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 [...,...].
    description Rank Gene Hugo Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1758 to 1807 of 8289 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Filtered  : 1
    description
    		Rank
    		Hugo
    		Interaction Map
    		red
    		green
    		network_comparison
    cytochrome p450 3a43 (ec 1.14.14.1). [swissprot;acc:q9hb55] 669 CYP3A43 Low confidence 203.712 198.082 1.02842
    cytochrome p450 3a5 (ec 1.14.14.1) (cypiiia5) (p450-pcn3). [swissprot;acc:p20815] 675 CYP3A5 203.702 198.095 1.0283
    cytochrome p450 3a7 (ec 1.14.14.1) (cypiiia7) (p450-hfla). [swissprot;acc:p24462] 672 CYP3A7 203.727 198.116 1.02832
    cytochrome p450 4a11 precursor (ec 1.14.15.3) (cypiva11) (fatty acid omega-hydroxylase) (p-450 hk omega) (lauric acid omega-hydroxylase) (cyp4aii) (p450-hl-omega). [swissprot;acc:q02928] 449 CYP4A11 203.077 196.283 1.03461
    1280 High confidence 218.368 213.22 1.02414
    cytochrome p450 4b1 (ec 1.14.14.1) (cypivb1) (p450-hp). [swissprot;acc:p13584] 441 CYP4B1 Low confidence 203.045 196.204 1.03487
    1288 High confidence 218.368 213.22 1.02414
    cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] 584 CYP4F11 Low confidence 203.163 197.102 1.03075
    1286 High confidence 218.368 213.22 1.02414
    cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] 565 CYP4F12 Low confidence 203.157 197.064 1.03092
    1284 High confidence 218.368 213.22 1.02414
    cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] 583 CYP4F2 Low confidence 203.166 197.101 1.03077
    1285 High confidence 218.368 213.22 1.02414
    cytochrome p450 4f3 (ec 1.14.13.30) (cypivf3) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:q08477] 582 CYP4F3 Low confidence 203.164 197.1 1.03077
    1281 High confidence 218.368 213.22 1.02414
    cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] 563 CYP4F8 Low confidence 203.155 197.018 1.03115
    1282 High confidence 218.368 213.22 1.02414
    cytochrome p450 51a1 (ec 1.14.13.70) (cypli) (p450li) (sterol 14-alpha demethylase) (lanosterol 14-alpha demethylase) (ldm) (p450-14dm). [swissprot;acc:q16850] 234 CYP51A1 Low confidence 208.851 199.38 1.0475
    cytoglobin (histoglobin) (hgb) (stellate cell activation-associated protein). [swissprot;acc:q8wwm9] 516 CYGB 205.156 198.715 1.03241
    cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 3 PSCD1 High confidence 15 28 1.86667
    5049 Low confidence 177.3 177.3 1
    cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 4 PSCD2 High confidence 15 28 1.86667
    5017 Low confidence 177.563 177.538 1.00014
    cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 6 PSCD3 High confidence 15 28 1.86667
    5018 Low confidence 177.568 177.543 1.00014
    cytohesin 4. [swissprot;acc:q9uia0] 5 PSCD4 High confidence 15 28 1.86667
    4997 Low confidence 177.9 177.845 1.00031
    cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569] 1170 no value High confidence 219.399 213.784 1.02626
    3991 Low confidence 203.948 206.371 1.01188
    cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] 797 High confidence 224.244 234.511 1.04578
    3802 Low confidence 202.443 199.787 1.01329
    cytoplasmic antiproteinase 3 (cap3) (cap-3) (protease inhibitor 9) (serpin b9). [swissprot;acc:p50453] 791 SERPINB9 High confidence 224.244 234.511 1.04578
    3795 Low confidence 202.443 199.787 1.01329
    cytoplasmic cysteine conjugate-beta lyase; glutamine-phenylpyruvate aminotransferase. [refseq;acc:nm_004059] 1816 CCBL1 196.857 192.989 1.02004
    2029 High confidence 189.999 191.677 1.00883
    cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] 847 DYNLT1 147.211 153.371 1.04184
    3866 Low confidence 194.792 197.306 1.01291
    cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] 54 CPEB3 267.448 240.822 1.11056
    136 High confidence 350 290 1.2069
    cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] 55 CPEB4 Low confidence 267.376 240.78 1.11046
    135 High confidence 350 290 1.2069
    cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [swissprot;acc:p16333] 1370 NCK1 205.185 200.784 1.02192
    1726 Low confidence 200.211 196.199 1.02045
    cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [swissprot;acc:o43639] 1323 NCK2 High confidence 205.225 200.625 1.02293
    1680 Low confidence 200.124 196.081 1.02062
    cytoskeleton related vitamin a responsive protein; glutamate transporter eeac1-associated protein; dermal papilla derived protein 11; putative mapk activating protein pm27. [refseq;acc:nm_006407] 1335 ARL6IP5 High confidence 199.771 204.287 1.02261
    1657 Low confidence 203.451 199.326 1.02069
    cytosolic nonspecific dipeptidase (glutamate carboxypeptidase-like protein 1). [swissprot;acc:q96kp4] 1648 CNDP2 199.862 195.806 1.02071
    2350 High confidence 209.811 210.733 1.00439
    cytosolic ovarian carcinoma antigen 1 (apk1 antigen). [swissprot;acc:q16206] 3578 ENOX2 Low confidence 203.012 200.111 1.0145

    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/