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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2001 to 2050 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		red
    		green
    		network_comparison
    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] 225.02 222.948 1.00929
    2002 u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579] 214.775 216.769 1.00928
    2003 axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] 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] 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] 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]
    2007 2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [swissprot;acc:q9uj83] 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]
    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] 216.201 214.245 1.00913
    2010 tubulin-specific chaperone c (tubulin-folding cofactor c) (cfc). [swissprot;acc:q15814] 193.517 191.766
    2011 putative acyl-coa thioester hydrolase cgi-16 (ec 3.1.2.-). [swissprot;acc:q9y305]
    2012 dead-box protein. [refseq;acc:nm_018665]
    2013 protein phosphatase 1, regulatory (inhibitor) subunit 12b isoform a; myosin phosphatase regulatory subunit; myosin phosphatase, target subunit 2. [refseq;acc:nm_002481] 217.662 215.693
    2014 protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [refseq;acc:nm_002480] 217.676 215.709 1.00912
    2015 dna topoisomerase iii alpha (ec 5.99.1.2). [swissprot;acc:q13472] 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] 199.092 197.301
    2017 ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] 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]
    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] 215.799 213.865 1.00904
    2020 putative eukaryotic translation initiation factor 3 subunit (eif-3) (fragment). [swissprot;acc:o75153] 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] 208.601 210.464 1.00893
    2022 atp synthase coupling factor b, mitochondrial precursor. [swissprot;acc:q99766]
    2023 guanine deaminase (ec 3.5.4.3) (guanase) (guanine aminase) (guanine aminohydrolase) (gah) (p51-nedasin). [swissprot;acc:q9y2t3]
    2024 vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] 215.553 213.663 1.00885
    2025 alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] 189.987 191.668
    2026 vacuolar protein sorting 11 (hvps11) (pp3476). [swissprot;acc:q9h270] 215.553 213.663
    2027 lin-7 homolog c; lin-7 protein 3. [refseq;acc:nm_018362] 225.015 223.041
    2028 vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] 215.553 213.663
    2029 cytoplasmic cysteine conjugate-beta lyase; glutamine-phenylpyruvate aminotransferase. [refseq;acc:nm_004059] 189.999 191.677 1.00883
    2030 alanine aminotransferase 2; glutamic-pyruvate transaminase 2. [refseq;acc:nm_133443]
    2031 traf and tnf receptor-associated protein; ets1-associated protein 2. [refseq;acc:nm_016614] 218.466 216.562 1.00879
    2032 f-actin capping protein alpha-3 subunit (capz alpha-3) (germ cell- specific protein 3). [swissprot;acc:q96kx2] 215.322 213.46 1.00872
    2033 f-actin capping protein beta subunit (capz beta). [swissprot;acc:p47756]
    2034 centaurin beta 5 (cnt-b5). [swissprot;acc:q96p50] 218.919 220.812 1.00865
    2035 centaurin beta 2 (cnt-b2). [swissprot;acc:q15057]
    2036 lamin b1. [swissprot;acc:p20700] 220.813
    2037 centaurin beta 1 (cnt-b1). [swissprot;acc:q15027] 220.812
    2038 lamin a/c (70 kda lamin). [swissprot;acc:p02545] 218.92 220.811 1.00864
    2039 acetyl-coenzyme a synthetase, cytoplasmic (ec 6.2.1.1) (acetate--coa ligase) (acyl-activating enzyme) (acetyl-coa synthetase) (acs) (acecs). [swissprot;acc:q9nr19] 190.551 192.191 1.00861
    2040 brachyury protein (t protein). [swissprot;acc:o15178] 210.586 208.803 1.00854
    2041 ataxin-1 ubiquitin-like interacting protein. [refseq;acc:nm_020131] 196.808 195.141
    2042 t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806] 210.586 208.803
    2043 ubiquilin 1 isoform 1. [refseq;acc:nm_013438] 196.837 195.173 1.00853
    2044 adapter-related protein complex 3 beta 1 subunit (beta-adaptin 3a) (ap-3 complex beta-3a subunit) (beta-3a-adaptin). [swissprot;acc:o00203] 199.928 198.24 1.00851
    2045 ny-ren-24 antigen (fragment). [sptrembl;acc:q9y5a4]
    2046 adapter-related protein complex 3 beta 2 subunit (beta-adaptin 3b) (ap-3 complex beta-3b subunit) (beta-3b-adaptin) (neuron-specific vesicle coat protein beta-nap). [swissprot;acc:q13367]
    2047 solute carrier family 2, facilitated glucose transporter, member 6 (glucose transporter type 6) (glucose transporter type 9). [swissprot;acc:q9ugq3] 224.124 226.003 1.00838
    2048 solute carrier family 2, facilitated glucose transporter, member 8 (glucose transporter type 8) (glucose transporter type x1). [swissprot;acc:q9ny64]
    2049 translation initiation factor eif-2b beta subunit (eif-2b gdp-gtp exchange factor) (s20i15) (s20iii15). [swissprot;acc:p49770] 220.787 222.634 1.00837
    2050 sh3 domain-binding glutamic acid-rich protein (sh3bgr protein) (21- glutamic acid-rich protein) (21-garp). [swissprot;acc:p55822] 218.79 216.981 1.00834

    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
    - 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/