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The iPSC proteomic compendium

https://doi.org/10.1101/469916
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What this work says

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

inferredcites →https://doi.org/10.1002/jcb.21809openalex-snapshot
p21 activated kinase 5 activates Raf‐1 and targets it to mitochondria
inferredcites →https://doi.org/10.1002/pmic.201200451openalex-snapshot
The challenge of the proteome dynamic range and its implications for in‐depth proteomics
inferredcites →https://doi.org/10.1002/stem.1133openalex-snapshot
High Basal γH2AX Levels Sustain Self-Renewal of Mouse Embryonic and Induced Pluripotent Stem Cells
inferredcites →https://doi.org/10.1002/stem.1724openalex-snapshot
JMJD5 Regulates Cell Cycle and Pluripotency in Human Embryonic Stem Cells
inferredcites →https://doi.org/10.1007/978-1-4419-7037-4_5openalex-snapshot
Preservation of Genomic Integrity in Mouse Embryonic Stem Cells
inferredcites →https://doi.org/10.1016/j.bbrc.2013.05.078openalex-snapshot
Evidence that P12, a specific variant of P16INK4A, plays a suppressive role in human pancreatic carcinogenesis
inferredcites →https://doi.org/10.1016/j.cell.2007.11.019openalex-snapshot
Induction of Pluripotent Stem Cells from Adult Human Fibroblasts by Defined Factors
inferredcites →https://doi.org/10.1016/j.cell.2013.08.031openalex-snapshot
The Cell-Cycle State of Stem Cells Determines Cell Fate Propensity
inferredcites →https://doi.org/10.1016/j.cell.2016.08.008openalex-snapshot
Cellular Metabolism and Induced Pluripotency
inferredcites →https://doi.org/10.1016/j.cell.2018.01.029openalex-snapshot
The Human Transcription Factors
inferredcites →https://doi.org/10.1016/j.celrep.2015.12.037openalex-snapshot
Essential Function of Dicer in Resolving DNA Damage in the Rapidly Dividing Cells of the Developing and Malignant Cerebellum
inferredcites →https://doi.org/10.1016/j.celrep.2016.04.066openalex-snapshot
Discovery of a Small-Molecule BMP Sensitizer for Human Embryonic Stem Cell Differentiation
inferredcites →https://doi.org/10.1016/j.cmet.2015.02.002openalex-snapshot
Glycolysis-Mediated Changes in Acetyl-CoA and Histone Acetylation Control the Early Differentiation of Embryonic Stem Cells
inferredcites →https://doi.org/10.1016/j.jmb.2017.04.013openalex-snapshot
Protein Kinases in Pluripotency—Beyond the Usual Suspects
inferredcites →https://doi.org/10.1016/j.molcel.2013.11.002openalex-snapshot
PRP19 Transforms into a Sensor of RPA-ssDNA after DNA Damage and Drives ATR Activation via a Ubiquitin-Mediated Circuitry
inferredcites →https://doi.org/10.1016/j.molcel.2017.04.006openalex-snapshot
DNA Damage in Stem Cells
inferredcites →https://doi.org/10.1016/j.neuron.2014.02.015openalex-snapshot
Calcineurin Signaling Regulates Neural Induction through Antagonizing the BMP Pathway
inferredcites →https://doi.org/10.1016/j.stem.2008.07.001openalex-snapshot
NANOG Is a Direct Target of TGFβ/Activin-Mediated SMAD Signaling in Human ESCs
inferredcites →https://doi.org/10.1016/j.stem.2016.05.009openalex-snapshot
LIN28 Regulates Stem Cell Metabolism and Conversion to Primed Pluripotency
inferredcites →https://doi.org/10.1016/j.tibs.2011.05.002openalex-snapshot
How dormant origins promote complete genome replication
inferredcites →https://doi.org/10.1016/s0021-9258(19)68900-3openalex-snapshot
Energy metabolism of tumor cells. Requirement for a form of hexokinase with a propensity for mitochondrial binding.
inferredcites →https://doi.org/10.1038/cdd.2013.44openalex-snapshot
A human iPSC model of Ligase IV deficiency reveals an important role for NHEJ-mediated-DSB repair in the survival and genomic stability of induced pluripotent stem cells and emerging haematopoietic progenitors
inferredcites →https://doi.org/10.1038/cdd.2016.84openalex-snapshot
CDK1-PDK1-PI3K/Akt signaling pathway regulates embryonic and induced pluripotency
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/nbt.2839openalex-snapshot
ProteomeXchange provides globally coordinated proteomics data submission and dissemination
inferredcites →https://doi.org/10.1038/ncb2897openalex-snapshot
Causes and consequences of replication stress
inferredcites →https://doi.org/10.1038/ncb2928openalex-snapshot
Impact of genomic damage and ageing on stem cell function
inferredcites →https://doi.org/10.1038/ncomms2254openalex-snapshot
The RB family is required for the self-renewal and survival of human embryonic stem cells
inferredcites →https://doi.org/10.1038/ncomms4901openalex-snapshot
Mixed lineage kinases activate MEK independently of RAF to mediate resistance to RAF inhibitors
inferredcites →https://doi.org/10.1038/ng.2222openalex-snapshot
Vitamin C improves the quality of somatic cell reprogramming
inferredcites →https://doi.org/10.1038/nmeth.1580openalex-snapshot
A bioinformatic assay for pluripotency in human cells
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/sj.onc.1204614openalex-snapshot
Independent control of cell survival by Raf-1 and Bcl-2 at the mitochondria
inferredcites →https://doi.org/10.1042/bj20121627openalex-snapshot
The cell cycle and pluripotency
inferredcites →https://doi.org/10.1074/jbc.m908959199openalex-snapshot
Oxidative Stress Induces Protein Kinase D Activation in Intact Cells
inferredcites →https://doi.org/10.1074/mcp.m113.037309openalex-snapshot
A “Proteomic Ruler” for Protein Copy Number and Concentration Estimation without Spike-in Standards
inferredcites →https://doi.org/10.1083/jcb.201408106openalex-snapshot
Stemness factor Sall4 is required for DNA damage response in embryonic stem cells
inferredcites →https://doi.org/10.1089/ars.2016.6871openalex-snapshot
A Peroxidase Peroxiredoxin 1-Specific Redox Regulation of the Novel FOXO3 microRNA Target let-7
inferredcites →https://doi.org/10.1093/bioinformatics/bty823openalex-snapshot
The Encyclopedia of Proteome Dynamics: the KinoViewer
inferredcites →https://doi.org/10.1093/carcin/bgs300openalex-snapshot
Superoxide dismutase 3 is induced by antioxidants, inhibits oxidative DNA damage and is associated with inhibition of estrogen-induced breast cancer
inferredcites →https://doi.org/10.1093/nar/gkh131openalex-snapshot
UniProt: the Universal Protein knowledgebase
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/gkv1145openalex-snapshot
2016 update of the PRIDE database and its related tools
inferredcites →https://doi.org/10.1093/nar/gkv1351openalex-snapshot
The Reactome pathway Knowledgebase
inferredcites →https://doi.org/10.1093/nar/gkw1099openalex-snapshot
UniProt: the universal protein knowledgebase
inferredcites →https://doi.org/10.1093/nar/gkw1125openalex-snapshot
Protein dynamics of human RPA and RAD51 on ssDNA during assembly and disassembly of the RAD51 filament
inferredcites →https://doi.org/10.1093/nar/gkx807openalex-snapshot
The Encyclopedia of Proteome Dynamics: a big data ecosystem for (prote)omics
inferredcites →https://doi.org/10.1111/j.1365-2184.2011.00753.xopenalex-snapshot
Cdc2: a monopotent or pluripotent CDK?
inferredcites →https://doi.org/10.1126/scisignal.aag1796openalex-snapshot
Genomics and evolution of protein phosphatases
inferredcites →https://doi.org/10.1128/mcb.24.15.6645-6652.2004openalex-snapshot
Vitamin C Is a Kinase Inhibitor: Dehydroascorbic Acid Inhibits IκBα Kinase β
inferredcites →https://doi.org/10.1152/physiolgenomics.00031.2016openalex-snapshot
Comprehensive database of human E3 ubiquitin ligases: application to aquaporin-2 regulation
inferredcites →https://doi.org/10.1371/journal.pone.0020914openalex-snapshot
Energy Metabolism in Human Pluripotent Stem Cells and Their Differentiated Counterparts
inferredcites →https://doi.org/10.1371/journal.pone.0056289openalex-snapshot
Sustained Levels of FGF2 Maintain Undifferentiated Stem Cell Cultures with Biweekly Feeding
inferredcites →https://doi.org/10.1371/journal.pone.0184861openalex-snapshot
DUSP5 and DUSP6, two ERK specific phosphatases, are markers of a higher MAPK signaling activation in BRAF mutated thyroid cancers
inferredcites →https://doi.org/10.1371/journal.pone.0185637openalex-snapshot
Cyclin D/CDK4/6 activity controls G1 length in mammalian cells
inferredcites →https://doi.org/10.15252/embj.201490446openalex-snapshot
Pluripotent stem cell energy metabolism: an update
inferredcites →https://doi.org/10.3389/fnins.2015.00022openalex-snapshot
Lactate is always the end product of glycolysis
inferredcites →https://doi.org/10.4161/cc.10.9.15421openalex-snapshot
The cell cycle inhibitor p27Kip1controls self-renewal and pluripotency of human embryonic stem cells by regulating the cell cycle,BrachyuryandTwist

What points at this work

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

inferred← citeshttps://doi.org/10.1074/mcp.ra119.001472openalex-snapshot
Multibatch TMT Reveals False Positives, Batch Effects and Missing Values
inferred← citeshttps://doi.org/10.1080/14789450.2024.2334033openalex-snapshot
Proteomics applications in next generation induced pluripotent stem cell models
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/10.1371/journal.pone.0323953openalex-snapshot
Screening for variable drug responses using human iPSC cohorts
inferred← citeshttps://doi.org/10.3390/cells8070703openalex-snapshot
Proteomics in the World of Induced Pluripotent Stem Cells
inferred← citeshttps://doi.org/10.7554/elife.57390openalex-snapshot
Population-scale proteome variation in human induced pluripotent stem cells
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