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MIXTURE: an improved algorithm for immune tumor microenvironment estimation based on gene expression data

https://doi.org/10.1101/726562
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1016/j.breast.2016.09.002openalex-snapshot
Tumor microenvironment-mediated chemoresistance in breast cancer
inferredcites →https://doi.org/10.1016/j.cell.2017.09.028openalex-snapshot
Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab
inferredcites →https://doi.org/10.1016/j.celrep.2019.01.041openalex-snapshot
RNA-Seq Signatures Normalized by mRNA Abundance Allow Absolute Deconvolution of Human Immune Cell Types
inferredcites →https://doi.org/10.1016/j.ctrv.2018.08.010openalex-snapshot
Tumor-associated macrophages in breast cancer: Innocent bystander or important player?
inferredcites →https://doi.org/10.1016/j.immuni.2016.04.023openalex-snapshot
Targeting T Cell Co-receptors for Cancer Therapy
inferredcites →https://doi.org/10.1016/j.it.2017.10.003openalex-snapshot
PD-1 hi CXCR5 − CD4 + T FH Cells Play Defense in Cancer and Offense in Arthritis
inferredcites →https://doi.org/10.1016/j.semcancer.2017.11.003openalex-snapshot
Breast cancer genomics and immuno-oncological markers to guide immune therapies
inferredcites →https://doi.org/10.1016/s0140-6736(86)90837-8openalex-snapshot
STATISTICAL METHODS FOR ASSESSING AGREEMENT BETWEEN TWO METHODS OF CLINICAL MEASUREMENT
inferredcites →https://doi.org/10.1038/cmi.2016.55openalex-snapshot
Human γδT-cell subsets and their involvement in tumor immunity
inferredcites →https://doi.org/10.1038/nature07205openalex-snapshot
Cancer-related inflammation
inferredcites →https://doi.org/10.1038/nature11412openalex-snapshot
Comprehensive molecular portraits of human breast tumours
inferredcites →https://doi.org/10.1038/nature13954openalex-snapshot
PD-1 blockade induces responses by inhibiting adaptive immune resistance
inferredcites →https://doi.org/10.1038/nature14011openalex-snapshot
Predictive correlates of response to the anti-PD-L1 antibody MPDL3280A in cancer patients
inferredcites →https://doi.org/10.1038/nature25501openalex-snapshot
TGFβ attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells
inferredcites →https://doi.org/10.1038/ncomms3612openalex-snapshot
Inferring tumour purity and stromal and immune cell admixture from expression data
inferredcites →https://doi.org/10.1038/ni.2703openalex-snapshot
Innate and adaptive immune cells in the tumor microenvironment
inferredcites →https://doi.org/10.1038/nm.3909openalex-snapshot
The prognostic landscape of genes and infiltrating immune cells across human cancers
inferredcites →https://doi.org/10.1038/nmeth.1830openalex-snapshot
Gene expression deconvolution in linear space
inferredcites →https://doi.org/10.1038/nmeth.1831openalex-snapshot
Gene expression deconvolution in linear space
inferredcites →https://doi.org/10.1038/nmeth.3337openalex-snapshot
Robust enumeration of cell subsets from tissue expression profiles
inferredcites →https://doi.org/10.1038/nrc3245openalex-snapshot
The immune contexture in human tumours: impact on clinical outcome
inferredcites →https://doi.org/10.1038/nrclinonc.2016.217openalex-snapshot
Tumour-associated macrophages as treatment targets in oncology
inferredcites →https://doi.org/10.1038/nrclinonc.2017.101openalex-snapshot
The immune contexture in cancer prognosis and treatment
inferredcites →https://doi.org/10.1038/nri3904openalex-snapshot
γδ T cells in cancer
inferredcites →https://doi.org/10.1038/onc.2008.251openalex-snapshot
Prediction of future metastasis and molecular characterization of head and neck squamous-cell carcinoma based on transcriptome and genome analysis by microarrays
inferredcites →https://doi.org/10.1038/s41568-019-0116-xopenalex-snapshot
The evolving landscape of biomarkers for checkpoint inhibitor immunotherapy
inferredcites →https://doi.org/10.1038/s41577-019-0127-6openalex-snapshot
Macrophages as regulators of tumour immunity and immunotherapy
inferredcites →https://doi.org/10.1038/s41587-019-0114-2openalex-snapshot
Determining cell type abundance and expression from bulk tissues with digital cytometry
inferredcites →https://doi.org/10.1080/2162402x.2016.1151594openalex-snapshot
CTLA4 blockade reduces immature myeloid cells in head and neck squamous cell carcinoma
inferredcites →https://doi.org/10.1093/bioinformatics/btt351openalex-snapshot
CellMix: a comprehensive toolbox for gene expression deconvolution
inferredcites →https://doi.org/10.1093/bioinformatics/btw704openalex-snapshot
A novel non-parametric method for uncertainty evaluation of correlation-based molecular signatures: its application on PAM50 algorithm
inferredcites →https://doi.org/10.1093/bioinformatics/bty019openalex-snapshot
Computational deconvolution of transcriptomics data from mixed cell populations
inferredcites →https://doi.org/10.1093/bioinformatics/bty926openalex-snapshot
dtangle: accurate and robust cell type deconvolution
inferredcites →https://doi.org/10.1093/jnci/djw192openalex-snapshot
Relevance of Tumor-Infiltrating Immune Cell Composition and Functionality for Disease Outcome in Breast Cancer
inferredcites →https://doi.org/10.1111/apm.12356openalex-snapshot
Peripheral blood monocyte and T‐lymphocyte activation levels at diagnosis predict long‐term survival in head and neck squamous cell carcinoma patients
inferredcites →https://doi.org/10.1111/his.12607openalex-snapshot
High numbers of macrophages, especially M2‐like ( CD 163‐positive), correlate with hyaluronan accumulation and poor outcome in breast cancer
inferredcites →https://doi.org/10.1126/science.1129139openalex-snapshot
Type, Density, and Location of Immune Cells Within Human Colorectal Tumors Predict Clinical Outcome
inferredcites →https://doi.org/10.1126/science.342.6165.1432openalex-snapshot
Cancer Immunotherapy
inferredcites →https://doi.org/10.1158/1078-0432.ccr-14-2926openalex-snapshot
Orchestration and Prognostic Significance of Immune Checkpoints in the Microenvironment of Primary and Metastatic Renal Cell Cancer
inferredcites →https://doi.org/10.1158/2326-6066.cir-14-0205openalex-snapshot
Immunity in Head and Neck Cancer
inferredcites →https://doi.org/10.1159/000046955openalex-snapshot
Using Artificial Intelligence to Predict the Equilibrated Postdialysis Blood Urea Concentration
inferredcites →https://doi.org/10.1172/jci67428openalex-snapshot
CD4+ follicular helper T cell infiltration predicts breast cancer survival
inferredcites →https://doi.org/10.1186/s12967-017-1378-2openalex-snapshot
Gamma-delta (γδ) T cells: friend or foe in cancer development?
inferredcites →https://doi.org/10.1186/s13045-017-0430-2openalex-snapshot
Tumor-associated macrophages: from basic research to clinical application
inferredcites →https://doi.org/10.1186/s13059-016-1028-7openalex-snapshot
Comprehensive analyses of tumor immunity: implications for cancer immunotherapy
inferredcites →https://doi.org/10.1186/s13059-016-1070-5openalex-snapshot
Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression
inferredcites →https://doi.org/10.1186/s13059-017-1256-5openalex-snapshot
Revisit linear regression-based deconvolution methods for tumor gene expression data
inferredcites →https://doi.org/10.1186/s13059-017-1349-1openalex-snapshot
xCell: digitally portraying the tissue cellular heterogeneity landscape
inferredcites →https://doi.org/10.1186/s40425-015-0088-7openalex-snapshot
nCounter® PanCancer Immune Profiling Panel (NanoString Technologies, Inc., Seattle, WA)
inferredcites →https://doi.org/10.1371/journal.pmed.1002194openalex-snapshot
Patterns of Immune Infiltration in Breast Cancer and Their Clinical Implications: A Gene-Expression-Based Retrospective Study
inferredcites →https://doi.org/10.1371/journal.pone.0006098openalex-snapshot
Deconvolution of Blood Microarray Data Identifies Cellular Activation Patterns in Systemic Lupus Erythematosus
inferredcites →https://doi.org/10.14670/hh-11-916openalex-snapshot
The role of tumor-associated macrophage in breast cancer biology.
inferredcites →https://doi.org/10.18632/oncotarget.13051openalex-snapshot
γδ T cells in cancer immunotherapy
inferredcites →https://doi.org/10.3389/fcell.2018.00038openalex-snapshot
Targeting Tumor-Associated Macrophages as a Potential Strategy to Enhance the Response to Immune Checkpoint Inhibitors
inferredcites →https://doi.org/10.3389/fimmu.2017.00828openalex-snapshot
Reprogramming of Tumor-Associated Macrophages with Anticancer Therapies: Radiotherapy versus Chemo- and Immunotherapies
inferredcites →https://doi.org/10.3389/fimmu.2018.01395openalex-snapshot
γδ T Cells and Tumor Microenvironment: From Immunosurveillance to Tumor Evasion
inferredcites →https://doi.org/10.5772/23133openalex-snapshot
Bedside Linear Regression Equations to Estimate Equilibrated Blood Urea

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1093/bib/bbaa358openalex-snapshot
Progress and challenge for computational quantification of tissue immune cells
inferred← citeshttps://doi.org/10.1101/2020.06.08.140764openalex-snapshot
Aging Interacts with Tumor Biology to Produce Major Changes in the Immune Tumor Microenvironment
inferred← citeshttps://doi.org/10.1186/s13059-021-02363-6openalex-snapshot
Multi-omic profiling of lung and liver tumor microenvironments of metastatic pancreatic cancer reveals site-specific immune regulatory pathways
inferred← citeshttps://doi.org/10.1214/20-aoas1395openalex-snapshot
The role of scale in the estimation of cell-type proportions
inferred← citeshttps://doi.org/10.3390/cancers12082227openalex-snapshot
Pre-Existing Tumoral B Cell Infiltration and Impaired Genome Maintenance Correlate with Response to Chemoradiotherapy in Locally Advanced Rectal Cancer
inferred← citeshttps://doi.org/10.3390/cancers12092710openalex-snapshot
Landscape of Genome-Wide DNA Methylation of Colorectal Cancer Metastasis
inferred← citeshttps://doi.org/10.3390/cells10010045openalex-snapshot
Pan-Cancer Molecular Patterns and Biological Implications Associated with a Tumor-Specific Molecular Signature
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