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 WITHDRAWN AND REPLACED — the entry was wrong, and a corrected version of it appears in the entries below.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 An entry we have WITHDRAWN is removed from this page and kept in the record, with its reason.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 | how much of each immune and stromal cell population is present in a tissue sample, read out of a bulk transcriptome - and what kind of comparison the resulting number licenses 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 markers exist that are expressed in one and only one cell population, and whether their average expression tracks that population's abundance well enough to compare samples 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 | MCP-counter - ten populations scored from data-driven transcriptomic markers selected against curated negative controls, validated against in vitro RNA mixtures and against immunohistochemical cell densities, and explicitly scoped to inter-sample comparison in arbitrary units 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 bulk transcriptome averaging signals from every cell type present, so that the composition of the tissue is recoverable only through markers that belong to one population and nothing else 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 | if a gene is expressed in exactly one cell type and at a stable level within it, then its expression in a mixture is proportional to how much of that cell type is there - no unmixing, no reference matrix, no dependence on what else is in the sample. The whole method is that one property, and the paper says such genes are not guaranteed to exist 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 | a marker qualifies by separating positive from negative samples, so a population with no purified counter-example in a public repository cannot be given markers at all. Effector memory CD4 T cells are named as a casualty: they would need central memory CD4 and effector memory CD8 controls, and those were not available Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: the controls decide the vocabulary | mechanisms[1] | 0.95 | the tagger's words |
| mechanisms | 21 cancer types among the negative controls make the markers portable across tissues and remove any marker that any of those tissues expresses. NCAM1/CD56, a standard NK marker, is discarded because nervous malignant cells carry it - which protects every other tissue and gives up NK quantification in brain 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 | the score is a log2 mean of marker expression, so it moves with abundance and has no absolute meaning. Two consequences the paper states: the units depend on the measurement platform, and mapping them onto percentages would require calibrating samples of known composition - which is the step aran2017 later takes Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: a scale with no zero and no unit | mechanisms[3] | 0.95 | the tagger's words |
| limitations | the scores are in arbitrary units that depend on the gene expression platform, so only samples produced on the same platform can be compared 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 | transcriptomic markers are not guaranteed to exist for a given population, because the definition requires expression in one and only one cell type 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 | populations without publicly available negative controls were dropped from the method regardless of their interest 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 breadth of the control set discards markers that would work in a restricted setting - NCAM1 is lost because nervous malignant cells express it 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 | spatial localisation is lost relative to immunohistochemistry, and histological confirmation may be needed where contamination by surrounding tissue is unavoidable 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 | accuracy depends on the quality of the expression summary, and the populations estimated are usually rare, so high sequencing depth may be required Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[5] | 0.95 | the tagger's words |
| limitations | the prognostic meta-analysis is univariate and unadjusted for stage or treatment Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[6] | 0.95 | the tagger's words |
| limitations | surprising tissue-level results are referred back to histopathological knowledge rather than defended - the authors say the method should be compared against it Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[7] | 0.95 | the tagger's words |
| limitations | the cytotoxic lymphocyte population's mRNA was not controlled in the mixture experiment, so its validation is a linear model on the other populations rather than a direct calibration Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[8] | 0.95 | the tagger's words |
| transfers | the latin square, carried from agricultural experimental design into the layout of an RNA mixture so that no two populations' concentrations are collinear 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 | the ROC curve and the signal-to-noise ratio, carried from signal detection into the selection criteria for a gene marker 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 | 742 tumour cell line samples from 21 non-hematopoietic cancer types included as negative controls, with no hematopoietic line included and the reason stated Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: a marker that is merely abundant being taken for a marker that is specific - and the exclusion of hematopoietic lines removes a control that would have looked like the positive class · outcome: held | controls[0] | 0.95 | the tagger's words |
| controls | three simultaneous thresholds per candidate feature - a log2 expression difference, an AUC for identifying positive samples, and a signal-to-noise ratio Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: a feature qualifying on one favourable statistic; all three must be met at once, which is what makes the marker set conservative rather than large · outcome: held | controls[1] | 0.95 | the tagger's words |
| controls | two independent validation series on different array platforms, 4804 samples, with the selection criteria re-applied to see whether the same markers come out Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: the marker sets being an artefact of the discovery data or of one array platform - the overlap is tested for significance rather than eyeballed · outcome: held | controls[2] | 0.95 | the tagger's words |
| controls | an in vitro RNA mixture experiment with the populations laid out in two transposed latin squares Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: collinearity between the populations - without the latin square, a score could track its own population or any other that happened to co-vary with it · outcome: held | controls[3] | 0.95 | the tagger's words |
| controls | immunohistochemical digital quantification of three cell densities on tissue sections from 38 colorectal tumours, compared against the corresponding scores Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: in vitro mixtures standing in for tissue - purified RNA mixed in a tube is not a tumour, and the ex vivo check is on real infiltrate · outcome: held | controls[4] | 0.95 | the tagger's words |
| controls | a simulation in which the within-leukocyte proportions are held constant and equal while the tumour fraction varies, run through both methods Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: the two methods being compared on a case that cannot separate them - this one is built so that the correct answers differ, and both give theirs · outcome: held | controls[5] | 0.95 | the tagger's words |
| controls | marker sets from two previously published methods scored on the same three microenvironment series as this one Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: the comparison being against the competitors' published numbers rather than against their markers on identical data · outcome: held | controls[6] | 0.95 | the tagger's words |
| controls | a limit of detection established per population against non-hematopoietic control samples Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: a score being read as presence at any level - below the stated fraction the method cannot distinguish the population from a sample containing none · outcome: held | controls[7] | 0.95 | the tagger's words |
| controls | the same tumour analysis repeated on three transcriptomic platforms across more than 19,000 samples Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: a platform-specific artefact being reported as biology, within the constraint that the units themselves are not comparable across platforms · outcome: partial | controls[8] | 0.95 | the tagger's words |
| controls | the discovery set spanning 344 different culture conditions, purification methods and cell treatments Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: marker genes selected because of the conditions the reference cells were grown in rather than because of the cell type · outcome (stated by the tagger, no quotation): held | controls[9] | 0.95 | the tagger's words |
| concepts | MCP-counter Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: MCP-counter | concepts[0] | 0.95 | the paper's words |
| concepts | transcriptomic markers Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: transcriptomic markers | concepts[1] | 0.95 | the paper's words |
| concepts | cell population Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: cell population | concepts[2] | 0.95 | the paper's words |
| concepts | negative controls Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: negative controls | concepts[3] | 0.95 | the paper's words |
| concepts | arbitrary units Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: arbitrary units | concepts[4] | 0.95 | the paper's words |
| concepts | CIBERSORT Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: CIBERSORT | concepts[5] | 0.95 | the paper's words |
| concepts | flow cytometry Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: flow cytometry | concepts[6] | 0.95 | the paper's words |
| concepts | limit of detection Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: limit of detection | concepts[7] | 0.95 | the paper's words |
| concepts | immunohistochemical Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: immunohistochemical | concepts[8] | 0.95 | the paper's words |
| senses | what an MCP-counter score is - IN THE ABSTRACT: a robust quantification of the ABSOLUTE abundance of ten cell populations 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 | what an MCP-counter score is - IN THE RESULTS: a measure of the INTER-SAMPLE RELATIVE abundance of one population 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 | what an MCP-counter score is - IN THE DISCUSSION: linearly correlated with abundance, in ARBITRARY UNITS that depend on the gene expression platform, comparable only between samples run on the same platform 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 | what the score answers - MCP-COUNTER: is there more of this cell type in sample A than in sample B 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 | what the score answers - CIBERSORT: what share of the leukocytes in THIS sample are of this cell type. The paper's own simulation shows both answering correctly at once Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[4] | 0.95 | the tagger's words |
| claim_relations | critiques → methods that characterise proportions of immune populations within the leukocyte fraction while omitting the overall abundance of leukocytes in the sample 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 - not as wrong but as answering a different question; the paper's own simulation has it estimating stable within-leukocyte proportions correctly while total abundance changes 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 | qualifies → its own headline - the abstract says absolute abundance and the discussion says arbitrary, platform-dependent units comparable only within a platform 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 | extends → immunohistochemistry, which MCP-counter is said to be conceptually closest to - ten populations from one experiment, at the cost of all spatial information 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 | MCP-counter —distinct-from→ CIBERSORT Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. differs in: whether the comparison licensed is between cell types inside one sample or between samples for one cell type · the relation itself is separately evidenced · strength of the relation: 0.95 · differs in (stated by the tagger, no quotation): whether the comparison licensed is between cell types inside one sample or between samples for one cell type · the relation stated: one measures proportions within a sample, the other abundance of one population across samples, and the second pays for it in arbitrary units also in: MCP-counter · CIBERSORT | concept_edges[0] | 0.95 | the tagger's words |
| concept_edges | MCP-counter —distinct-from→ flow cytometry Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. differs in: which axis of comparison the measurement is built for · the relation itself is separately evidenced · strength of the relation: 0.95 · differs in (stated by the tagger, no quotation): which axis of comparison the measurement is built for · the relation stated: flow-cytometry-inspired methods describe the relative proportions of populations within one sample; this one is designed for the other axis also in: MCP-counter · flow cytometry | concept_edges[1] | 0.95 | the tagger's words |
| content_tags | in a simulation where within-leukocyte proportions are constant and tumour content varies, MCP-counter tracks abundance and CIBERSORT accurately reports stable proportions - both are right about different questions 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 | transcriptomic markers are not guaranteed to exist for a population, because the definition demands expression in one and only one cell type 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 | Populations lacking publicly available negative controls, with few positive samples, or with no identified markers were discarded. 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 | The screening discarded NCAM1 (CD56), a common NK-cell marker, because nervous malignant cells also express it. 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 | Scores correlated with known cell proportions in the RNA mixtures at Pearson 0.94 to 0.99. Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[5] | 0.95 | the tagger's words |
| content_tags | the limit of detection is below 2% of total sample RNA for every population assayed Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[6] | 0.95 | the tagger's words |
| content_tags | mapping the scores onto percentages would require calibrating samples of known composition, and setting-specific tuning may still be needed Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[7] | 0.95 | the tagger's words |
| content_tags | gene expression features expressed in one and only one cell population and whose expression shows little variation within that population - a definition the authors note is restrictive enough that such markers may not exist for a given population Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: transcriptomic markers | content_tags.definitions[0] | 0.95 | the tagger's words |
| content_tags | the scale of an MCP-counter score: linearly correlated with abundance, dependent on the gene expression platform, and comparable only between samples run on the same platform Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: arbitrary units | content_tags.definitions[1] | 0.95 | the tagger's words |
| content_tags | the Pearson correlations between scores and known RNA proportions in the in vitro mixtures 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 AUC floor for every signature across 4804 validation samples 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 upper bound on the limit of detection for every population assayed - from 1/950 to 1/50 of total RNA depending on which Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: 2 % | content_tags.quantities[2] | 0.95 | the tagger's words |
| content_tags | tumour cell line samples included as negative controls, from 21 non-hematopoietic cancer types 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 | AUC Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: AUC | content_tags.statistics[0] | 0.95 | the tagger's words |
| content_tags | Pearson Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: Pearson | content_tags.statistics[1] | 0.95 | the tagger's words |
| content_tags | arbitrary units Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: arbitrary units | content_tags.variables[0] | 0.95 | the tagger's words |
| content_tags | limit of detection Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: limit of detection | content_tags.variables[1] | 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.