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.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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description Rank Gene Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 701 to 750 of 3228 in total
Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
description
Rank
red
network_comparison
green
cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] 2685 3953.53 1.00475 3972.32
cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [swissprot;acc:q15070] 1299 5589.33 1.08204 6047.9
cytochrome p450 24a1, mitochondrial precursor (ec 1.14.-.-) (p450- cc24) (vitamin d(3) 24-hydroxylase) (1,25-dihydroxyvitamin d(3) 24- hydroxylase) (24-ohase). [swissprot;acc:q07973] 3211 0.00001 1 0.00001
cytochrome p450 27, mitochondrial precursor (ec 1.14.-.-) (cytochrome p-450c27/25) (sterol 26-hydroxylase) (sterol 27-hydroxylase) (vitamin d(3) 25-hydroxylase) (5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol 27-hydroxylase). [swissprot;acc:q02318] 2977
cytochrome p450 2d6 (ec 1.14.14.1) (cypiid6) (p450-db1) (debrisoquine 4-hydroxylase). [swissprot;acc:p10635] 1877 6076.66 1.0636 6463.12
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] 1286 5655.85 1.08218 6120.64
cytochrome p450 4b1 (ec 1.14.14.1) (cypivb1) (p450-hp). [swissprot;acc:p13584] 1295
cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] 1292
cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] 1290
cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] 1291
cytochrome p450 4f3 (ec 1.14.13.30) (cypivf3) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:q08477] 1287
cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] 1288
cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 221 41482.5 1.24361 33356.5
cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 222
cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 224
cytohesin 4. [swissprot;acc:q9uia0] 223
cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569] 1147 6281.21 1.08858 6837.61
cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] 2410 5078.5 1.03884 5275.76
cytoplasmic antiproteinase 3 (cap3) (cap-3) (protease inhibitor 9) (serpin b9). [swissprot;acc:p50453] 2404
cytoplasmic cysteine conjugate-beta lyase; glutamine-phenylpyruvate aminotransferase. [refseq;acc:nm_004059] 2413 6956.32 1.03836 7223.14
cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] 732 13241.4 1.1161 11864
cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] 13 398.5 3.21581 1281.5
cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] 12
cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [swissprot;acc:p16333] 892 6784.67 1.10182 7475.48
cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [swissprot;acc:o43639] 847 6776.85 1.10458 7485.55
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] 2654 7118.22 1.0089 7055.43
cytosolic nonspecific dipeptidase (glutamate carboxypeptidase-like protein 1). [swissprot;acc:q96kp4] 1285 6207.57 1.08234 6718.7
d(4) dopamine receptor (d(2c) dopamine receptor). [swissprot;acc:p21917] 1880 6076.66 1.0636 6463.12
d-3-phosphoglycerate dehydrogenase (ec 1.1.1.95) (3-pgdh). [swissprot;acc:o43175] 1101 6133.83 1.0907 6690.18
dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] 11 398.5 3.21581 1281.5
dachshund homolog isoform a. [refseq;acc:nm_080759] 2847 0.00001 1 0.00001
daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] 1239 5654.53 1.08457 6132.76
db83 protein. [swissprot;acc:p57088] 8 1153.5 3.39764 339.5
dc11 protein. [refseq;acc:nm_020186] 1908 6858.84 1.06246 7287.27
dc12 protein. [refseq;acc:nm_020187] 2774 0.00001 1 0.00001
dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] 431 3849.94 1.15102 4431.36
dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804] 777 5874.74 1.11211 6533.34
dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355] 2284 5783.73 1.04585 6048.91
dead-box protein 4 (vasa homolog). [swissprot;acc:q9nqi0] 990 5147.9 1.09584 5641.25
dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] 2033 6101.12 1.05716 6449.87
dead-box protein. [refseq;acc:nm_018665] 1064 5719.01 1.0926 6248.6
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] 2497 7002.3 1.02713 7192.25
defender against cell death 1 (dad-1). [swissprot;acc:p46966] 2391 6327.14 1.03987 6579.38
deformed epidermal autoregulatory factor 1 homolog (nuclear deaf-1 related transcriptional regulator) (nudr) (suppressin) (zinc finger mynd domain containing protein 5). [swissprot;acc:o75398] 2584 4180.32 1.0175 4253.46
dehydrodolichyl diphosphate synthase. [refseq;acc:nm_024887] 1280 6350.81 1.08252 6874.88
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] 1488 5573.64 1.07499 5991.58
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] 2309 6960.96 1.04493 7273.7
delta-aminolevulinic acid dehydratase (ec 4.2.1.24) (porphobilinogen synthase) (aladh). [swissprot;acc:p13716] 1158 5489.18 1.08797 5972.09
delta-interacting protein a (hepatitis delta antigen interacting protein a). [swissprot;acc:q15834] 1410 6274.62 1.07748 6760.78
delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q92629] 738 5768.32 1.11554 6434.78

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/