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 Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered green red 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
    		Hugo
    		description
    		green
    		red
    		network_comparison
    1980 SERINC1 tumor differentially expressed 1 protein like. [swissprot;acc:q9nrx5] 207.529 209.539 1.00969
    1981 PHGDH d-3-phosphoglycerate dehydrogenase (ec 1.1.1.95) (3-pgdh). [swissprot;acc:o43175]
    1982 no value 40s ribosomal protein s28. [swissprot;acc:p25112] 198.427 200.343 1.00966
    1983 PDLIM5 lim protein (similar to rat protein kinase c-binding enigma); enigma homolog. [refseq;acc:nm_006457] 217.175 219.25 1.00955
    1984 EP400 e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409] 217.193 219.26 1.00952
    1985 MRPL24 mitochondrial ribosomal protein l24. [refseq;acc:nm_024540]
    1986 YAP1 65 kda yes-associated protein (yap65). [swissprot;acc:p46937]
    1987 LIN7A lin-7 homolog a; vertebrate lin7 homolog 1; tax interaction protein 33; mammalian lin-7 1. [refseq;acc:nm_004664] 222.9 225.022
    1988 CCDC130 9 kda protein. [swissprot;acc:p13994] 217.193 219.26
    1989 COL4A3 collagen alpha 3(iv) chain precursor (goodpasture antigen). [swissprot;acc:q01955] 217.195 219.261 1.00951
    1990 no value collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400] 217.194 219.26
    1991 WWTR1 transcriptional co-activator with pdz-binding motif (taz). [refseq;acc:nm_015472]
    1992 LDB3 zasp protein (fragment). [sptrembl;acc:q9y4z3] 217.207 219.267 1.00948
    1993 HIP1R huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146] 190.835 189.052 1.00943
    1994 COL4A3BP 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] 190.787 189.011 1.0094
    1995 HIP1 huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291] 190.73 188.961 1.00936
    1996 SLC5A5 sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911] 202.784 204.682
    1997 PRODH2 kidney and liver proline oxidase 1. [refseq;acc:nm_021232] 202.759 204.651 1.00933
    1998 C15orf15 ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] 198.37 200.219 1.00932
    1999 SLC5A8 solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913] 202.748 204.636 1.00931
    2000 SLC5A6 sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289] 202.739 204.626
    2001 LIN7B 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] 222.948 225.02 1.00929
    2002 SNRPB2 u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579] 216.769 214.775 1.00928
    2003 DNALI1 axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] 206.41 208.315 1.00923
    2004 ERBB4 receptor protein-tyrosine kinase erbb-4 precursor (ec 2.7.1.112) (p180erbb4) (tyrosine kinase-type cell surface receptor her4). [swissprot;acc:q15303] 222.969 225.019 1.00919
    2005 EGFR epidermal growth factor receptor precursor (ec 2.7.1.112) (receptor protein-tyrosine kinase erbb-1). [swissprot;acc:p00533] 222.971
    2006 ERBB2 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]
    2007 HACL1 2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [swissprot;acc:q9uj83] 222.969
    2008 ERBB3 receptor protein-tyrosine kinase erbb-3 precursor (ec 2.7.1.112) (c-erbb3) (tyrosine kinase-type cell surface receptor her3). [swissprot;acc:p21860]
    2009 CTRL 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] 214.245 216.201 1.00913
    2010 TBCC tubulin-specific chaperone c (tubulin-folding cofactor c) (cfc). [swissprot;acc:q15814] 191.766 193.517
    2011 ACOT9 putative acyl-coa thioester hydrolase cgi-16 (ec 3.1.2.-). [swissprot;acc:q9y305]
    2012 DDX43 dead-box protein. [refseq;acc:nm_018665]
    2013 PPP1R12B protein phosphatase 1, regulatory (inhibitor) subunit 12b isoform a; myosin phosphatase regulatory subunit; myosin phosphatase, target subunit 2. [refseq;acc:nm_002481] 215.693 217.662
    2014 PPP1R12A protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [refseq;acc:nm_002480] 215.709 217.676 1.00912
    2015 TOP3A dna topoisomerase iii alpha (ec 5.99.1.2). [swissprot;acc:q13472] 215.979 217.941 1.00908
    2016 ETFDH 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] 197.301 199.092
    2017 RRS1 ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] 128.553 127.397 1.00907
    2018 PPP1CA serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129]
    2019 no value 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] 213.865 215.799 1.00904
    2020 KIAA0664 putative eukaryotic translation initiation factor 3 subunit (eif-3) (fragment). [swissprot;acc:o75153] 221.176 223.168 1.00901
    2021 COQ3 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] 210.464 208.601 1.00893
    2022 ATP5S atp synthase coupling factor b, mitochondrial precursor. [swissprot;acc:q99766]
    2023 GDA guanine deaminase (ec 3.5.4.3) (guanase) (guanine aminase) (guanine aminohydrolase) (gah) (p51-nedasin). [swissprot;acc:q9y2t3]
    2024 VPS33B vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] 213.663 215.553 1.00885
    2025 GPT alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] 191.668 189.987
    2026 VPS11 vacuolar protein sorting 11 (hvps11) (pp3476). [swissprot;acc:q9h270] 213.663 215.553
    2027 LIN7C lin-7 homolog c; lin-7 protein 3. [refseq;acc:nm_018362] 223.041 225.015
    2028 VPS33A vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] 213.663 215.553
    2029 CCBL1 cytoplasmic cysteine conjugate-beta lyase; glutamine-phenylpyruvate aminotransferase. [refseq;acc:nm_004059] 191.677 189.999 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/