Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • Navigation/Query Panel:
    Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
    Rank description Gene Hugo Value Type Network Comparison Type Interaction Map red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 1980 to 2029 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    1980 tumor differentially expressed 1 protein like. [swissprot;acc:q9nrx5] SERINC1 209.539 207.529 1.00969
    1981 d-3-phosphoglycerate dehydrogenase (ec 1.1.1.95) (3-pgdh). [swissprot;acc:o43175] PHGDH
    1982 40s ribosomal protein s28. [swissprot;acc:p25112] no value 200.343 198.427 1.00966
    1983 lim protein (similar to rat protein kinase c-binding enigma); enigma homolog. [refseq;acc:nm_006457] PDLIM5 219.25 217.175 1.00955
    1984 e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409] EP400 219.26 217.193 1.00952
    1985 mitochondrial ribosomal protein l24. [refseq;acc:nm_024540] MRPL24
    1986 65 kda yes-associated protein (yap65). [swissprot;acc:p46937] YAP1
    1987 lin-7 homolog a; vertebrate lin7 homolog 1; tax interaction protein 33; mammalian lin-7 1. [refseq;acc:nm_004664] LIN7A 225.022 222.9
    1988 9 kda protein. [swissprot;acc:p13994] CCDC130 219.26 217.193
    1989 collagen alpha 3(iv) chain precursor (goodpasture antigen). [swissprot;acc:q01955] COL4A3 219.261 217.195 1.00951
    1990 collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400] no value 219.26 217.194
    1991 transcriptional co-activator with pdz-binding motif (taz). [refseq;acc:nm_015472] WWTR1
    1992 zasp protein (fragment). [sptrembl;acc:q9y4z3] LDB3 219.267 217.207 1.00948
    1993 huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146] HIP1R 189.052 190.835 1.00943
    1994 goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4] COL4A3BP 189.011 190.787 1.0094
    1995 huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291] HIP1 188.961 190.73 1.00936
    1996 sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911] SLC5A5 204.682 202.784
    1997 kidney and liver proline oxidase 1. [refseq;acc:nm_021232] PRODH2 204.651 202.759 1.00933
    1998 ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] C15orf15 200.219 198.37 1.00932
    1999 solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913] SLC5A8 204.636 202.748 1.00931
    2000 sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289] SLC5A6 204.626 202.739
    2001 lin-7 homolog b; lin-7b protein; likely ortholog of mouse lin-7b; mammalian lin-7 protein 2; likely orholog of mouse lin 7 homolog b (c. elegans). [refseq;acc:nm_022165] LIN7B 225.02 222.948 1.00929
    2002 u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579] SNRPB2 214.775 216.769 1.00928
    2003 axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] DNALI1 208.315 206.41 1.00923
    2004 receptor protein-tyrosine kinase erbb-4 precursor (ec 2.7.1.112) (p180erbb4) (tyrosine kinase-type cell surface receptor her4). [swissprot;acc:q15303] ERBB4 225.019 222.969 1.00919
    2005 epidermal growth factor receptor precursor (ec 2.7.1.112) (receptor protein-tyrosine kinase erbb-1). [swissprot;acc:p00533] EGFR 222.971
    2006 receptor protein-tyrosine kinase erbb-2 precursor (ec 2.7.1.112) (p185erbb2) (neu proto-oncogene) (c-erbb-2) (tyrosine kinase-type cell surface receptor her2) (mln 19). [swissprot;acc:p04626] ERBB2
    2007 2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [swissprot;acc:q9uj83] HACL1 222.969
    2008 receptor protein-tyrosine kinase erbb-3 precursor (ec 2.7.1.112) (c-erbb3) (tyrosine kinase-type cell surface receptor her3). [swissprot;acc:p21860] ERBB3
    2009 proteasome subunit beta type 10 precursor (ec 3.4.25.1) (proteasome mecl-1) (macropain subunit mecl-1) (multicatalytic endopeptidase complex subunit mecl-1). [swissprot;acc:p40306] CTRL 216.201 214.245 1.00913
    2010 tubulin-specific chaperone c (tubulin-folding cofactor c) (cfc). [swissprot;acc:q15814] TBCC 193.517 191.766
    2011 putative acyl-coa thioester hydrolase cgi-16 (ec 3.1.2.-). [swissprot;acc:q9y305] ACOT9
    2012 dead-box protein. [refseq;acc:nm_018665] DDX43
    2013 protein phosphatase 1, regulatory (inhibitor) subunit 12b isoform a; myosin phosphatase regulatory subunit; myosin phosphatase, target subunit 2. [refseq;acc:nm_002481] PPP1R12B 217.662 215.693
    2014 protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [refseq;acc:nm_002480] PPP1R12A 217.676 215.709 1.00912
    2015 dna topoisomerase iii alpha (ec 5.99.1.2). [swissprot;acc:q13472] TOP3A 217.941 215.979 1.00908
    2016 electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial precursor (ec 1.5.5.1) (etf-qo) (etf-ubiquinone oxidoreductase) (etf dehydrogenase) (electron-transferring- flavoprotein dehydrogenase). [swissprot;acc:q16134] ETFDH 199.092 197.301
    2017 ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] RRS1 127.397 128.553 1.00907
    2018 serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] PPP1CA
    2019 acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954] no value 215.799 213.865 1.00904
    2020 putative eukaryotic translation initiation factor 3 subunit (eif-3) (fragment). [swissprot;acc:o75153] KIAA0664 223.168 221.176 1.00901
    2021 hexaprenyldihydroxybenzoate methyltransferase, mitochondrial precursor (ec 2.1.1.114) (dihydroxyhexaprenylbenzoate methyltransferase) (3,4- dihydroxy-5-hexaprenylbenzoate methyltransferase) (dhhb methyltransferase) (dhhb-mt) (dhhb-mtase). [swissprot;acc:q9nzj6] COQ3 208.601 210.464 1.00893
    2022 atp synthase coupling factor b, mitochondrial precursor. [swissprot;acc:q99766] ATP5S
    2023 guanine deaminase (ec 3.5.4.3) (guanase) (guanine aminase) (guanine aminohydrolase) (gah) (p51-nedasin). [swissprot;acc:q9y2t3] GDA
    2024 vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] VPS33B 215.553 213.663 1.00885
    2025 alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] GPT 189.987 191.668
    2026 vacuolar protein sorting 11 (hvps11) (pp3476). [swissprot;acc:q9h270] VPS11 215.553 213.663
    2027 lin-7 homolog c; lin-7 protein 3. [refseq;acc:nm_018362] LIN7C 225.015 223.041
    2028 vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] VPS33A 215.553 213.663
    2029 cytoplasmic cysteine conjugate-beta lyase; glutamine-phenylpyruvate aminotransferase. [refseq;acc:nm_004059] CCBL1 189.999 191.677 1.00883

    Legend:
    - Rank is the rank after comparing the two networks
    - Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
    - Hugo is the HGNC identifier if it exists
    - Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
    - Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
    - Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
    - Filtered specifies whether we only included the high confidence microarry measurements or not.
    - http://analysis.yellowcouch.org/