standOff, and the article is at its publisher via the link below. 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 WITHDRAWN AND REPLACED — the entry was wrong, and a corrected version of it appears in the entries below.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 An entry we have WITHDRAWN is removed from this page and kept in the record, with its reason.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.| 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 | 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 |
This record holds no relations between concepts. A layer is empty when the tagger recorded nothing in it — which is not the same as the paper having nothing to record.
| facet | tag | field | conf. | whose words |
|---|---|---|---|---|
| object_of_study | immune cell composition of tumours - a quantity that is inferred from bulk transcriptome rather than counted, by six different algorithms 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 immune-infiltration estimates from public tumour data usable without committing to any one inference algorithm 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 platform that runs six estimation algorithms over uniformly pre-processed TCGA data and shows their outputs side by side 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 | tumour immune infiltration, whose direct measurement is limited enough that the field works from computational inference instead 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 | gene-signature methods score cell-type-specific gene sets INDEPENDENTLY per cell type; deconvolution methods model the tissue's expression as a WEIGHTED SUM of the component cells' profiles. Two different mathematical objects behind one output name Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | mechanisms[0] | 0.95 | the tagger's words |
| limitations | THE QUANTITY IS NOT MEASURED. `Due to the limitations of direct measurement methods, computational algorithms are often used to infer immune cell composition` - and the transcriptome `does not immediately indicate` it 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 | SIX ALGORITHMS, ONE OUTPUT NAME, AND ONLY TWO PRODUCE A QUANTITY ON A MEANINGFUL SCALE: `EPIC and quanTIseq have the advantage of directly generating scores interpreted as cell fractions`. The other four produce enrichment scores displayed beside them 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 | each algorithm is named with its own failure: TIMER handles tissue specificity but covers only six cell types, xCell covers more but MAY FAIL TO DETECT SIGNALS FROM HOMOGENEOUS SAMPLES 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 |
| limitations | the justification for running all six is a HOPE, in the authors' own word: `We hope that evaluating estimations from multiple algorithms might help the user gain more comprehensive and robust results` Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[3] | 0.95 | the tagger's words |
| limitations | and the cross-species use is caveated where it is offered: mouse estimations `should be interpreted with caution since human and the mouse tumors may have different immune properties` Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[4] | 0.95 | the tagger's words |
| controls | all TCGA samples are pre-processed UNIFORMLY before the six algorithms run, so the estimates differ by algorithm and not by pipeline Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: disagreement between algorithms that is really disagreement between normalisations - which is the only way the side-by-side display could mean anything · outcome: held | controls[0] | 0.95 | the tagger's words |
| controls | whether the six estimates are on the same scale Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: nothing - EPIC and quanTIseq generate cell fractions and the rest do not, and the platform shows all six together without reconciling them · outcome: failed | controls[1] | 0.95 | the tagger's words |
| controls | whether running six algorithms actually yields more robust results Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: nothing that is demonstrated here - the claim is 'We hope ... might help', with no comparison against single-algorithm use reported · outcome: absent-declared-unreported | controls[2] | 0.95 | the tagger's words |
| concepts | deconvolution Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: deconvolution | concepts[0] | 0.95 | the paper's words |
| concepts | cell fractions Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: cell fractions | concepts[1] | 0.95 | the paper's words |
| concepts | xCell Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: xCell | concepts[2] | 0.95 | the paper's words |
| concepts | TIMER Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: TIMER | concepts[3] | 0.95 | the paper's words |
| senses | immune infiltration level - AS DELIVERED BY THIS PLATFORM, SIX DIFFERENT QUANTITIES UNDER ONE HEADING. Two are cell fractions, four are enrichment scores, and the platform's design is to show them together rather than to reconcile them. THE NAME IS THE ONLY THING THE SIX SHARE 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 | estimation, AS OPPOSED TO MEASUREMENT - the paper's own framing throughout, and it is honest: direct measurement is limited, so the field infers. Every number this server is cited for is downstream of that sentence 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 | robustness, AS THIS PLATFORM OPERATIONALISES IT: agreement across six algorithms, displayed for the user to judge. Not a statistic, not a test - A LAYOUT. And the authors say they HOPE it helps 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 |
| claim_relations | critiques → reliance on any single immune-infiltration algorithm, since the two families have variable performance advantages across cell types and tumours Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | claim_relations[0] | 0.95 | the tagger's words |
| claim_relations | extends → the original TIMER web server, which used one algorithm where this uses six Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | claim_relations[1] | 0.95 | the tagger's words |
| content_tags | THE QUANTITY IS INFERRED, NOT MEASURED: due to the limitations of direct measurement methods, immune cell composition is computed from bulk transcriptome 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 | EPIC and quanTIseq directly generate scores interpreted as cell fractions 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 | each algorithm carries its own failure mode - TIMER covers only six cell types, xCell may fail to detect signals from homogeneous samples 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 | the reason for running all six is stated as a HOPE: `We hope that evaluating estimations from multiple algorithms might help the user gain more comprehensive and robust results` Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[3] | 0.95 | the tagger's words |
| content_tags | mouse estimations SHOULD BE INTERPRETED WITH CAUTION because human and mouse tumours may have different immune properties - the caveat is placed where the feature is offered Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[4] | 0.95 | the tagger's words |
| content_tags | methods that model the gene expression of a tissue sample as the weighted sum of the expression profiles from the cells in the population mix Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: Deconvolution | content_tags.definitions[0] | 0.95 | the tagger's words |
| content_tags | deconvolution Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: deconvolution | content_tags.statistics[0] | 0.95 | the tagger's words |
| content_tags | tissue specificity Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: tissue specificity | content_tags.variables[0] | 0.95 | the tagger's words |
Tags that could not be placed 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.