GEPIA2: an enhanced web server for large-scale expression profiling and interactive analysis

Zefang Tang, Boxi Kang, Chenwei Li, Tianxiang Chen, Zemin Zhang · Nucleic Acids Research · 2019 · genetics · 10.1093/nar/gkz430 · record tang2019-gepia2-an-enhanced-web-server-for
tag layer · index · concepts · authors · עברית

Where this record's text came from. 2026-08-20 and 2026-08-28 schema-0.3 passes: every quote verified as an exact substring of the staged text and anchored at merge time; concept terms verified present; every edge endpoint an existing node.

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Other fields define these differently the same word, defined another way in another discipline
alternative splicing 2 fields · statistical significance 2 fields · TCGA 2 fields · TPM 2 fields

Tags on this paper

Every tag the record carries, each linking to every other paper in the corpus that carries it. A tag appears here whether or not its words occur in the article — the spans below are only the ones a sentence in this paper licenses. Of the 104 concept tags on this paper, all 104 are grounded in a quoted sentence. All carry the tagger's gloss of what the term means in this paper, which is not something the article can license.

signature score isoform usage survival map hazard ratios cancer subtype MSI MSS Quantile-normalization Pfam triple-negative breast cancer MAPK6 TPM log2(TPM + 1) cancer type breast cancer subtypes GEPIA2 GenomeSpace isoform protein domain structure plots GEPIA (Gene Expression Profiling Interactive Analysis) web server tumor and normal samples TCGA GTEx databases updated and enhanced version higher resolution 198 619 isoforms 84 cancer subtypes gene expression quantification gene level transcript level gene signature quantification single-cell sequencing studies customized analysis own RNA-seq data API for batch process easy retrieval of the analysis results data mining gene functions Survival analysis gene expression levels prognostic outcomes clinical relevance of a given gene differential expression analysis similar gene identification potential biomarkers therapeutic targets alternative splicing different isoform usages UCSC Xena recomputed data coding non-coding transcripts heterogeneous subtypes with distinct prognosis single-cell sequencing gene signatures composition of tumor microenvironment functional status of infiltrating immune content curated list of signatures Expression Analysis Custom Data Analysis eight tabs two tabs Cancer Subtype Classifier Expression Comparison python package survival analyses custom cancer types heat map statistical significance context-dependent prognostic impact users’ custom data public cancer genomic data other two additional normalization strategies uploaded dataset target dataset on the server boxplot gene expression TCGA expression data probability of this sample belonging to each subtype two modes more sensitive result cancer with unknown origin isoform symbol Ensembl ID differentially expressed isoforms prognostic isoforms correlation between two isoforms HTML5, JavaScript, and PHP R and Perl scripts uniform pipeline MySQL relational database GEPIA2 python API multiple requests efficiency of users 5 functionalities immune-cell clusters pan-cancer manner Th1-like signature stomach tumors adjacent normal tissues isoform quantification cancer subtype information isoform usage profiling big cancer genomics data isoform switching cross-dataset normalisation Stacked Separated Comparing Across Subtypes isoform expression level hazard ratio hazard ratio in log10 scale P = 0.022 P = 0.15 system-or-tool-building

Method, as described: interactive analysis over UCSC Xena recomputed TCGA and GTEx RNA-seq, served from a relational database

Legend

relation to other work	`claim_relations`	how this paper stands to another: agrees, contradicts, extends, qualifies
claim type	`claim_type`	the shape of the claim: existence, mechanism, method, critique, prediction, null
concept edge	`concept_edges`	an asserted relation between two concepts, with the sentence asserting it
concept	`concepts`	an idea the paper works with, quoted where the paper uses it
content tag	`content_tags`	a finding, definition, quantity, statistic or variable named in the paper
contribution	`contribution`	what the paper claims to add
control	`controls`	an experiment run to eliminate a rival explanation
limitation	`limitations`	what the paper says its evidence cannot support
mechanism	`mechanisms`	how the reported effect is said to come about
method	`method`	how the paper produced its evidence
object of study	`object_of_study`	what the paper is about — the thing it investigates
phenomenon	`phenomenon`	the effect or regularity under study
research question	`research_question`	the question the paper sets itself
sense	`senses`	a distinct use of a term, quoted where the paper fixes it
transfer	`transfers`	a method or concept carried in from another field
unrecordable relation	`unhoused_relations`	a relation the paper asserts that this vocabulary cannot express, with the reason

The paper

The full text is not reproduced here. This article is not cleared for redistribution, so the page carries the tag layer only. Its evidence sentences are withheld; the grounding status remains with each tag, and the article itself is at https://doi.org/10.1093/nar/gkz430. The reading view exists for the papers whose licence permits it.

Every tag on this page

claim_relations 2 · claim_type 1 · concept_edges 11 · concepts 104 · content_tags 23 · contribution 1 · controls 2 · limitations 3 · mechanisms 2 · method 1 · object_of_study 1 · phenomenon 1 · research_question 1 · senses 14 · transfers 1 · unhoused_relations 6

Relations on this page carry a quotation for the claim. Where a relation was separately evidenced — and so tested against the vocabulary for its type — the row says so; 7 of 11 relations here carry that mark. The rest are the tagger’s reading of the sentence quoted beside them.

facet	tag	field	conf.	whose words
object_of_study	gene- and isoform-level expression across TCGA tumour and GTEx normal samples Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`object_of_study`		the paper's words
research_question	how to make expression, survival and signature analysis of TCGA/GTEx available at isoform and cancer-subtype resolution Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`research_question`		the paper's words
contribution	a web server extending expression quantification from the gene to the transcript level and to 84 cancer subtypes, with user-uploaded data comparison and a python API Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`contribution`		the paper's words
claim_type	method Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`claim_type`		the paper's words
phenomenon	prognostic associations that appear only at cancer-subtype resolution Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`phenomenon`		the paper's words
method	system-or-tool-building Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: system-or-tool-building	`method`		the paper's words
mechanisms	alternative splicing shifts which isoform of a gene predominates, and the shift can be specific to a cancer type Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: isoform switching	`mechanisms[0]`	0.85	the tagger's words
mechanisms	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 record is not cleared for redistribution. The sentence is in the paper at the link above. also in: cross-dataset normalisation	`mechanisms[1]`	0.95	the tagger's words
limitations	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 record is not cleared for redistribution. The sentence is in the paper at the link above.	`limitations[0]`	0.95	the tagger's words
limitations	the two classifier modes trade sensitivity against coverage, and the paper states the trade-off without quantifying either side Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`limitations[1]`	0.95	the tagger's words
limitations	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 record is not cleared for redistribution. The sentence is in the paper at the link above.	`limitations[2]`	0.95	the tagger's words
transfers	gene signature quantification, taken from single-cell sequencing practice into bulk TCGA/GTEx analysis Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`transfers[0]`	0.85	the tagger's words
controls	any accuracy, precision, recall or held-out validation figure for the Cancer-subtype Classifier Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: 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' · outcome: absent-declared-unreported	`controls[0]`	0.95	the tagger's words
controls	the same MAPK6 survival test run at whole-breast-cancer level alongside the Lumina A subtype level Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: a survival signal that exists only in one subtype being reported as a property of the cancer type · outcome: held	`controls[1]`	0.95	the tagger's words
concepts	signature score Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: signature score	`concepts[0]`	0.95	the paper's words
concepts	isoform usage Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: isoform usage	`concepts[1]`	0.95	the paper's words
concepts	survival map Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: survival map	`concepts[2]`	0.85	the paper's words
concepts	hazard ratios Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: hazard ratios	`concepts[3]`	0.85	the paper's words
concepts	cancer subtype Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: cancer subtype	`concepts[4]`	0.85	the paper's words
concepts	MSI Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: MSI	`concepts[5]`	0.95	the paper's words
concepts	MSS Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: MSS	`concepts[6]`	0.95	the paper's words
concepts	Quantile-normalization Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: Quantile-normalization	`concepts[7]`	0.95	the paper's words
concepts	Pfam Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: Pfam	`concepts[8]`	0.95	the paper's words
concepts	triple-negative breast cancer Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: triple-negative breast cancer	`concepts[9]`	0.95	the paper's words
concepts	MAPK6 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: MAPK6	`concepts[10]`	0.95	the paper's words
concepts	TPM Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: TPM	`concepts[11]`	0.95	the paper's words
concepts	log2(TPM + 1) Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: log2(TPM + 1)	`concepts[12]`	0.95	the paper's words
concepts	cancer type Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: cancer type	`concepts[13]`	0.95	the paper's words
concepts	breast cancer subtypes Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: breast cancer subtypes	`concepts[14]`	0.95	the paper's words
concepts	GEPIA2 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: GEPIA2	`concepts[15]`	0.95	the paper's words
concepts	GenomeSpace Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: GenomeSpace	`concepts[16]`	0.95	the paper's words
concepts	isoform protein domain structure plots Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: isoform protein domain structure plots	`concepts[17]`	0.95	the paper's words
concepts	GEPIA (Gene Expression Profiling Interactive Analysis) web server Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: GEPIA (Gene Expression Profiling Interactive Analysis) web server	`concepts[18]`	0.95	the paper's words
concepts	tumor and normal samples Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: tumor and normal samples	`concepts[19]`	0.95	the paper's words
concepts	TCGA Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: TCGA	`concepts[20]`	0.95	the paper's words
concepts	GTEx databases Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: GTEx databases	`concepts[21]`	0.95	the paper's words
concepts	updated and enhanced version Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: updated and enhanced version	`concepts[22]`	0.95	the paper's words
concepts	higher resolution Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: higher resolution	`concepts[23]`	0.95	the paper's words
concepts	198 619 isoforms Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: 198 619 isoforms	`concepts[24]`	0.95	the paper's words
concepts	84 cancer subtypes Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: 84 cancer subtypes	`concepts[25]`	0.95	the paper's words
concepts	gene expression quantification Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: gene expression quantification	`concepts[26]`	0.95	the paper's words
concepts	gene level Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: gene level	`concepts[27]`	0.95	the paper's words
concepts	transcript level Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: transcript level	`concepts[28]`	0.95	the paper's words
concepts	gene signature quantification Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: gene signature quantification	`concepts[29]`	0.95	the paper's words
concepts	single-cell sequencing studies Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: single-cell sequencing studies	`concepts[30]`	0.95	the paper's words
concepts	customized analysis Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: customized analysis	`concepts[31]`	0.95	the paper's words
concepts	own RNA-seq data Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: own RNA-seq data	`concepts[32]`	0.95	the paper's words
concepts	API for batch process Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: API for batch process	`concepts[33]`	0.95	the paper's words
concepts	easy retrieval of the analysis results Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: easy retrieval of the analysis results	`concepts[34]`	0.95	the paper's words
concepts	data mining Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: data mining	`concepts[35]`	0.95	the paper's words
concepts	gene functions Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: gene functions	`concepts[36]`	0.95	the paper's words
concepts	Survival analysis Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: Survival analysis	`concepts[37]`	0.95	the paper's words
concepts	gene expression levels Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: gene expression levels	`concepts[38]`	0.95	the paper's words
concepts	prognostic outcomes Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: prognostic outcomes	`concepts[39]`	0.95	the paper's words
concepts	clinical relevance of a given gene Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: clinical relevance of a given gene	`concepts[40]`	0.95	the paper's words
concepts	differential expression analysis Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: differential expression analysis	`concepts[41]`	0.95	the paper's words
concepts	similar gene identification Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: similar gene identification	`concepts[42]`	0.95	the paper's words
concepts	potential biomarkers Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: potential biomarkers	`concepts[43]`	0.95	the paper's words
concepts	therapeutic targets Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: therapeutic targets	`concepts[44]`	0.95	the paper's words
concepts	alternative splicing Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: alternative splicing	`concepts[45]`	0.95	the paper's words
concepts	different isoform usages Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: different isoform usages	`concepts[46]`	0.95	the paper's words
concepts	UCSC Xena recomputed data Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: UCSC Xena recomputed data	`concepts[47]`	0.95	the paper's words
concepts	coding Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: coding	`concepts[48]`	0.95	the paper's words
concepts	non-coding transcripts Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: non-coding transcripts	`concepts[49]`	0.95	the paper's words
concepts	heterogeneous subtypes with distinct prognosis Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: heterogeneous subtypes with distinct prognosis	`concepts[50]`	0.95	the paper's words
concepts	single-cell sequencing Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: single-cell sequencing	`concepts[51]`	0.95	the paper's words
concepts	gene signatures Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: gene signatures	`concepts[52]`	0.95	the paper's words
concepts	composition of tumor microenvironment Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: composition of tumor microenvironment	`concepts[53]`	0.95	the paper's words
concepts	functional status of infiltrating immune content Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: functional status of infiltrating immune content	`concepts[54]`	0.95	the paper's words
concepts	curated list of signatures Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: curated list of signatures	`concepts[55]`	0.95	the paper's words
concepts	Expression Analysis Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: Expression Analysis	`concepts[56]`	0.95	the paper's words
concepts	Custom Data Analysis Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: Custom Data Analysis	`concepts[57]`	0.95	the paper's words
concepts	eight tabs Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: eight tabs	`concepts[58]`	0.95	the paper's words
concepts	two tabs Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: two tabs	`concepts[59]`	0.95	the paper's words
concepts	Cancer Subtype Classifier Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: Cancer Subtype Classifier	`concepts[60]`	0.95	the paper's words
concepts	Expression Comparison Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: Expression Comparison	`concepts[61]`	0.95	the paper's words
concepts	python package Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: python package	`concepts[62]`	0.95	the paper's words
concepts	survival analyses Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: survival analyses	`concepts[63]`	0.95	the paper's words
concepts	custom cancer types Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: custom cancer types	`concepts[64]`	0.95	the paper's words
concepts	heat map Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: heat map	`concepts[65]`	0.95	the paper's words
concepts	statistical significance Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: statistical significance	`concepts[66]`	0.95	the paper's words
concepts	context-dependent Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: context-dependent	`concepts[67]`	0.95	the paper's words
concepts	prognostic impact Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: prognostic impact	`concepts[68]`	0.95	the paper's words
concepts	users’ custom data Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: users’ custom data	`concepts[69]`	0.95	the paper's words
concepts	public cancer genomic data Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: public cancer genomic data	`concepts[70]`	0.95	the paper's words
concepts	other two additional normalization strategies Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: other two additional normalization strategies	`concepts[71]`	0.95	the paper's words
concepts	uploaded dataset Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: uploaded dataset	`concepts[72]`	0.95	the paper's words
concepts	target dataset on the server Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: target dataset on the server	`concepts[73]`	0.95	the paper's words
concepts	boxplot Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: boxplot	`concepts[74]`	0.95	the paper's words
concepts	gene expression Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: gene expression	`concepts[75]`	0.95	the paper's words
concepts	TCGA expression data Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: TCGA expression data	`concepts[76]`	0.95	the paper's words
concepts	probability of this sample belonging to each subtype Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: probability of this sample belonging to each subtype	`concepts[77]`	0.95	the paper's words
concepts	two modes Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: two modes	`concepts[78]`	0.95	the paper's words
concepts	more sensitive result Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: more sensitive result	`concepts[79]`	0.95	the paper's words
concepts	cancer with unknown origin Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: cancer with unknown origin	`concepts[80]`	0.95	the paper's words
concepts	isoform symbol Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: isoform symbol	`concepts[81]`	0.95	the paper's words
concepts	Ensembl ID Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: Ensembl ID	`concepts[82]`	0.95	the paper's words
concepts	differentially expressed isoforms Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: differentially expressed isoforms	`concepts[83]`	0.95	the paper's words
concepts	prognostic isoforms Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: prognostic isoforms	`concepts[84]`	0.95	the paper's words
concepts	correlation between two isoforms Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: correlation between two isoforms	`concepts[85]`	0.95	the paper's words
concepts	HTML5, JavaScript, and PHP Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: HTML5, JavaScript, and PHP	`concepts[86]`	0.95	the paper's words
concepts	R and Perl scripts Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: R and Perl scripts	`concepts[87]`	0.95	the paper's words
concepts	uniform pipeline Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: uniform pipeline	`concepts[88]`	0.95	the paper's words
concepts	MySQL relational database Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: MySQL relational database	`concepts[89]`	0.95	the paper's words
concepts	GEPIA2 python API Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: GEPIA2 python API	`concepts[90]`	0.95	the paper's words
concepts	multiple requests Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: multiple requests	`concepts[91]`	0.95	the paper's words
concepts	efficiency of users Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: efficiency of users	`concepts[92]`	0.95	the paper's words
concepts	5 functionalities Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: 5 functionalities	`concepts[93]`	0.95	the paper's words
concepts	immune-cell clusters Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: immune-cell clusters	`concepts[94]`	0.95	the paper's words
concepts	pan-cancer manner Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: pan-cancer manner	`concepts[95]`	0.95	the paper's words
concepts	Th1-like signature Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: Th1-like signature	`concepts[96]`	0.95	the paper's words
concepts	stomach tumors Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: stomach tumors	`concepts[97]`	0.95	the paper's words
concepts	adjacent normal tissues Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: adjacent normal tissues	`concepts[98]`	0.95	the paper's words
concepts	isoform quantification Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: isoform quantification	`concepts[99]`	0.95	the paper's words
concepts	cancer subtype information Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: cancer subtype information	`concepts[100]`	0.95	the paper's words
concepts	isoform usage profiling Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: isoform usage profiling	`concepts[101]`	0.95	the paper's words
concepts	custom data analysis Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: custom data analysis	`concepts[102]`	0.95	the paper's words
concepts	big cancer genomics data Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: big cancer genomics data	`concepts[103]`	0.95	the paper's words
unhoused_relations	GEPIA2 → GEPIA (Gene Expression Profiling Interactive Analysis) web server Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. GEPIA2 is the updated and enhanced version of GEPIA. Version-of is absent from the eight edge types.	`unhoused_relations[0]`	0.95	the tagger's words
unhoused_relations	gene signature quantification → single-cell sequencing studies Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. GEPIA2's signature quantification is inspired by techniques from single-cell sequencing studies. Inspired-by is absent.	`unhoused_relations[1]`	0.95	the tagger's words
unhoused_relations	Cancer Subtype Classifier → TCGA expression data Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. The classifier is trained on TCGA expression data. Trained-on is absent from the governed types.	`unhoused_relations[2]`	0.95	the tagger's words
unhoused_relations	HTML5, JavaScript, and PHP → GEPIA2 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. The website's interactive controls are implemented with HTML5, JavaScript and PHP. Implemented-with is absent.	`unhoused_relations[3]`	0.95	the tagger's words
unhoused_relations	R and Perl scripts → GEPIA2 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. GEPIA2 accesses and processes server-side data using R and Perl scripts. Implemented-with is absent.	`unhoused_relations[4]`	0.95	the tagger's words
unhoused_relations	GEPIA2 python API → 5 functionalities Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. The Python package provides access to five named GEPIA2 functions. Provides-access-to is absent from the edge registry.	`unhoused_relations[5]`	0.95	the tagger's words
senses	signature score = mean log2(TPM + 1) across a signature's genes Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`senses[0]`	0.95	the tagger's words
senses	'Stacked' = pool the selected subtypes, then compare the pool with normal samples Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`senses[1]`	0.95	the tagger's words
senses	'Separated' = compare each selected subtype with normal samples on its own Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`senses[2]`	0.95	the tagger's words
senses	'Comparing Across Subtypes' = compare the selected subtypes with each other, not with normal Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`senses[3]`	0.95	the tagger's words
senses	isoform 'switch' = the isoform carrying most of a gene's expression differs by cancer type Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`senses[4]`	0.85	the tagger's words
senses	GEPIA2 - enhanced GEPIA with transcript-level, subtype-level, uploaded-data, and batch-API analysis Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`senses[5]`	0.95	the tagger's words
senses	Resolution shift - expression quantification moves from gene level to individual transcripts and cancer subtypes Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`senses[6]`	0.95	the tagger's words
senses	Survival analysis - links expression level to prognostic outcome to assess clinical relevance Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`senses[7]`	0.95	the tagger's words
senses	Gene signature - curated gene set used to interrogate tumor-microenvironment composition or infiltrating-immune functional state Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`senses[8]`	0.95	the tagger's words
senses	Survival map - context-sensitive gene or isoform prognosis summarized across selected cancer types Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`senses[9]`	0.95	the tagger's words
senses	Uploaded expression comparison - normalize a user matrix with a public target and return differential expression as a boxplot Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`senses[10]`	0.95	the tagger's words
senses	Classifier modes - known cancer type gives sensitive subtype prediction; unrestricted mode addresses unknown origin Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`senses[11]`	0.95	the tagger's words
senses	Isoform analysis - profile expression, differential status, prognosis, and pairwise correlation using transcript identifiers Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`senses[12]`	0.95	the tagger's words
senses	Python API - batch requests and streamlined retrieval for five analysis functions Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`senses[13]`	0.95	the tagger's words
claim_relations	extends → GEPIA (Tang et al. 2017), the previous version of this server Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. note: the whole paper is a version increment; the extension named first is gene level to transcript level	`claim_relations[0]`		the tagger's words
claim_relations	qualifies → prognostic gene lists identified at the level of a general cancer type Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. note: not a contradiction - the paper accepts those lists and argues they are at the wrong resolution	`claim_relations[1]`		the tagger's words
concept_edges	signature score —operationalised-as→ log2(TPM + 1) Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. the relation itself is separately evidenced · strength of the relation: 0.95 · the relation stated: the signature score IS DEFINED AS the mean of this transformed value over a signature's genes also in: signature score · log2(TPM + 1)	`concept_edges[0]`		the tagger's words
concept_edges	MSI —distinct-from→ MSS Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. differs in: response to chemotherapy and immunotherapy · strength of the relation: 0.95 also in: MSI · MSS	`concept_edges[1]`		the tagger's words
concept_edges	triple-negative breast cancer —distinct-from→ breast cancer subtypes Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. differs in: five-year survival rate, about 15% lower · strength of the relation: 0.85 also in: triple-negative breast cancer · breast cancer subtypes	`concept_edges[2]`		the tagger's words
concept_edges	cancer subtype —part-of→ cancer type Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. the relation itself is separately evidenced · strength of the relation: 0.95 · the relation stated: a cancer is COMPRISED BY its subtypes, so a subtype sits inside a 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'. also in: cancer subtype · cancer type	`concept_edges[3]`		the tagger's words
concept_edges	GEPIA2 —contrasted-with→ GenomeSpace Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. strength of the relation: 0.95 · note: the paper's only named alternative, and it concedes the alternative can do the same analyses also in: GEPIA2 · GenomeSpace	`concept_edges[4]`		the tagger's words
concept_edges	Pfam —operationalised-as→ isoform protein domain structure plots Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. strength of the relation: 0.85 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. also in: Pfam · isoform protein domain structure plots	`concept_edges[5]`		the tagger's words
concept_edges	alternative splicing —causes→ different isoform usages Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. the relation itself is separately evidenced · strength of the relation: 1 · note: The paper states that alternative splicing results in different isoform usages. also in: alternative splicing · different isoform usages	`concept_edges[6]`	0.95	the tagger's words
concept_edges	GEPIA (Gene Expression Profiling Interactive Analysis) web server —causes→ potential biomarkers Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. the relation itself is separately evidenced · strength of the relation: 1 · note: GEPIA use led to identification of 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'. also in: GEPIA (Gene Expression Profiling Interactive Analysis) web server · potential biomarkers	`concept_edges[7]`	0.95	the tagger's words
concept_edges	GEPIA (Gene Expression Profiling Interactive Analysis) web server —causes→ therapeutic targets Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. the relation itself is separately evidenced · strength of the relation: 1 · note: GEPIA use also led to identification of 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'. also in: GEPIA (Gene Expression Profiling Interactive Analysis) web server · therapeutic targets	`concept_edges[8]`	0.95	the tagger's words
concept_edges	GEPIA2 python API —causes→ efficiency of users Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. the relation itself is separately evidenced · strength of the relation: 1 · note: The API boosts efficiency through batch processing and streamlined retrieval. also in: GEPIA2 python API · efficiency of users	`concept_edges[9]`	0.95	the tagger's words
concept_edges	stomach tumors —distinct-from→ adjacent normal tissues Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. the relation itself is separately evidenced · strength of the relation: 1 · note: The Th1-like signature is significantly higher in tumors than adjacent normal tissue. 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. also in: stomach tumors · adjacent normal tissues	`concept_edges[10]`	0.95	the tagger's words
content_tags	MAPK6 shows no association with breast cancer survival overall, and a significant unfavourable association within the Lumina A subtype Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`content_tags.findings[0]`	0.95	the tagger's words
content_tags	the Th1-like signature score is significantly higher in stomach tumours than in adjacent normal tissue Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`content_tags.findings[1]`	0.95	the tagger's words
content_tags	gene survival analyses are context-dependent, which is the stated reason for scanning many cancer types at once Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`content_tags.findings[2]`	0.95	the tagger's words
content_tags	signature score Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: signature score	`content_tags.definitions[0]`	0.95	the tagger's words
content_tags	isoform usage Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: isoform usage	`content_tags.definitions[1]`	0.95	the tagger's words
content_tags	Stacked Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: Stacked	`content_tags.definitions[2]`	0.95	the tagger's words
content_tags	Separated Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: Separated	`content_tags.definitions[3]`	0.95	the tagger's words
content_tags	Comparing Across Subtypes Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: Comparing Across Subtypes	`content_tags.definitions[4]`	0.95	the tagger's words
content_tags	198 619 isoforms — None Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`content_tags.quantities[0]`	0.95	the tagger's words
content_tags	84 cancer subtypes — None Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`content_tags.quantities[1]`	0.95	the tagger's words
content_tags	about 15% lower five-year survival in triple-negative breast cancer — None Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`content_tags.quantities[2]`	0.95	the tagger's words
content_tags	414 citations of GEPIA by May 2019, per Google Scholar — None Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`content_tags.quantities[3]`	0.95	the tagger's words
content_tags	about 400 000 analysis requests from about 110 000 distinct IP addresses — None Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`content_tags.quantities[4]`	0.95	the tagger's words
content_tags	5 functionalities in the python package — None Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`content_tags.quantities[5]`	0.95	the tagger's words
content_tags	MySQL version 5.7.17 — None Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`content_tags.quantities[6]`	0.95	the tagger's words
content_tags	log2(TPM + 1) Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: log2(TPM + 1)	`content_tags.statistics[0]`	0.95	the tagger's words
content_tags	hazard ratio in log10 scale Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: hazard ratio in log10 scale	`content_tags.statistics[1]`	0.95	the tagger's words
content_tags	P = 0.022 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: P = 0.022	`content_tags.statistics[2]`	0.95	the tagger's words
content_tags	P = 0.15 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: P = 0.15	`content_tags.statistics[3]`	0.95	the tagger's words
content_tags	Quantile-normalization Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: Quantile-normalization	`content_tags.statistics[4]`	0.95	the tagger's words
content_tags	isoform expression level Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: isoform expression level	`content_tags.variables[0]`	0.95	the tagger's words
content_tags	signature score Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: signature score	`content_tags.variables[1]`	0.95	the tagger's words
content_tags	hazard ratio Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: hazard ratio	`content_tags.variables[2]`	0.95	the tagger's words

Interpretive choices

Tags that could not be placed in the text:

none — every tag was located in the text

What was deliberately not tagged, and why, is recorded per paper by the tagger. Where a paper has no such record, this page says so rather than implying that nothing was declined.