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 [...,...].
    Gene description Rank Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 708 to 757 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		green
    		network_comparison
    cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] 1286 CYP4F11 218.368 213.22 1.02414
    cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] 1284 CYP4F12
    cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] 1285 CYP4F2
    cytochrome p450 4f3 (ec 1.14.13.30) (cypivf3) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:q08477] 1281 CYP4F3
    cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] 1282 CYP4F8
    cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 3 PSCD1 15 28 1.86667
    cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 4 PSCD2
    cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 6 PSCD3
    cytohesin 4. [swissprot;acc:q9uia0] 5 PSCD4
    cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569] 1170 no value 219.399 213.784 1.02626
    cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] 797 224.244 234.511 1.04578
    cytoplasmic antiproteinase 3 (cap3) (cap-3) (protease inhibitor 9) (serpin b9). [swissprot;acc:p50453] 791 SERPINB9
    cytoplasmic cysteine conjugate-beta lyase; glutamine-phenylpyruvate aminotransferase. [refseq;acc:nm_004059] 2029 CCBL1 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
    cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] 136 CPEB3 350 290 1.2069
    cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] 135 CPEB4
    cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [swissprot;acc:p16333] 1370 NCK1 205.185 200.784 1.02192
    cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [swissprot;acc:o43639] 1323 NCK2 205.225 200.625 1.02293
    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 199.771 204.287 1.02261
    cytosolic nonspecific dipeptidase (glutamate carboxypeptidase-like protein 1). [swissprot;acc:q96kp4] 2350 CNDP2 209.811 210.733 1.00439
    d(4) dopamine receptor (d(2c) dopamine receptor). [swissprot;acc:p21917] 1261 DRD4 219.354 224.7 1.02437
    d-3-phosphoglycerate dehydrogenase (ec 1.1.1.95) (3-pgdh). [swissprot;acc:o43175] 1981 PHGDH 209.539 207.529 1.00969
    dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] 134 DAB2IP 350 290 1.2069
    dachshund homolog isoform a. [refseq;acc:nm_080759] 2847 DACH1 0.00001 0.00001 1
    daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] 1215 DAZAP1 218.268 212.916 1.02514
    db83 protein. [swissprot;acc:p57088] 76 TMEM33 288 362 1.25694
    dc11 protein. [refseq;acc:nm_020186] 2489 no value 194.527 195.08 1.00284
    dc12 protein. [refseq;acc:nm_020187] 2774 C3orf37 0.00001 0.00001 1
    dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] 527 DDX31 248.56 232.579 1.06871
    dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804] 1140 DDX39 218.484 212.675 1.02731
    dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355] 1385 no value 218.47 213.875 1.02148
    dead-box protein 4 (vasa homolog). [swissprot;acc:q9nqi0] 1689 DDX4 228.277 225.163 1.01383
    dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] 634 no value 226.523 213.786 1.05958
    dead-box protein. [refseq;acc:nm_018665] 2012 DDX43 193.517 191.766 1.00913
    dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [refseq;acc:nm_030655] 1720 DDX12 187.205 189.679 1.01322
    defender against cell death 1 (dad-1). [swissprot;acc:p46966] 1740 DAD1 206.595 209.258 1.01289
    deformed epidermal autoregulatory factor 1 homolog (nuclear deaf-1 related transcriptional regulator) (nudr) (suppressin) (zinc finger mynd domain containing protein 5). [swissprot;acc:o75398] 920 DEAF1 236.741 245.547 1.0372
    dehydrodolichyl diphosphate synthase. [refseq;acc:nm_024887] 2275 DHDDS 207.319 208.44 1.00541
    delta 1-pyrroline-5-carboxylate synthetase (p5cs) [includes: glutamate 5-kinase (ec 2.7.2.11) (gamma-glutamyl kinase) (gk); gamma-glutamyl phosphate reductase (gpr) (ec 1.2.1.41) (glutamate-5-semialdehyde dehydrogenase) (glutamyl-gamma-semialdehyde dehydrogenase)]. [swissprot;acc:p54886] 2305 ALDH18A1 217.392 218.498 1.00509
    delta(14)-sterol reductase (ec 1.3.1.70) (c-14 sterol reductase) (sterol c14-reductase) (delta14-sr) (transmembrane 7 superfamily member 2) (another new gene 1) (putative sterol reductase sr-1). [swissprot;acc:o76062] 1901 TM7SF2 191.411 193.39 1.01034
    delta-aminolevulinic acid dehydratase (ec 4.2.1.24) (porphobilinogen synthase) (aladh). [swissprot;acc:p13716] 2252 ALAD 217.185 218.498 1.00605
    delta-interacting protein a (hepatitis delta antigen interacting protein a). [swissprot;acc:q15834] 2097 CCDC85B 214.979 213.39 1.00745
    delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q92629] 1178 SGCD 218.186 212.672 1.02593
    delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011] 667 ECH1 229.072 216.576 1.0577
    deltex 2. [refseq;acc:nm_020892] 110 DTX2 333.144 267.393 1.2459
    deltex homolog 1; hdx-1. [refseq;acc:nm_004416] 111 DTX1 332.925 267.274 1.24563
    dendritic cell protein. [refseq;acc:nm_006360] 713 EIF3M 223.121 211.685 1.05402
    density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] 267 DENR 241.07 267.88 1.11121
    deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [swissprot;acc:p32321] 779 DCTD 230.516 241.641 1.04826
    deoxyhypusine synthase (ec 2.5.1.46) (dhs). [swissprot;acc:p49366] 2755 DHPS 212.403 212.401 1.00001

    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/