MK5 Microarray Data

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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Network Comparison Type	Gene	Value Type	Rank	Interaction Map	description	red	network_comparison	green	Filtered

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Showing element 1413 to 1462 of 3228 in total

Network Comparison Type  : Divided
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1

Rank	description	red	network_comparison	green
1413	histone deacetylase 9 (hd9) (hd7b) (hd7). [swissprot;acc:q9ukv0]	5813.88	1.07742	6263.97
1414	histone deacetylase 4 (hd4). [swissprot;acc:p56524]		1.07741	6263.96
1415	14-3-3 protein zeta/delta (protein kinase c inhibitor protein-1) (kcip-1) (factor activating exoenzyme s) (fas). [swissprot;acc:p29312]	5815.33	1.0774	6265.44
1416	xpmc2 prevents mitotic catastrophe 2 homolog; xenopus prevents mitotic catastrophe 2 homolog. [refseq;acc:nm_020385]	6123.75		6597.71
1417	isocitrate dehydrogenase [nad] subunit alpha, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [swissprot;acc:p50213]	5360.39	1.07739	5775.24
1418	isocitrate dehydrogenase [nad] subunit beta, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [swissprot;acc:o43837]
1419	isocitrate dehydrogenase [nad] subunit gamma, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [swissprot;acc:p51553]
1420	zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [swissprot;acc:q15915]	5658.51	1.07735	6096.21
1421	importin 7; ran-binding protein 7. [refseq;acc:nm_006391]	5628.53	1.0773	6063.61
1422	importin 8; ran-binding protein 8. [refseq;acc:nm_006390]
1423	brefeldin a-inhibited guanine nucleotide-exchange protein 2 (brefeldin a-inhibited gep 2). [swissprot;acc:q9y6d5]
1424	hsgcn1 (fragment). [sptrembl;acc:q99736]
1425	brefeldin a-inhibited guanine nucleotide-exchange protein 1 (brefeldin a-inhibited gep 1) (p200 arf-gep1) (p200 arf guanine nucleotide exchange factor). [swissprot;acc:q9y6d6]
1426	glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [swissprot;acc:q06210]	5362.85	1.07729	5777.33
1427	zinc finger protein zic 3 (zinc finger protein of the cerebellum 3). [swissprot;acc:o60481]	5658.55	1.07728	6095.85
1428	dual specificity mitogen-activated protein kinase kinase 1 (ec 2.7.1.-) (map kinase kinase 1) (mapkk 1) (erk activator kinase 1) (mapk/erk kinase 1) (mek1). [swissprot;acc:q02750]	5880.37	1.07726	6334.71
1429	similar to kinase suppressor of ras (fragment). [sptrembl;acc:q8ivt5]
1430	dual specificity mitogen-activated protein kinase kinase 2 (ec 2.7.1.-) (map kinase kinase 2) (mapkk 2) (erk activator kinase 2) (mapk/erk kinase 2) (mek2). [swissprot;acc:p36507]
1431	limkain beta 2. [refseq;acc:nm_025140]	5796.03	1.07725	6243.78
1432	zinc finger protein zic 2 (zinc finger protein of the cerebellum 2). [swissprot;acc:o95409]	5658.58	1.07723	6095.62
1433	dna topoisomerase iii alpha (ec 5.99.1.2). [swissprot;acc:q13472]	5692.34	1.07719	6131.71
1434	myosin viia. [swissprot;acc:q13402]	5759.68	1.07708	6203.63
1435	ubiquitin-conjugating enzyme e2 b (ec 6.3.2.19) (ubiquitin-protein ligase b) (ubiquitin carrier protein b) (hr6b) (hhr6b) (e2-17 kda). [swissprot;acc:p23567]
1436	ubiquitin-conjugating enzyme e2 a (ec 6.3.2.19) (ubiquitin-protein ligase a) (ubiquitin carrier protein a) (hr6a) (hhr6a). [swissprot;acc:p49459]
1437	glycerol-3-phosphate dehydrogenase, mitochondrial precursor (ec 1.1.99.5) (gpd-m) (gpdh-m). [swissprot;acc:p43304]	6089.43	1.07695	6558.02
1438	exocyst complex component sec10 (hsec10). [swissprot;acc:o00471]	6721.25	1.07693	7238.34
1439	camp response element-binding protein cre-bpa. [refseq;acc:nm_004904]	5658.8	1.07683	6093.56
1440	peroxisomal membrane protein pex14 (peroxin-14) (peroxisomal membrane anchor protein pex14) (pts1 receptor docking protein). [swissprot;acc:o75381]	6522.96	1.07678	7023.77
1441	proteasome subunit alpha type 7 (ec 3.4.25.1) (proteasome subunit rc6-1) (proteasome subunit xapc7). [swissprot;acc:o14818]	6216.12		6693.38
1442	proteasome subunit alpha type 7-like (ec 3.4.25.1). [swissprot;acc:q8taa3]	6216.13	1.07674	6693.13
1443	ketohexokinase (ec 2.7.1.3) (hepatic fructokinase). [swissprot;acc:p50053]	5450.9	1.07672	5869.07
1444	purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491]
1445	cd109; gov system alloantigens on platelets. [refseq;acc:nm_133493]	5117.85	1.07671	5510.45
1446	peptidyl-prolyl cis-trans isomerase nima-interacting 1 (ec 5.2.1.8) (rotamase pin1) (ppiase pin1). [swissprot;acc:q13526]
1447	iroquois-class homeodomain protein irx-4 (iroquois homeobox protein 4). [swissprot;acc:p78413]
1448	dpy-30-like protein. [swissprot;acc:q9c005]	5602.01	1.07659	6031.05
1449	rab coupling protein; rab-interacting recycling protein; rab effector protein; rab11-family interacting protein 1. [refseq;acc:nm_025151]
1450	gamma-snap-associated factor 1; rab11-interacting protein. [refseq;acc:nm_015470]
1451	neighbor of cox4. [swissprot;acc:o43402]
1452	protein c14orf122 (cgi-112). [swissprot;acc:q9y3b6]
1453	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]
1454	ubiquitin-like protein sumo-1 conjugating enzyme (ec 6.3.2.19) (sumo- 1-protein ligase) (ubiquitin carrier protein) (ubiquitin-conjugating enzyme ubce2a) (p18). [swissprot;acc:p50550]	5770.74	1.07623	6210.65
1455	lim protein (similar to rat protein kinase c-binding enigma); enigma homolog. [refseq;acc:nm_006457]	5672.68	1.07615	6104.68
1456	e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409]	5672.25	1.07612	6104.01
1457	collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400]	5672.23		6103.98
1458	mitochondrial ribosomal protein l24. [refseq;acc:nm_024540]	5672.25		6104.01
1459	65 kda yes-associated protein (yap65). [swissprot;acc:p46937]
1460	p29ing4; candidate tumor suppressor p33 ing1 homolog. [refseq;acc:nm_016162]	5696.65		6130.26
1461	9 kda protein. [swissprot;acc:p13994]	5672.25		6104.01
1462	transcriptional co-activator with pdz-binding motif (taz). [refseq;acc:nm_015472]	5672.24		6103.99

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.