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 [...,...].
    Network Comparison Type Rank Gene Value Type description Hugo Interaction Map network_comparison Filtered red green
    Results: HTML CSV LaTeX Showing element 332 to 381 of 66312 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Value Type
    		description
    		Hugo
    		Interaction Map
    		network_comparison
    		red
    		green
    42 Ranked proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] FOS High confidence 1.2714 204.641 160.957
    Squared melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] MAGEC1 Low confidence 1.33073 82347.8 61881.5
    microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] MAP1LC3A High confidence 1.78561 144911 81154.7
    Rooted guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] GNB5 1.62821 40.225 24.7051
    protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] PPP1R14D Low confidence 1.13601 55.7075 63.2842
    43 Measured cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] ATG4A 1.16122 13689.1 11788.6
    guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] GNB3 High confidence 1.83093 1881.02 1027.36
    Ranked jun dimerization protein. [refseq;acc:nm_130469] no value 1.2714 204.641 160.957
    regulator of g-protein signaling 12 (rgs12). [swissprot;acc:o14924] RGS12 Low confidence 1.12703 247.768 219.841
    Squared cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] ATG4B High confidence 1.78558 144876 81136.5
    melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] MAGEA4 Low confidence 1.33073 82347.8 61881.5
    Rooted ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] FCN2 1.13601 55.7075 63.2842
    guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] GNB1 High confidence 1.59677 40.6302 25.4452
    44 Measured 1.82652 1931.34 1057.39
    transcription factor jun-d. [swissprot;acc:p17535] JUND Low confidence 1.16112 6614.51 7680.25
    Ranked fos-related antigen 2. [swissprot;acc:p15408] FOSL2 High confidence 1.2707 204.641 161.046
    protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] PPP1R14A Low confidence 1.11751 242.742 217.217
    Squared gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] GABARAP High confidence 1.78117 139741 78454.6
    melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] no value Low confidence 1.33073 82347.8 61881.5
    Rooted guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] GNB4 High confidence 1.59556 40.5691 25.4263
    protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] no value Low confidence 1.13601 55.7075 63.2842
    45 Measured guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] GNB4 High confidence 1.82448 1926.69 1056.02
    transcription factor jun-b. [swissprot;acc:p17275] JUNB Low confidence 1.16109 6613.42 7678.76
    Ranked microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] MFAP4 1.11751 242.742 217.217
    protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] FOSB High confidence 1.27066 204.641 161.051
    Squared gaba-a receptor-associated protein. [sptrembl;acc:q9by60] no value 1.77148 129597 73157.5
    melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] MAGEA10 Low confidence 1.33073 82347.8 61881.5
    Rooted guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] GNB3 High confidence 1.59339 40.081 25.1546
    proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] FOS Low confidence 1.13252 66.5831 75.4064
    46 Measured neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] NEUROD2 High confidence 1.78438 779.167 1390.33
    transcription regulator protein bach1 (btb and cnc homolog 1) (ha2303). [swissprot;acc:o14867] BACH1 Low confidence 1.16027 8313.02 9645.34
    Ranked fos-related antigen 1 (fra-1). [swissprot;acc:p15407] FOSL1 High confidence 1.27053 204.642 161.068
    protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] PPP1R14D Low confidence 1.11751 242.742 217.217
    Squared apg3p; pc3-96 protein. [refseq;acc:nm_022488] ATG3 High confidence 1.77148 129597 73157.5
    melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] MAGEB4 Low confidence 1.33073 82347.8 61881.5
    Rooted deltex 2. [refseq;acc:nm_020892] DTX2 High confidence 1.5909 27.634 43.9629
    jun dimerization protein. [refseq;acc:nm_130469] no value Low confidence 1.13252 66.5831 75.4064
    47 Measured chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] CHD3 High confidence 1.78438 779.167 1390.33
    nuclear factor erythroid 2 related factor 2 (nf-e2 related factor 2) (nfe2-related factor 2) (nuclear factor, erythroid derived 2, like 2) (hebp1). [swissprot;acc:q16236] NFE2L2 Low confidence 1.16027 8313.02 9645.34
    Ranked ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] FCN2 1.11751 242.742 217.217
    gbp protein isoform a. [refseq;acc:nm_017870] TMEM132A High confidence 1.26938 325.586 256.492
    Squared melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] MAGED2 Low confidence 1.33073 82347.8 61881.5
    ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] no value High confidence 1.73059 98517.9 56927.2
    Rooted deltex homolog 1; hdx-1. [refseq;acc:nm_004416] DTX1 1.58861 27.7078 44.017
    fos-related antigen 2. [swissprot;acc:p15408] FOSL2 Low confidence 1.13105 66.6469 75.3812
    48 Measured doc-1 related protein (doc-1r). [swissprot;acc:o75956] CDK2AP2 High confidence 1.78438 779.167 1390.33
    transcription regulator protein bach2 (btb and cnc homolog 2). [swissprot;acc:q9byv9] BACH2 Low confidence 1.16027 8313.02 9645.34
    Ranked gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] GABARAP High confidence 1.26868 65.4586 83.0461
    protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] no value Low confidence 1.11751 242.742 217.217
    Squared lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] LASS2 High confidence 1.69891 6300.2 10703.5

    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/