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

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Showing element 1430 to 1479 of 3228 in total

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

Rank	description	red	green	network_comparison
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]	5880.37	6334.71	1.07726
1431	limkain beta 2. [refseq;acc:nm_025140]	5796.03	6243.78	1.07725
1432	zinc finger protein zic 2 (zinc finger protein of the cerebellum 2). [swissprot;acc:o95409]	5658.58	6095.62	1.07723
1433	dna topoisomerase iii alpha (ec 5.99.1.2). [swissprot;acc:q13472]	5692.34	6131.71	1.07719
1434	myosin viia. [swissprot;acc:q13402]	5759.68	6203.63	1.07708
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	6558.02	1.07695
1438	exocyst complex component sec10 (hsec10). [swissprot;acc:o00471]	6721.25	7238.34	1.07693
1439	camp response element-binding protein cre-bpa. [refseq;acc:nm_004904]	5658.8	6093.56	1.07683
1440	peroxisomal membrane protein pex14 (peroxin-14) (peroxisomal membrane anchor protein pex14) (pts1 receptor docking protein). [swissprot;acc:o75381]	6522.96	7023.77	1.07678
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	6693.13	1.07674
1443	ketohexokinase (ec 2.7.1.3) (hepatic fructokinase). [swissprot;acc:p50053]	5450.9	5869.07	1.07672
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	5510.45	1.07671
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	6031.05	1.07659
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	6210.65	1.07623
1455	lim protein (similar to rat protein kinase c-binding enigma); enigma homolog. [refseq;acc:nm_006457]	5672.68	6104.68	1.07615
1456	e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409]	5672.25	6104.01	1.07612
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
1463	collagen alpha 3(iv) chain precursor (goodpasture antigen). [swissprot;acc:q01955]	5672.2	6103.92	1.07611
1464	zasp protein (fragment). [sptrembl;acc:q9y4z3]	5671.93	6103.49	1.07609
1465	glycerol-3-phosphate dehydrogenase [nad+], cytoplasmic (ec 1.1.1.8) (gpd-c) (gpdh-c). [swissprot;acc:p21695]	5686.74	6119.36	1.07608
1466	proteasome subunit beta type 5 precursor (ec 3.4.25.1) (proteasome epsilon chain) (macropain epsilon chain) (multicatalytic endopeptidase complex epsilon chain) (proteasome subunit x) (proteasome chain 6) (proteasome subunit mb1). [swissprot;acc:p28074]	6523.17	7019.44
1467	p47 protein isoform a. [refseq;acc:nm_016143]	6444.4	6932.39	1.07572
1468	sphingosine-1-phosphate lyase 1; sphingosine-1-phosphate lyase. [refseq;acc:nm_003901]	5473.09	5887.45	1.07571
1469	4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404]
1470	ornithine aminotransferase, mitochondrial precursor (ec 2.6.1.13) (ornithine--oxo-acid aminotransferase). [swissprot;acc:p04181]
1471	40s ribosomal protein s8. [swissprot;acc:p09058]	5659.45	6087.55	1.07564
1472	26s proteasome non-atpase regulatory subunit 6 (26s proteasome regulatory subunit s10) (p42a) (proteasome regulatory particle subunit p44s10). [swissprot;acc:q15008]	5984.47	6435.42	1.07535
1473	calmegin precursor. [swissprot;acc:o14967]	5910.06	6355.08	1.0753
1474	calnexin precursor (major histocompatibility complex class i antigen-binding protein p88) (p90) (ip90). [swissprot;acc:p27824]
1475	soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825]
1476	rna (guanine-7-) methyltransferase. [refseq;acc:nm_003799]
1477	palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5]	3687.37	3429.37	1.07523
1478	cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [swissprot;acc:p17544]	5659.22	6084.68	1.07518
1479	hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317]	5787.03	6221.72	1.07511

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.