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Population-scale proteome variation in human induced pluripotent stem cells

https://doi.org/10.1101/439216
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What this work says

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

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Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells
inferredcites →https://doi.org/10.1016/j.cels.2017.08.013openalex-snapshot
Widespread Post-transcriptional Attenuation of Genomic Copy-Number Variation in Cancer
inferredcites →https://doi.org/10.1016/j.msard.2017.10.017openalex-snapshot
Vaccinia Related Kinase 2 (VRK2) expression in neurological disorders: schizophrenia, epilepsy and multiple sclerosis
inferredcites →https://doi.org/10.1016/j.stem.2016.11.005openalex-snapshot
Analysis of Transcriptional Variability in a Large Human iPSC Library Reveals Genetic and Non-genetic Determinants of Heterogeneity
inferredcites →https://doi.org/10.1016/j.stem.2017.01.011openalex-snapshot
A Drug Screen using Human iPSC-Derived Hepatocyte-like Cells Reveals Cardiac Glycosides as a Potential Treatment for Hypercholesterolemia
inferredcites →https://doi.org/10.1016/j.stem.2017.03.009openalex-snapshot
Large-Scale Profiling Reveals the Influence of Genetic Variation on Gene Expression in Human Induced Pluripotent Stem Cells
inferredcites →https://doi.org/10.1016/j.stem.2018.06.002openalex-snapshot
Human iPSC-Derived Natural Killer Cells Engineered with Chimeric Antigen Receptors Enhance Anti-tumor Activity
inferredcites →https://doi.org/10.1016/j.stemcr.2017.03.012openalex-snapshot
iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types
inferredcites →https://doi.org/10.1021/ac0262560openalex-snapshot
Tandem Mass Tags: A Novel Quantification Strategy for Comparative Analysis of Complex Protein Mixtures by MS/MS
inferredcites →https://doi.org/10.1021/ac502040vopenalex-snapshot
MultiNotch MS3 Enables Accurate, Sensitive, and Multiplexed Detection of Differential Expression across Cancer Cell Line Proteomes
inferredcites →https://doi.org/10.1021/pr101065jopenalex-snapshot
Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment
inferredcites →https://doi.org/10.1038/mp.2015.23openalex-snapshot
A novel Alzheimer disease locus located near the gene encoding tau protein
inferredcites →https://doi.org/10.1038/mp.2016.212openalex-snapshot
Common variants on 2p16.1, 6p22.1 and 10q24.32 are associated with schizophrenia in Han Chinese population
inferredcites →https://doi.org/10.1038/msb.2010.106openalex-snapshot
Defining the transcriptome and proteome in three functionally different human cell lines
inferredcites →https://doi.org/10.1038/msb.2011.84openalex-snapshot
The quantitative proteomes of human‐induced pluripotent stem cells and embryonic stem cells
inferredcites →https://doi.org/10.1038/nature10098openalex-snapshot
Global quantification of mammalian gene expression control
inferredcites →https://doi.org/10.1038/nature12223openalex-snapshot
Variation and genetic control of protein abundance in humans
inferredcites →https://doi.org/10.1038/nature13302openalex-snapshot
A draft map of the human proteome
inferredcites →https://doi.org/10.1038/nature15393openalex-snapshot
A global reference for human genetic variation
inferredcites →https://doi.org/10.1038/nature18270openalex-snapshot
Defining the consequences of genetic variation on a proteome-wide scale
inferredcites →https://doi.org/10.1038/nature22403openalex-snapshot
Common genetic variation drives molecular heterogeneity in human iPSCs
inferredcites →https://doi.org/10.1038/nbt.1511openalex-snapshot
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
inferredcites →https://doi.org/10.1038/nmeth.1699openalex-snapshot
Proteomic and phosphoproteomic comparison of human ES and iPS cells
inferredcites →https://doi.org/10.1038/nmeth.4197openalex-snapshot
Salmon provides fast and bias-aware quantification of transcript expression
inferredcites →https://doi.org/10.1038/nprot.2011.457openalex-snapshot
Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses
inferredcites →https://doi.org/10.1038/nprot.2016.136openalex-snapshot
The MaxQuant computational platform for mass spectrometry-based shotgun proteomics
inferredcites →https://doi.org/10.1038/nrg3185openalex-snapshot
Insights into the regulation of protein abundance from proteomic and transcriptomic analyses
inferredcites →https://doi.org/10.1038/s41586-018-0175-2openalex-snapshot
Genomic atlas of the human plasma proteome
inferredcites →https://doi.org/10.1038/s41588-017-0005-8openalex-snapshot
Molecular and functional variation in iPSC-derived sensory neurons
inferredcites →https://doi.org/10.1080/15476278.2015.1011921openalex-snapshot
Large-scale generation of human iPSC-derived neural stem cells/early neural progenitor cells and their neuronal differentiation
inferredcites →https://doi.org/10.1093/bioinformatics/btp616openalex-snapshot
edgeR : a Bioconductor package for differential expression analysis of digital gene expression data
inferredcites →https://doi.org/10.1093/bioinformatics/bts635openalex-snapshot
STAR: ultrafast universal RNA-seq aligner
inferredcites →https://doi.org/10.1093/bioinformatics/btt656openalex-snapshot
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
inferredcites →https://doi.org/10.1093/bioinformatics/btu655openalex-snapshot
SNPsnap: a Web-based tool for identification and annotation of matched SNPs
inferredcites →https://doi.org/10.1093/bioinformatics/btv722openalex-snapshot
Fast and efficient QTL mapper for thousands of molecular phenotypes
inferredcites →https://doi.org/10.1093/humrep/dem411openalex-snapshot
Expression of pluripotent stem cell markers in the human fetal ovary
inferredcites →https://doi.org/10.1093/nar/gkp914openalex-snapshot
CORUM: the comprehensive resource of mammalian protein complexes—2009
inferredcites →https://doi.org/10.1093/nar/gkt1115openalex-snapshot
The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases
inferredcites →https://doi.org/10.1093/nar/gkw1133openalex-snapshot
The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog)
inferredcites →https://doi.org/10.1093/nar/gkw937openalex-snapshot
The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible
inferredcites →https://doi.org/10.1093/nar/gkx1098openalex-snapshot
Ensembl 2018
inferredcites →https://doi.org/10.1101/003905openalex-snapshot
LIMIX: genetic analysis of multiple traits
inferredcites →https://doi.org/10.1126/science.1136800openalex-snapshot
Clustering by Passing Messages Between Data Points
inferredcites →https://doi.org/10.1126/science.1260793openalex-snapshot
Impact of regulatory variation from RNA to protein
inferredcites →https://doi.org/10.1192/bjp.bp.115.161950openalex-snapshot
VRK2 gene expression in schizophrenia, bipolar disorder and healthy controls
inferredcites →https://doi.org/10.1371/journal.pgen.1000888openalex-snapshot
Trait-Associated SNPs Are More Likely to Be eQTLs: Annotation to Enhance Discovery from GWAS
inferredcites →https://doi.org/10.1371/journal.pgen.1004192openalex-snapshot
Protein Quantitative Trait Loci Identify Novel Candidates Modulating Cellular Response to Chemotherapy
inferredcites →https://doi.org/10.1371/journal.pgen.1004432openalex-snapshot
Genetic Background Drives Transcriptional Variation in Human Induced Pluripotent Stem Cells
inferredcites →https://doi.org/10.1634/stemcells.2007-0605openalex-snapshot
Expression of Pluripotent Stem Cell Markers in the Human Fetal Testis
inferredcites →https://doi.org/10.3233/jad-2011-111163openalex-snapshot
Potential Roles of Peroxisomes in Alzheimer's Disease and in Dementia of the Alzheimer's Type

What points at this work

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

inferred← citeshttps://doi.org/10.1007/s10557-021-07175-1openalex-snapshot
Integration of Transformative Platforms for the Discovery of Causative Genes in Cardiovascular Diseases
inferred← citeshttps://doi.org/10.1016/j.tips.2020.02.005openalex-snapshot
Multiparametric Assays for Accelerating Early Drug Discovery
inferred← citeshttps://doi.org/10.1038/s41467-020-14457-zopenalex-snapshot
Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression
inferred← citeshttps://doi.org/10.1038/s42003-022-03831-wopenalex-snapshot
Shared regulation and functional relevance of local gene co-expression revealed by single cell analysis
inferred← citeshttps://doi.org/10.1074/mcp.ra118.001280openalex-snapshot
Multi-omics Characterization of Interaction-mediated Control of Human Protein Abundance levels
inferred← citeshttps://doi.org/10.1101/497396openalex-snapshot
Optimising multi-batch TMT analysis to mitigate inflation of missing values, false positives and diminished inter batch accuracy
inferred← citeshttps://doi.org/10.1101/630996openalex-snapshot
Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression
inferred← citeshttps://doi.org/10.1242/dmm.042317openalex-snapshot
Addressing variability in iPSC-derived models of human disease: guidelines to promote reproducibility
inferred← citeshttps://doi.org/10.1371/journal.pgen.1008785openalex-snapshot
Linking protein to phenotype with Mendelian Randomization detects 38 proteins with causal roles in human diseases and traits
inferred← citeshttps://doi.org/10.3390/genes15040495openalex-snapshot
Heritability of Gene Expression Measured from Peripheral Blood in Older Adults
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