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 1400 to 1449 of 3228 in total

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

Rank	description	red	green	network_comparison
1400	heterogeneous nuclear ribonucleoprotein h3 (hnrnp h3) (hnrnp 2h9). [swissprot;acc:p31942]	5803.45	6256.43	1.07805
1401	hepatocyte nuclear factor 3-gamma (hnf-3g) (forkhead box protein a3) (fork head-related protein fkh h3). [swissprot;acc:p55318]	5728.92	6175.99	1.07804
1402	43 kda receptor-associated protein of the synapse (rapsyn) (acetylcholine receptor-associated 43 kda protein) (43 kda postsynaptic protein). [swissprot;acc:q13702]	6160.06	6640.78
1403	importin 4. [refseq;acc:nm_024658]	5613.16	6050.16	1.07785
1404	mesoderm induction early response 1. [refseq;acc:nm_020948]	6291.89	6781.6	1.07783
1405	proteasome subunit alpha type 3 (ec 3.4.25.1) (proteasome component c8) (macropain subunit c8) (multicatalytic endopeptidase complex subunit c8). [swissprot;acc:p25788]
1406	ribokinase (ec 2.7.1.15). [swissprot;acc:q9h477]	6210.51	6693.49	1.07777
1407	transketolase (ec 2.2.1.1) (tk). [swissprot;acc:p29401]	5692.53	6134.64	1.07766
1408	serologically defined colon cancer antigen 16. [refseq;acc:nm_006649]	6268.94	6755.57	1.07763
1409	glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 2 (ec 2.6.1.16) (hexosephosphate aminotransferase 2) (d-fructose-6- phosphate amidotransferase 2) (gfat 2) (gfat2). [swissprot;acc:o94808]	5358.19	5773.37	1.07749
1410	delta-interacting protein a (hepatitis delta antigen interacting protein a). [swissprot;acc:q15834]	6274.62	6760.78	1.07748
1411	14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [swissprot;acc:p31946]	5812.02	6262.07	1.07743
1412	histone deacetylase 5 (hd5) (antigen ny-co-9). [swissprot;acc:q9uql6]	5813.84	6263.92	1.07742
1413	histone deacetylase 9 (hd9) (hd7b) (hd7). [swissprot;acc:q9ukv0]	5813.88	6263.97
1414	histone deacetylase 4 (hd4). [swissprot;acc:p56524]		6263.96	1.07741
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	6265.44	1.0774
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	5775.24	1.07739
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	6096.21	1.07735
1421	importin 7; ran-binding protein 7. [refseq;acc:nm_006391]	5628.53	6063.61	1.0773
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	5777.33	1.07729
1427	zinc finger protein zic 3 (zinc finger protein of the cerebellum 3). [swissprot;acc:o60481]	5658.55	6095.85	1.07728
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	6334.71	1.07726
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	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]

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.