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DNA methylation-based immune cell deconvolution in solid tumors

https://doi.org/10.1101/619965

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What this work says

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

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ggplot2: Elegant Graphics for Data Analysis

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CircRNA circ-BANP-mediated miR-503/LARP1 signaling contributes to lung cancer progression

inferredcites →https://doi.org/10.1016/j.biopha.2016.12.097openalex-snapshot

Circular BANP, an upregulated circular RNA that modulates cell proliferation in colorectal cancer

inferredcites →https://doi.org/10.1016/j.cell.2009.04.013openalex-snapshot

Cyfip1 Is a Putative Invasion Suppressor in Epithelial Cancers

inferredcites →https://doi.org/10.1016/j.cell.2011.02.003openalex-snapshot

Activation of Multiple Proto-oncogenic Tyrosine Kinases in Breast Cancer via Loss of the PTPN12 Phosphatase

inferredcites →https://doi.org/10.1016/j.immuni.2013.10.003openalex-snapshot

Spatiotemporal Dynamics of Intratumoral Immune Cells Reveal the Immune Landscape in Human Cancer

inferredcites →https://doi.org/10.1016/s0002-9440(10)65173-5openalex-snapshot

Vascular Channel Formation by Human Melanoma Cells in Vivo and in Vitro: Vasculogenic Mimicry

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/ncomms9971openalex-snapshot

Systematic pan-cancer analysis of tumour purity

inferredcites →https://doi.org/10.1038/nmeth.3337openalex-snapshot

Robust enumeration of cell subsets from tissue expression profiles

inferredcites →https://doi.org/10.1038/nrclinonc.2017.101openalex-snapshot

The immune contexture in cancer prognosis and treatment

inferredcites →https://doi.org/10.1038/s41467-018-05570-1openalex-snapshot

Pan-cancer deconvolution of tumour composition using DNA methylation

inferredcites →https://doi.org/10.1056/nejmoa1406498openalex-snapshot

Genetic Basis for Clinical Response to CTLA-4 Blockade in Melanoma

inferredcites →https://doi.org/10.1093/bioinformatics/btu049openalex-snapshot

Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays

inferredcites →https://doi.org/10.1093/hmg/ddx275openalex-snapshot

Cell-type deconvolution from DNA methylation: a review of recent applications

inferredcites →https://doi.org/10.1093/nar/gkw124openalex-snapshot

DNA methylation in human epigenomes depends on local topology of CpG sites

inferredcites →https://doi.org/10.1111/j.1467-985x.2010.00676_9.xopenalex-snapshot

ggplot2: Elegant Graphics for Data Analysis

inferredcites →https://doi.org/10.1111/j.1467-9868.2010.00740.xopenalex-snapshot

Stability Selection

inferredcites →https://doi.org/10.1126/science.1203486openalex-snapshot

Cancer Immunoediting: Integrating Immunity’s Roles in Cancer Suppression and Promotion

inferredcites →https://doi.org/10.1126/science.aaa1348openalex-snapshot

Mutational landscape determines sensitivity to PD-1 blockade in non–small cell lung cancer

inferredcites →https://doi.org/10.1128/mcb.23.21.7600-7610.2003openalex-snapshot

Fibroblast Growth Factor 2-Mediated Translational Control of IAPs Blocks Mitochondrial Release of Smac/DIABLO and Apoptosis in Small Cell Lung Cancer Cells

inferredcites →https://doi.org/10.1172/jci80008openalex-snapshot

Tumor neoantigens: building a framework for personalized cancer immunotherapy

inferredcites →https://doi.org/10.1186/1471-2105-10-48openalex-snapshot

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

inferredcites →https://doi.org/10.1186/1471-2105-13-86openalex-snapshot

DNA methylation arrays as surrogate measures of cell mixture distribution

inferredcites →https://doi.org/10.1186/1471-2105-14-7openalex-snapshot

GSVA: gene set variation analysis for microarray and RNA-Seq data

inferredcites →https://doi.org/10.1186/1756-9966-27-48openalex-snapshot

Role of Smac/DIABLO in cancer progression

inferredcites →https://doi.org/10.1186/s12916-016-0705-4openalex-snapshot

Novel algorithmic approach predicts tumor mutation load and correlates with immunotherapy clinical outcomes using a defined gene mutation set

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/s13059-016-1092-zopenalex-snapshot

Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures

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/10.1214/10-aoas377openalex-snapshot

Random lasso

inferredcites →https://doi.org/10.1371/journal.pone.0085592openalex-snapshot

Decreased Expression of PTPN12 Correlates with Tumor Recurrence and Poor Survival of Patients with Hepatocellular Carcinoma

inferredcites →https://doi.org/10.18632/oncotarget.3588openalex-snapshot

Tyrosine-protein phosphatase non-receptor type 12 expression is a good prognostic factor in resectable non-small cell lung cancer

inferredcites →https://doi.org/10.18637/jss.v033.i01openalex-snapshot

Regularization Paths for Generalized Linear Models via Coordinate Descent

inferredcites →https://doi.org/10.5114/wo.2014.47136openalex-snapshot

Review The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge

What points at this work

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

inferred← citeshttps://doi.org/10.1002/mc.23501openalex-snapshot

Plasma cell‐free DNA methylome profiling in pre‐ and post‐surgery oral cavity squamous cell carcinoma

inferred← citeshttps://doi.org/10.1016/bs.mie.2020.01.001openalex-snapshot

Computational methods in tumor immunology

inferred← citeshttps://doi.org/10.3390/cancers12103054openalex-snapshot

A Methylation-Based Reclassification of Bladder Cancer Based on Immune Cell Genes

inferred← citeshttps://doi.org/10.3390/genes12060854openalex-snapshot

A Sparse and Low-Rank Regression Model for Identifying the Relationships Between DNA Methylation and Gene Expression Levels in Gastric Cancer and the Prediction of Prognosis

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