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 WITHDRAWN AND REPLACED — the entry was wrong, and a corrected version of it appears in the entries below.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 An entry we have WITHDRAWN is removed from this page and kept in the record, with its reason.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 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 |
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; 2 of 2 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 | inferring which cell types are present in a tissue from its bulk gene expression - and how far such an inference can be trusted 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 | whether enrichment scores can be made comparable across cell types and freed of the correlation between closely related ones, which is what signature methods could not previously do 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 | xCell - 489 signatures for 64 cell types chosen on held-out data, a power-law calibration onto a common scale, a spillover compensation borrowed from flow cytometry, and a null distribution for absence 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 | a measurement that returns a non-zero score for cell types that are not in the sample, and scores that look like proportions without being them 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 | closely related cell types share marker genes, so a signature for one is partly satisfied by the other - formally the same problem as fluorophores whose emission spectra overlap, and correctable by the same device, a compensation matrix estimated from mixtures where the true answer is known 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 |
| mechanisms | before compensation each cell type's score is computed alone, so one wrong inference cannot contaminate the rest; the correction couples them, which is exactly the property that makes deconvolution fragile - the paper accepts a limited amount of it and says how limited Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | mechanisms[1] | 0.95 | the tagger's words |
| mechanisms | a signature returns a score for any input, so a cell type absent from the mixture still receives one; only a null distribution built from mixtures that exclude it can say whether the score means presence Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | mechanisms[2] | 0.95 | the tagger's words |
| mechanisms | signatures are learned from cells isolated and profiled alone, and applied to cells sitting in tissue; if marker expression differs between those two states the method is calibrated on a population it never meets Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | mechanisms[3] | 0.95 | the tagger's words |
| limitations | the outputs are enrichment scores and cannot be interpreted as proportions, although they are calibrated to resemble them 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 | every method, this one included, performs significantly better on simulated mixtures than on real ones, and the real-data correlations are called far from perfect 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 | 56.4% of scores for cell types absent from a test mixture were non-negligible; the significance test brings that to 28.8% and costs 13.5 points of the true positives 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 spillover correction removes the independence between cell type inferences that was the signature approach's main protection - limited, and the authors say so 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 | on CD8+ T cells the method is beaten by using CD8A expression alone, with the caveat that the single gene may not be reliable in cancer 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 |
| limitations | for five cell types the null distribution degenerated to zero and was replaced by a hand-set constant of 0.001 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[5] | 0.85 | the tagger's words |
| transfers | spillover compensation, carried from flow cytometry - where fluorophore emission spectra overlap - into gene signature scoring, where marker genes overlap Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | transfers[0] | 0.95 | the tagger's words |
| transfers | null-distribution fitting for a presence test, carried from statistical hypothesis testing to ask whether a cell type is in a mixture at all Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | transfers[1] | 0.95 | the tagger's words |
| controls | signatures selected only if they hold up in a data source they were NOT trained on Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: overfitting to the source a signature was learned from as the explanation of its performance - the reliance on reference data that the paper names as the first of the field's seven problems · outcome: held | controls[0] | 0.95 | the tagger's words |
| controls | simulated mixtures built from an independent data source never used in development (GSE60424), scored before and after spillover compensation Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: the development data as the source of the improvement - a correction tuned on the training sources could otherwise be measuring itself · outcome: held | controls[1] | 0.95 | the tagger's words |
| controls | comparison against 53 previously published signatures and against CIBERSORT, a deconvolution method, on the same mixtures Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: the possibility that any signature set would score as well - the comparison is to named alternatives on identical inputs rather than to nothing · outcome: held | controls[2] | 0.95 | the tagger's words |
| controls | validation against cytometry immunophenotyping in 165 individuals across two independent studies, rather than against simulations alone Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: in-silico mixing as the reason the method works - arithmetic admixtures cannot test whether marker expression survives being in real tissue · outcome: partial | controls[3] | 0.95 | the tagger's words |
| controls | a null distribution per cell type, learned from random mixtures that EXCLUDE that cell type and its relatives, to test whether a score means presence at all Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: a non-zero score as evidence of presence - without this the method reports something for every cell type in every sample · outcome: partial | controls[4] | 0.95 | the tagger's words |
| controls | the significance threshold set at 20% and the trade-off stated, rather than chosen silently Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: a threshold tuned to flatter the result - the cost in true-positive power is reported alongside the gain in false-positive suppression · outcome: held | controls[5] | 0.95 | the tagger's words |
| concepts | enrichment scores Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: enrichment scores | concepts[0] | 0.95 | the paper's words |
| concepts | proportions Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: proportions | concepts[1] | 0.95 | the paper's words |
| concepts | spillover effect Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: spillover effect | concepts[2] | 0.95 | the paper'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[3] | 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[4] | 0.95 | the paper's words |
| concepts | simulated mixtures Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: simulated mixtures | concepts[5] | 0.95 | the paper's words |
| concepts | real mixtures Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: real mixtures | concepts[6] | 0.95 | the paper's words |
| concepts | tumor microenvironment Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: tumor microenvironment | concepts[7] | 0.95 | the paper's words |
| concepts | CD8A Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: CD8A | concepts[8] | 0.95 | the paper's words |
| concepts | ssGSEA Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: ssGSEA | concepts[9] | 0.95 | the paper's words |
| senses | xCell's performance - IN SIMULATED MIXTURES: outperforms every compared method in the large majority of cell types, across data sources and platforms 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 | xCell's performance - IN REAL MIXTURES: significantly better than the alternatives and still, in the authors' words, far from perfect - and beaten outright on CD8+ T cells by using one gene 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 | an xCell score - AS COMPUTED: a single-sample gene-set enrichment score, interpretable only against other samples 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 | an xCell score - AS CALIBRATED: deliberately transformed to resemble a proportion so cell types can be compared, and explicitly not usable as a proportion 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 |
| claim_relations | critiques → in-silico cell-type dissection methods generally, on seven named grounds including reliance on the reference source, narrow cell-type coverage, and validation on few cell types in few samples 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 | qualifies → CIBERSORT and other deconvolution approaches, whose strict inter-cell-type dependencies make them fragile on tumour expression profiles and tied to their reference matrix 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 |
| claim_relations | extends → gene set enrichment analysis, by calibrating its scores onto a common scale and compensating the correlation between related signatures Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | claim_relations[2] | 0.95 | the tagger's words |
| claim_relations | qualifies → its own results and every comparable method's - digital dissection findings must be validated by other technologies before they are believed Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | claim_relations[3] | 0.95 | the tagger's words |
| concept_edges | enrichment scores —distinct-from→ proportions Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. differs in: whether the value can be read as a share of the mixture · the relation itself is separately evidenced · strength of the relation: 0.95 · differs in (stated by the tagger, no quotation): whether the value can be read as a share of the mixture · the relation stated: the score is calibrated to resemble a fraction and cannot be used as one also in: enrichment scores · proportions | concept_edges[0] | 0.95 | the tagger's words |
| concept_edges | simulated mixtures —contrasted-with→ real mixtures Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. differs in: whether the cells were mixed by arithmetic or by biology · the relation itself is separately evidenced · strength of the relation: 0.95 · differs in (stated by the tagger, no quotation): whether the cells were mixed by arithmetic or by biology · the relation stated: every method scores better on in-silico admixtures than on tissue also in: simulated mixtures · real mixtures | concept_edges[1] | 0.95 | the tagger's words |
| content_tags | every method, including this one, performs significantly better on simulated mixtures than on real ones 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 scores are calibrated to resemble proportions and cannot be used as proportions 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 | 56.4% of scores for cell types absent from a mixture were non-negligible before the significance test, and 28.8% after 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 | Spillover correction removes the strict independence between cell-type inferences, though compensation is limited and most inferences stay independent. 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 | on CD8+ T cells a single gene outperforms the whole method, with the caveat that the gene may be unreliable in cancer 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 | a cell type's score showing enrichment because a closely related cell type is present - the same shape as spectral overlap between fluorophores in flow cytometry Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: spillover effect | content_tags.definitions[0] | 0.95 | the tagger's words |
| content_tags | the inferences this method produces - strictly scores, calibrated to resemble proportions and explicitly not interpretable as them Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: enrichment scores | content_tags.definitions[1] | 0.95 | the tagger's words |
| content_tags | scores for cell types absent from the mixture that were nonetheless non-negligible 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 | the share of genes xCell requires that were actually present in one validation study 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 | the significance threshold, chosen as a stated trade-off 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 | ssGSEA Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: ssGSEA | content_tags.statistics[0] | 0.95 | the tagger's words |
| content_tags | p value Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: p value | content_tags.statistics[1] | 0.95 | the tagger's words |
| content_tags | enrichment scores Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: enrichment scores | 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.