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CrossCheck: an open-source, high-throughput database analysis software

This software will find common hits between a high-throughput reference database* (A) and a user-defined high-throughput dataset (B):

    STEP 1

    (A) Select a CrossCheck reference database:
    View    

    OR


    (A) Upload your own reference database file (TSV file):
   


    STEP 2

    (B) Paste your dataset (a column of gene symbols):

   




*CrossCheck Reference Database:
      Total datasets: 16,231
      Total hits/interactions: 614,161
      Last updated: 05-Feb-2017

Major databases included in CrossCheck reference database (05-Feb-2017):
NCBI/Gene (used for protein-protein interaction database building)
NCBI/PubMed (used for 75 recent genome-wide and proteomics screen studies)
Uniprot (protein knowledgebase)
COSMIC (cancer mutation database)
BioGRID (protein-protein interaction database)
BioPlex (protein-protein interaction database)
PhosphoSitePlus (kinase-substrate database)
PhosphoNetworks (kinase-substrate database)
Proteome-wide kinase motif prediction database (CrossCheck)

Major high-throughput screen studies included in the CrossCheck reference database (05-Feb-2017):
Taxol apoptosis protectors (Díaz-Martínez, 2014, EMBO J; PMID: 25024437)
Taxol apoptosis sensitizers (Díaz-Martínez, 2014, EMBO J; PMID: 25024437)
Genes mediating TNF induced NFKB activity (Nickles et al, 2012, Mol Cell Biol; PMID: 22733992)
Genes inhibiting TNF induced NFKB activity (Nickles et al, 2012, Mol Cell Biol; PMID: 22733992)
897 genes expressed exclusively in Microglia (>20 FPKM) (http://web.stanford.edu/group/barres_lab/brain_rnaseq.html)
NFKB targets (http://www.bu.edu/nf-kb/gene-resources/target-genes/)
Autophagy flux inhibitors (Lipinski et al, 2010, Dev Cell; PMID: 20627085)
Candidates for positive regulators of normal growth (DESeq) (Beronja et al., 2013, Nature; PMID: 23945586)
Candidates for negative regulators of normal growth (DESeq) (Beronja et al., 2013, Nature; PMID: 23945586)
Candidates for positive regulators of oncogenic growth (DESeq) (Beronja et al., 2013, Nature; PMID: 23945586)
Candidates for negative regulators of oncogenic growth (DESeq) (Beronja et al., 2013, Nature; PMID: 23945586)
Knockdown causes sensitivity to tamoxifen (Mendes-Pereira et al., 2011, PNAS; PMID: 21482774)
Knockdown causes resistance to tamoxifen (Mendes-Pereira et al., 2011, PNAS; PMID: 21482774)
CRISPR screen for essential genes in the human genome - KBM7 cells, p<0.05 (Wang et al., 2015, Science; PMID: 26472758)
CRISPR screen for essential genes in the human genome - K562 cells, p<0.05 (Wang et al., 2015, Science; PMID: 26472758)
CRISPR screen for essential genes in the human genome - Jiyoye cells, p<0.05 (Wang et al., 2015, Science; PMID: 26472758)
CRISPR screen for essential genes in the human genome - Raji cells, p<0.05 (Wang et al., 2015, Science; PMID: 26472758)
Ca2+ influx mediators (Genome-wide RNAi screen in Drosophila cells) (Vig et al., 2006, Science; PMID: 16645049)
Modifiers of the Circadian Clock in Human Cells (Genome-wide RNAi screen; Zhang et al., 2009, Cell; PMID: 19765810)
Synthetic Lethal Interactions with the Ras Oncogene (Genome-wide RNAi screen; Luo et al., 2009, Cell; PMID: 19490893)
Mediators of Genome Stability (Genome-wide siRNA Screen; Significant gamma-H2AX Values; p<0.05) (Paulsen et al., 2009, Mol Cell; PMID: 19647519)
Camptothecin sensitivity (Genome-wide RNAi screen; O'Connell et al., 2010, Mol Cell; PMID: 21055985)
Modulators of ciliogenesis (Genome-wide RNAi screen; Kim et al., 2016, Biochimica et Biophysica Acta; PMID: 27033521)
Regulators of centriole biogenesis (Genome-wide RNAi screen; Balestra et al., 2010, Dev Cell; PMID: 23769972)
Regulators of beta-catenin-dependent WNT Signaling (Genome-wide RNAi screen; Madan et al., 2010, PNAS; PMID: 27162353)
Genes Essential for West-Nile-Virus-Induced Cell Death (Genome-wide RNAi screen; Ma et al., 2015, Cell Reports; PMID: 26190106)
Protector Hits from Taxol-Induced Mitotic Arrest and Apoptosis (Genome-wide RNAi screen; Díaz-Martínez et al., 2014, EMBO J; PMID: 25024437)
Sensitizer Hits from Taxol-Induced Mitotic Arrest and Apoptosis (Genome-wide RNAi screen; Díaz-Martínez et al., 2014, EMBO J; PMID: 25024437)
Modulators of Ca2+/NFAT signalling (Genome-wide RNAi screen; Sharma et al., 2013, Nature; PMID: 23792561)
Host Factors Necessary for Growth of the Parasite Toxoplasma gondii (Genome-wide RNAi screen; Moser et al., 2013, PLoS ONE; PMID: 23840822)
Host Factors Necessary for human papillomavirus infection (Genome-wide RNAi screen; Lipovsky et al., 2013, PNAS; PMID: 23569269)
Host Factors Necessary for poxvirus morphogenesis (Table S2 - Genome-wide RNAi screen; Sivan et al., 2013, PNAS; PMID: 23401514)
Host factors affecting C. burnetii growth phenotypes (Genome-wide RNAi screen; McDonough et al., 2013, MBio; PMID: 23362322)
Regulators of clathrin-coated vesicle formation (Kozik et al., 2013, Nat Cell Biol, PMID: 23263279)
Host Proteins Promoting Alphavirus Entry (Genome-wide RNAi screen; Ooi et al., 2013, PLoS Pathog, PMID: 24367265)
Host Proteins Inhibiting Alphavirus Entry (Genome-wide RNAi screen; Ooi et al., 2013, PLoS Pathog, PMID: 24367265)
SOD1 Regulators (Genome-wide RNAi screen; Somalinga et al., 2012, PLoS One, PMID: 22563406)
Modulators of Cell Death Induced by Proteasome Inhibitor Bortezomib (Genome-wide RNAi screen; Chen et al., 2010, Cancer Res, PMID: 20460535)
Regulators of human papillomavirus oncogene expression (Genome-wide RNAi screen; Smith et al., 2010, PNAS, PMID: 20133580)
Enhancers of a kinesin-5 inhibitor K5I (Genome-wide RNAi screen; Tsui et al., 2009, PLoS One, PMID: 19802393)
Suppressors of a kinesin-5 inhibitor K5I (Genome-wide RNAi screen; Tsui et al., 2009, PLoS One, PMID: 19802393)
Regulators of caspase activation (Genome-wide RNAi screen; Yi et al., 2007, J Cell Biol, PMID: 17998402)
Genes essential for cell division (Genome-wide RNAi screen; Kittler et al., 2004, Nature, PMID: 15616564)
Positive modulators of p62/Sqstm1/canonical macroautophagy (Genome-wide CRISPR screen; DeJesus et al., 2016, eLIFE, PMID: 27351204)
Negative modulators of p62/Sqstm1/canonical macroautophagy (Genome-wide CRISPR screen; DeJesus et al., 2016, eLIFE, PMID: 27351204)
Host factors required for diphteria toxin-mediated toxicity (Genome-wide RNAi screen; Virreira Winter et al., 2016, Sci Rep, PMID: 27351204)
Host factors required for Staphylococcus aureus α-hemolysin-mediated toxicity (Genome-wide RNAi screen; Virreira Winter et al., 2016, Sci Rep, PMID: 27351204)
Nigericin-resistant knockouts (1.5-fold sgRNA ratio) (Genome-wide CRISPR screen; Schmid-Burgk et al., 2016, J Biol Chem, PMID: 26553871)
Protein-coding genes affecting myeloid leukemia cell growth (MV4-11) (Genome-wide CRISPR screen; Wallace et al., 2016, PLoS One, PMID: 27081855)
miRNAs affecting myeloid leukemia cell growth (MV4-11) (Genome-wide CRISPR screen; Wallace et al., 2016, PLoS One, PMID: 27081855)
Novel modulators of HLA-I ERAD (Genome-wide RNAi screen; van de Weijer et al., 2014, Nat Commun, PMID: 24807418)
Crapome (Mellacheruvu et al., 2013, Nat Methods; PMID: 23921808)
Peripheral membrane proteins (Nastou et al, 2014, Biomed Res Int; PMID: 25057483)
Proteome of mouse photoreceptor sensory cilium (Liu et al, 2007, Mol Cell Proteomics; PMID: 17494944)
mTORC1 targets - Rapamycin >2-fold (Yu, 2011, Science; PMID: 21659605)
mTOR targets - Ku-0063794 >2-fold (Yu, 2011, Science; PMID: 21659605)
Complex-I TNF-5min/ctrl interactors (>1.5-fold) (Wagner, 2016, EMBO J, PMID: 27307491)
Complex-I TNF-15min/ctrl interactors (>1.5-fold) (Wagner, 2016, EMBO J, PMID: 27307491)
Complex-I TNF-5min/ctrl phosphorylated (>1.5-fold) (Wagner, 2016, EMBO J, PMID: 27307491)
Complex-I TNF-15min/ctrl phosphorylated (>1.5-fold) (Wagner, 2016, EMBO J, PMID: 27307491)
Complex-I TNF-5min/ctrl ubiquitinated (>1.5-fold) (Wagner, 2016, EMBO J, PMID: 27307491)
Complex-I TNF-15min/ctrl ubiquitinated (>1.5-fold) (Wagner, 2016, EMBO J, PMID: 27307491)
RIP3 WT/KO >1.5-fold (TNF-MEF) Wu et al 2012 MCP (PMID: 22942356)
RIP3 WT/KO >1.5-fold (LPS-macrophage) Wu et al 2012 MCP (PMID: 22942356)
Global Identification of Modular Cullin-Ring Ligase Substrates (Emanuele et al., 2011, Cell; PMID: 21963094)
AMPK substrates (Schaffer BE et al., 2015, Cell Metabolism; PMID: 26456332 )
Phosphorylated exclusively in G1-phase (Dephoure et al., 2008, PNAS; PMID: 18669648)
Phosphorylated exclusively in M-phase (Dephoure et al., 2008, PNAS; PMID: 18669648)
Phosphorylated in both G1-phase and in M-phase (Dephoure et al., 2008, PNAS; PMID: 18669648)
Ubiquitination in the DNA Damage Response (UV, >1.5-fold) (Elia et al., 2015, Mol Cell; PMID: 26051181)
Ubiquitination in the DNA Damage Response (IR, >1.5-fold) (Elia et al., 2015, Mol Cell; PMID: 26051181)
Phosphorylation in the DNA Damage Response (UV, >1.5-fold) (Elia et al., 2015, Mol Cell; PMID: 26051181)
Phosphorylation in the DNA Damage Response (IR, >1.5-fold) (Elia et al., 2015, Mol Cell; PMID: 26051181)
Proteins differentially phosphorylated upon CDKN3 knockdown (PhosphoScan proteomic platform (Cell Signaling Technology); Nalepa et al., 2013, J Cell Biol; PMID: 23775190)
The CRAPome - a contaminant repository for affinity purification-mass spectrometry data (Mellacheruvu et al., 2013, Nat Methods; PMID: 23921808)


Please email us at info[at]proteinguru.com to submit your published datasets to the CrossCheck reference database.

CrossCheck source codes