phenomenon · claim-type · cross-domain-transfer · mechanism · claim-relation · replication-status · limitation — grounded in the full text| phenomenon | prognostic associations that appear only at cancer-subtype resolution— “It is thus desirable to perform prognostic analysis at a higher resolution. Based on the outputs of GEPIA2, we found that MAPK6 showed no association with breast cancer survival while it exhibited significant association with unfavorable prognostic outcome in Lumina A subtype” | |
| claim-type | method— “GEPIA2 performs survival analyses based on gene or isoform expression levels. Given a list of custom cancer types, GEPIA2 would provide a heat map to show the survival analysis result based on multiple cancer types (Figure 2A).” | |
| method — evidence | — “In GEPIA2, we utilized the UCSC Xena recomputed data of TCGA and GTEx for 198,619 coding and a series of other non-coding transcripts, and developed new computational functionalities to explore such events.” | |
| object of study — evidence | — “Featuring 198 619 isoforms and 84 cancer subtypes, GEPIA2 has extended gene expression quantification from the gene level to the transcript level, and supports analysis of a specific cancer subtype, and comparison between subtypes.” | |
| research question — evidence | — “Featuring 198 619 isoforms and 84 cancer subtypes, GEPIA2 has extended gene expression quantification from the gene level to the transcript level, and supports analysis of a specific cancer subtype, and comparison between subtypes.” | |
| contribution — evidence | — “Featuring 198 619 isoforms and 84 cancer subtypes, GEPIA2 has extended gene expression quantification from the gene level to the transcript level, and supports analysis of a specific cancer subtype, and comparison between subtypes.” | |
| transfer | from single-cell sequencing: gene signature quantification, taken from single-cell sequencing practice into bulk TCGA/GTEx analysis | transfers[0] |
| mechanism | isoform switching alternative splicing shifts which isoform of a gene predominates, and the shift can be specific to a cancer type Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | mechanisms[0] |
| mechanism | cross-dataset normalisation a user's uploaded matrix and the server-side target set are quantile-normalised against each other before any differential test, so the comparison is between normalised distributions rather than raw counts Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | mechanisms[1] |
| extends | GEPIA (Tang et al. 2017), the previous version of this server Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[0] |
| qualifies | prognostic gene lists identified at the level of a general cancer type Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[1] |
| sense | signature score = mean log2(TPM + 1) across a signature's genes Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[0] |
| sense | 'Stacked' = pool the selected subtypes, then compare the pool with normal samples Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[1] |
| sense | 'Separated' = compare each selected subtype with normal samples on its own Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[2] |
| sense | 'Comparing Across Subtypes' = compare the selected subtypes with each other, not with normal Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[3] |
| sense | isoform 'switch' = the isoform carrying most of a gene's expression differs by cancer type Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[4] |
| sense | GEPIA2 - enhanced GEPIA with transcript-level, subtype-level, uploaded-data, and batch-API analysis Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[5] |
| sense | Resolution shift - expression quantification moves from gene level to individual transcripts and cancer subtypes Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[6] |
| sense | Survival analysis - links expression level to prognostic outcome to assess clinical relevance Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[7] |
| sense | Gene signature - curated gene set used to interrogate tumor-microenvironment composition or infiltrating-immune functional state Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[8] |
| sense | Survival map - context-sensitive gene or isoform prognosis summarized across selected cancer types Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[9] |
| sense | Uploaded expression comparison - normalize a user matrix with a public target and return differential expression as a boxplot Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[10] |
| sense | Classifier modes - known cancer type gives sensitive subtype prediction; unrestricted mode addresses unknown origin Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[11] |
| sense | Isoform analysis - profile expression, differential status, prognosis, and pairwise correlation using transcript identifiers Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[12] |
| sense | Python API - batch requests and streamlined retrieval for five analysis functions Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[13] |
| control | any accuracy, precision, recall or held-out validation figure for the Cancer-subtype Classifier — absent-declared-unreported Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. — rules out a classifier that is confidently wrong - no accuracy, precision, recall or held-out figure is given for a tool the sentence says predicts cancer subtype 'accurately' Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[0] |
| control | the same MAPK6 survival test run at whole-breast-cancer level alongside the Lumina A subtype level — held Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. — rules out a survival signal that exists only in one subtype being reported as a property of the cancer type Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[1] |
| note | GEPIA (Tang et al. 2017), the previous version of this server — the whole paper is a version increment; the extension named first is gene level to transcript level Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[0] |
| weight | GEPIA (Tang et al. 2017), the previous version of this server — 0.95 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[0] |
| note | prognostic gene lists identified at the level of a general cancer type — not a contradiction - the paper accepts those lists and argues they are at the wrong resolution Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[1] |
| weight | prognostic gene lists identified at the level of a general cancer type — 0.95 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[1] |
| relation | signature score —operationalised-as→ log2(TPM + 1) — the signature score IS DEFINED AS the mean of this transformed value over a signature's genes Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[0] |
| weight | signature score —operationalised-as→ log2(TPM + 1) — 0.95 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[0] |
| differs in | MSI —distinct-from→ MSS — response to chemotherapy and immunotherapy Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[1] |
| weight | MSI —distinct-from→ MSS — 0.95 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[1] |
| differs in | triple-negative breast cancer —distinct-from→ breast cancer subtypes — five-year survival rate, about 15% lower Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[2] |
| weight | triple-negative breast cancer —distinct-from→ breast cancer subtypes — 0.85 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[2] |
| audit | cancer subtype —part-of→ cancer type — Audit 2026-09-28: DOUBTFUL - read against its full span and kept, but the span writes 'cancers are often comprised by heterogeneous subtypes', not 'cancer subtype' / 'cancer type'. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[3] |
| relation | cancer subtype —part-of→ cancer type — a cancer is COMPRISED BY its subtypes, so a subtype sits inside a type Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[3] |
| weight | cancer subtype —part-of→ cancer type — 0.95 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[3] |
| note | GEPIA2 —contrasted-with→ GenomeSpace — the paper's only named alternative, and it concedes the alternative can do the same analyses Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[4] |
| weight | GEPIA2 —contrasted-with→ GenomeSpace — 0.95 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[4] |
| audit | Pfam —operationalised-as→ isoform protein domain structure plots — Audit 2026-09-28: DOUBTFUL - read against its full span and kept, but the span says the plots are BASED ON Pfam predictions; operationalised-as is loose. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[5] |
| weight | Pfam —operationalised-as→ isoform protein domain structure plots — 0.85 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[5] |
| note | alternative splicing —causes→ different isoform usages — The paper states that alternative splicing results in different isoform usages. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[6] |
| audit | GEPIA (Gene Expression Profiling Interactive Analysis) web server —causes→ potential biomarkers — Audit 2026-09-28: DOUBTFUL - read against its full span and kept, but the span writes 'the GEPIA web server', not 'GEPIA (Gene Expression Profiling Interactive Analysis) web server'. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[7] |
| note | GEPIA (Gene Expression Profiling Interactive Analysis) web server —causes→ potential biomarkers — GEPIA use led to identification of potential biomarkers. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[7] |
| audit | GEPIA (Gene Expression Profiling Interactive Analysis) web server —causes→ therapeutic targets — Audit 2026-09-28: DOUBTFUL - read against its full span and kept, but the span writes 'the GEPIA web server', not 'GEPIA (Gene Expression Profiling Interactive Analysis) web server'. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[8] |
| note | GEPIA (Gene Expression Profiling Interactive Analysis) web server —causes→ therapeutic targets — GEPIA use also led to identification of therapeutic targets. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[8] |
| note | GEPIA2 python API —causes→ efficiency of users — The API boosts efficiency through batch processing and streamlined retrieval. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[9] |
| audit | stomach tumors —distinct-from→ adjacent normal tissues — Audit 2026-09-28: DOUBTFUL - read against its full span and kept, but the span says the Th1-like signature is higher in stomach tumors than in adjacent normal tissue; distinct-from is loose. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[10] |
| note | stomach tumors —distinct-from→ adjacent normal tissues — The Th1-like signature is significantly higher in tumors than adjacent normal tissue. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[10] |
| outcome | control — absent-declared-unreported Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[0] |
| outcome | control — held Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[1] |
| no type for this | GEPIA2 → GEPIA (Gene Expression Profiling Interactive Analysis) web server — GEPIA2 is the updated and enhanced version of GEPIA. Version-of is absent from the eight edge types. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | unhoused_relations[0] |
| no type for this | gene signature quantification → single-cell sequencing studies — GEPIA2's signature quantification is inspired by techniques from single-cell sequencing studies. Inspired-by is absent. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | unhoused_relations[1] |
| no type for this | Cancer Subtype Classifier → TCGA expression data — The classifier is trained on TCGA expression data. Trained-on is absent from the governed types. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | unhoused_relations[2] |
| no type for this | HTML5, JavaScript, and PHP → GEPIA2 — The website's interactive controls are implemented with HTML5, JavaScript and PHP. Implemented-with is absent. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | unhoused_relations[3] |
| no type for this | R and Perl scripts → GEPIA2 — GEPIA2 accesses and processes server-side data using R and Perl scripts. Implemented-with is absent. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | unhoused_relations[4] |
| no type for this | GEPIA2 python API → 5 functionalities — The Python package provides access to five named GEPIA2 functions. Provides-access-to is absent from the edge registry. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | unhoused_relations[5] |
| limitation | the Cancer-subtype Classifier is described as predicting accurately, and the article reports no accuracy, no held-out split and no confusion matrix anywhere Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[0] |
| limitation | the two classifier modes trade sensitivity against coverage, and the paper states the trade-off without quantifying either side Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[1] |
| limitation | prognostic gene lists in the prior literature were derived at cancer-type level, so a subtype-specific effect is invisible in them Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[2] |
finding · quantity · variable · definition · key-term — grounded in the full text| finding | MAPK6 shows no association with breast cancer survival overall, and a significant unfavourable association within the Lumina A subtype Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[0] |
| finding | the Th1-like signature score is significantly higher in stomach tumours than in adjacent normal tissue Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[1] |
| finding | gene survival analyses are context-dependent, which is the stated reason for scanning many cancer types at once Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[2] |
| quantity | 198 619 isoforms — Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[0] |
| quantity | 84 cancer subtypes — Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[1] |
| quantity | about 15% lower five-year survival in triple-negative breast cancer — Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[2] |
| quantity | 414 citations of GEPIA by May 2019, per Google Scholar — Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[3] |
| quantity | about 400 000 analysis requests from about 110 000 distinct IP addresses — Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[4] |
| quantity | 5 functionalities in the python package — Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[5] |
| quantity | MySQL version 5.7.17 — Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[6] |
| variable | isoform expression level Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.variables[0] |
| variable | signature score Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.variables[1] |
| variable | hazard ratio Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.variables[2] |
| definition | signature score Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.definitions[0] |
| definition | isoform usage Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.definitions[1] |
| definition | Stacked Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.definitions[2] |
| definition | Separated Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.definitions[3] |
| definition | Comparing Across Subtypes Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.definitions[4] |
| concept | signature score — not defined in this paper's own words; the mean of log2(TPM + 1) over the genes of a signature set, in one sample Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[0] |
| concept | isoform usage — not defined in this paper's own words; the share of a gene's expression carried by each of its isoforms, 0% to 100% Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[1] |
| concept | survival map — not defined in this paper's own words; a heat map of one gene's or isoform's prognostic effect across many cancer types at once Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[2] |
| concept | hazard ratios — not defined in this paper's own words; plotted in logarithmic (log10) scale; red is higher risk, blue lower Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[3] |
| concept | cancer subtype — not defined in this paper's own words; a division below cancer type, carrying its own prognosis and treatment response Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[4] |
| concept | MSI — not defined in this paper's own words; microsatellite-instable colorectal cancer, contrasted here with MSS Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[5] |
| concept | MSS — not defined in this paper's own words; microsatellite-stable colorectal cancer, contrasted here with MSI Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[6] |
| concept | Quantile-normalization — not defined in this paper's own words; applied to a user's uploaded matrix and the target set before they are compared Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[7] |
| concept | Pfam — not defined in this paper's own words; the domain predictor behind the per-isoform protein structure plots Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[8] |
| concept | triple-negative breast cancer — not defined in this paper's own words; the subtype the paper uses to argue that subtype prognosis diverges from type prognosis Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[9] |
| concept | MAPK6 — not defined in this paper's own words; the worked example: no association at breast-cancer level, significant within Lumina A Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[10] |
| concept | TPM — not defined in this paper's own words; transcripts per million; every expression figure in the paper is log2(TPM + 1) Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[11] |
| concept | log2(TPM + 1) — not defined in this paper's own words; the transform every expression value in the paper is reported on Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[12] |
| concept | cancer type — not defined in this paper's own words; the level above subtype, and the level the prior prognostic literature worked at Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[13] |
| concept | breast cancer subtypes — not defined in this paper's own words; the comparison class for triple-negative breast cancer's survival deficit Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[14] |
| concept | GEPIA2 — not defined in this paper's own words; the web server this paper announces Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[15] |
| concept | GenomeSpace — not defined in this paper's own words; the one named alternative platform, conceded to allow similar analyses Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[16] |
| concept | isoform protein domain structure plots — not defined in this paper's own words; per-isoform domain diagrams, predicted rather than observed Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[17] |
| concept | GEPIA (Gene Expression Profiling Interactive Analysis) web server — not defined in this paper's own words; original interactive gene-expression analysis server Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[18] |
| concept | tumor and normal samples — not defined in this paper's own words; sample classes drawn from TCGA and GTEx Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[19] |
| concept | TCGA — not defined in this paper's own words; tumor genomics resource used by GEPIA2 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[20] |
| concept | GTEx databases — not defined in this paper's own words; normal-tissue expression resource used by GEPIA2 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[21] |
| concept | updated and enhanced version — not defined in this paper's own words; status assigned to GEPIA2 relative to GEPIA Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[22] |
| concept | higher resolution — not defined in this paper's own words; analytical granularity enabled by isoforms and subtypes Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[23] |
| concept | 198 619 isoforms — not defined in this paper's own words; transcript coverage advertised for GEPIA2 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[24] |
| concept | 84 cancer subtypes — not defined in this paper's own words; subtype coverage advertised for GEPIA2 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[25] |
| concept | gene expression quantification — not defined in this paper's own words; quantification extended from gene to transcript level Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[26] |
| concept | gene level — not defined in this paper's own words; coarser expression-analysis level Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[27] |
| concept | transcript level — not defined in this paper's own words; finer expression-analysis level Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[28] |
| concept | gene signature quantification — not defined in this paper's own words; analysis technique adapted from single-cell studies Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[29] |
| concept | single-cell sequencing studies — not defined in this paper's own words; source of inspiration for signature quantification Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[30] |
| concept | customized analysis — not defined in this paper's own words; comparison of uploaded RNA-seq data with public samples Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[31] |
| concept | own RNA-seq data — not defined in this paper's own words; user data accepted by the server Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[32] |
| concept | API for batch process — not defined in this paper's own words; programmatic batch-analysis interface Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[33] |
| concept | easy retrieval of the analysis results — not defined in this paper's own words; retrieval capability offered by the API Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[34] |
| concept | data mining — not defined in this paper's own words; use enabled by public cancer RNA-seq resources Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[35] |
| concept | gene functions — not defined in this paper's own words; biological target of deeper understanding Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[36] |
| concept | Survival analysis — not defined in this paper's own words; method linking expression with prognostic outcomes Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[37] |
| concept | gene expression levels — not defined in this paper's own words; predictor examined in survival analysis Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[38] |
| concept | prognostic outcomes — not defined in this paper's own words; clinical outcome linked to expression Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[39] |
| concept | clinical relevance of a given gene — not defined in this paper's own words; interpretive target of survival analysis Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[40] |
| concept | differential expression analysis — not defined in this paper's own words; original GEPIA functionality Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[41] |
| concept | similar gene identification — not defined in this paper's own words; original GEPIA functionality Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[42] |
| concept | potential biomarkers — not defined in this paper's own words; discovery outcome attributed to GEPIA use Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[43] |
| concept | therapeutic targets — not defined in this paper's own words; second discovery outcome attributed to GEPIA use Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[44] |
| concept | alternative splicing — not defined in this paper's own words; process producing different isoform usages Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[45] |
| concept | different isoform usages — not defined in this paper's own words; cancer-relevant result of alternative splicing Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[46] |
| concept | UCSC Xena recomputed data — not defined in this paper's own words; uniform transcript-level TCGA/GTEx data used by GEPIA2 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[47] |
| concept | coding — not defined in this paper's own words; one class of transcripts included Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[48] |
| concept | non-coding transcripts — not defined in this paper's own words; additional transcript class included Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[49] |
| concept | heterogeneous subtypes with distinct prognosis — not defined in this paper's own words; within-cancer heterogeneity motivating subtype analysis Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[50] |
| concept | single-cell sequencing — not defined in this paper's own words; widely available technology motivating signature paradigms Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[51] |
| concept | gene signatures — not defined in this paper's own words; sets used to interrogate tumor environments and immune content Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[52] |
| concept | composition of tumor microenvironment — not defined in this paper's own words; property interrogated with gene signatures Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[53] |
| concept | functional status of infiltrating immune content — not defined in this paper's own words; second property interrogated with signatures Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[54] |
| concept | curated list of signatures — not defined in this paper's own words; efficient signature-analysis resource integrated into GEPIA2 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[55] |
| concept | Expression Analysis — not defined in this paper's own words; major GEPIA2 feature topic for public data Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[56] |
| concept | Custom Data Analysis — not defined in this paper's own words; major GEPIA2 feature topic for uploaded data Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[57] |
| concept | eight tabs — not defined in this paper's own words; feature divisions contained in Expression Analysis Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[58] |
| concept | two tabs — not defined in this paper's own words; feature divisions contained in Custom Data Analysis Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[59] |
| concept | Cancer Subtype Classifier — not defined in this paper's own words; custom-data tab predicting type or subtype Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[60] |
| concept | Expression Comparison — not defined in this paper's own words; custom-data tab comparing uploaded expression Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[61] |
| concept | python package — not defined in this paper's own words; command-line access route to GEPIA2 analyses Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[62] |
| concept | survival analyses — not defined in this paper's own words; gene- or isoform-based prognostic analyses Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[63] |
| concept | custom cancer types — not defined in this paper's own words; user-selected cancers summarized in a survival map Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[64] |
| concept | heat map — not defined in this paper's own words; multi-cancer survival-result visualization Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[65] |
| concept | statistical significance — not defined in this paper's own words; status marked by dark frames Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[66] |
| concept | context-dependent — not defined in this paper's own words; property of gene survival effects across cancers Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[67] |
| concept | prognostic impact — not defined in this paper's own words; effect screened across cancer contexts Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[68] |
| concept | users’ custom data — not defined in this paper's own words; uploaded expression matrices linked to public genomics Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[69] |
| concept | public cancer genomic data — not defined in this paper's own words; TCGA/GTEx comparison target Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[70] |
| concept | other two additional normalization strategies — not defined in this paper's own words; alternatives offered alongside quantile normalization Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[71] |
| concept | uploaded dataset — not defined in this paper's own words; user-side matrix normalized against the target Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[72] |
| concept | target dataset on the server — not defined in this paper's own words; public comparison matrix Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[73] |
| concept | boxplot — not defined in this paper's own words; returned differential-expression visualization Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[74] |
| concept | gene expression — not defined in this paper's own words; features used to classify an uploaded sample Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[75] |
| concept | TCGA expression data — not defined in this paper's own words; training data for the subtype classifier Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[76] |
| concept | probability of this sample belonging to each subtype — not defined in this paper's own words; per-sample classifier output Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[77] |
| concept | two modes — not defined in this paper's own words; conditional and pan-subtype classifier options Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[78] |
| concept | more sensitive result — not defined in this paper's own words; advantage of specifying the cancer type first Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[79] |
| concept | cancer with unknown origin — not defined in this paper's own words; use case for unrestricted subtype prediction Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[80] |
| concept | isoform symbol — not defined in this paper's own words; one accepted identifier for isoform analysis Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[81] |
| concept | Ensembl ID — not defined in this paper's own words; alternative accepted isoform identifier Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[82] |
| concept | differentially expressed isoforms — not defined in this paper's own words; isoform-level discovery output Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[83] |
| concept | prognostic isoforms — not defined in this paper's own words; isoform-level survival output Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[84] |
| concept | correlation between two isoforms — not defined in this paper's own words; isoform-level association analysis Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[85] |
| concept | HTML5, JavaScript, and PHP — not defined in this paper's own words; interactive-control implementation technologies Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[86] |
| concept | R and Perl scripts — not defined in this paper's own words; server-side processing technologies Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[87] |
| concept | uniform pipeline — not defined in this paper's own words; UCSC Xena recomputation workflow Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[88] |
| concept | MySQL relational database — not defined in this paper's own words; storage system for expression and subtype datasets Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[89] |
| concept | GEPIA2 python API — not defined in this paper's own words; programmatic interface for server analyses Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[90] |
| concept | multiple requests — not defined in this paper's own words; batch workload targeted by the API Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[91] |
| concept | efficiency of users — not defined in this paper's own words; property boosted by batch processing and retrieval Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[92] |
| concept | 5 functionalities — not defined in this paper's own words; boxplot, similar, correlation, survival and survival-map API scope Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[93] |
| concept | immune-cell clusters — not defined in this paper's own words; single-cell-derived populations profiled pan-cancer Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[94] |
| concept | pan-cancer manner — not defined in this paper's own words; cross-cancer mode of signature profiling Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[95] |
| concept | Th1-like signature — not defined in this paper's own words; worked immune-cluster signature example Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[96] |
| concept | stomach tumors — not defined in this paper's own words; tumor context with elevated Th1-like score Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[97] |
| concept | adjacent normal tissues — not defined in this paper's own words; comparison tissue for the example Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[98] |
| concept | isoform quantification — not defined in this paper's own words; new data layer pushing analysis resolution Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[99] |
| concept | cancer subtype information — not defined in this paper's own words; new stratification layer pushing analysis resolution Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[100] |
| concept | isoform usage profiling — not defined in this paper's own words; new analysis method highlighted in conclusion Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[101] |
| concept | custom data analysis — not defined in this paper's own words; uploaded-data method highlighted in conclusion Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[102] |
| concept | big cancer genomics data — not defined in this paper's own words; resource domain explored with GEPIA2 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[103] |
| log2(TPM + 1) | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[0] |
| hazard ratio in log10 scale | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[1] |
| P = 0.022 | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[2] |
| P = 0.15 | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[3] |
| Quantile-normalization | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[4] |
When we have changed our mind. Some entries in the table begin with a word in capitals and the reason for it. EVIDENCE CORRECTED — the finding still stands, but we had quoted the wrong sentence from the paper, and the quotation has been replaced with the right one. RETRACTED — the entry itself was wrong; it stays on the page, marked, with the reason, rather than being deleted. WITHDRAWN AND REPLACED — the entry was wrong, and a corrected version of it appears in the entries below. Each mark carries its own reason, in brackets, because the reasons differ from one entry to the next. An entry we have WITHDRAWN is removed from this page and kept in the record, with its reason. A line reading Audit and a date is a later re-reading of the entry against its whole sentence: DOUBTFUL means it was kept, and the reason says what is loose about it. Quotation marks inside the tagger's sentence. Where a tag is the tagger's own sentence, a phrase in quotation marks inside it is borrowed from the paper — the tagger's wording around it is not. The paper's own sentence is the evidence quote for that row; on this page it is withheld with the article, and the article is at its publisher. Nothing inside quotation marks anywhere on this page is ours: if it is quoted, it is the paper's. Whose words a concept carries. A concept entry records a term the paper itself uses, so the term, the sense given for it, and its evidence are the paper's own words, quoted where the paper fixes them. This is the opposite of a sense entry in the tag table, which is the tagger's sentence about how the paper uses a term. Where a concept entry could not be grounded in the paper's words, the entry says so on its own row.
Tag layer © the Meta-Tagging Project, CC BY 4.0. The paper text is © its authors/publisher
and is linked, not reproduced. Excerpts shown are short quotations for identification and verification.
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