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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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1433 to 1482 of 3228 in total 
Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
1433	dna topoisomerase iii alpha (ec 5.99.1.2). [source:swissprot;acc:q13472]	5692.34	6131.71	1.07719	
1434	myosin viia. [source: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). [source:swissprot;acc:p23567]	5759.68	6203.63	1.07708	
1436	ubiquitin-conjugating enzyme e2 a (ec 6.3.2.19) (ubiquitin-protein ligase a) (ubiquitin carrier protein a) (hr6a) (hhr6a). [source:swissprot;acc:p49459]	5759.68	6203.63	1.07708	
1437	glycerol-3-phosphate dehydrogenase, mitochondrial precursor (ec 1.1.99.5) (gpd-m) (gpdh-m). [source:swissprot;acc:p43304]	6089.43	6558.02	1.07695	
1438	exocyst complex component sec10 (hsec10). [source:swissprot;acc:o00471]	6721.25	7238.34	1.07693	
1439	camp response element-binding protein cre-bpa. [source: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). [source: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). [source:swissprot;acc:o14818]	6216.12	6693.38	1.07678	
1442	proteasome subunit alpha type 7-like (ec 3.4.25.1). [source:swissprot;acc:q8taa3]	6216.13	6693.13	1.07674	
1443	ketohexokinase (ec 2.7.1.3) (hepatic fructokinase). [source:swissprot;acc:p50053]	5450.9	5869.07	1.07672	
1444	purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [source:swissprot;acc:p00491]	5450.9	5869.07	1.07672	
1445	cd109; gov system alloantigens on platelets. [source: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). [source:swissprot;acc:q13526]	5117.85	5510.45	1.07671	
1447	iroquois-class homeodomain protein irx-4 (iroquois homeobox protein 4). [source:swissprot;acc:p78413]	5117.85	5510.45	1.07671	
1448	dpy-30-like protein. [source: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. [source:refseq;acc:nm_025151]	5602.01	6031.05	1.07659	
1450	gamma-snap-associated factor 1; rab11-interacting protein. [source:refseq;acc:nm_015470]	5602.01	6031.05	1.07659	
1451	neighbor of cox4. [source:swissprot;acc:o43402]	5602.01	6031.05	1.07659	
1452	protein c14orf122 (cgi-112). [source:swissprot;acc:q9y3b6]	5602.01	6031.05	1.07659	
1453	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [source:swissprot;acc:o75110]	5602.01	6031.05	1.07659	
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). [source:swissprot;acc:p50550]	5770.74	6210.65	1.07623	
1455	lim protein (similar to rat protein kinase c-binding enigma); enigma homolog. [source: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. [source:refseq;acc:nm_015409]	5672.25	6104.01	1.07612	
1457	collagen alpha 5(iv) chain precursor. [source:swissprot;acc:p29400]	5672.23	6103.98	1.07612	
1458	mitochondrial ribosomal protein l24. [source:refseq;acc:nm_024540]	5672.25	6104.01	1.07612	
1459	65 kda yes-associated protein (yap65). [source:swissprot;acc:p46937]	5672.25	6104.01	1.07612	
1460	p29ing4; candidate tumor suppressor p33 ing1 homolog. [source:refseq;acc:nm_016162]	5696.65	6130.26	1.07612	
1461	9 kda protein. [source:swissprot;acc:p13994]	5672.25	6104.01	1.07612	
1462	transcriptional co-activator with pdz-binding motif (taz). [source:refseq;acc:nm_015472]	5672.24	6103.99	1.07612	
1463	collagen alpha 3(iv) chain precursor (goodpasture antigen). [source:swissprot;acc:q01955]	5672.2	6103.92	1.07611	
1464	zasp protein (fragment). [source: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). [source: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). [source:swissprot;acc:p28074]	6523.17	7019.44	1.07608	
1467	p47 protein isoform a. [source:refseq;acc:nm_016143]	6444.4	6932.39	1.07572	
1468	sphingosine-1-phosphate lyase 1; sphingosine-1-phosphate lyase. [source: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). [source:swissprot;acc:p80404]	5473.09	5887.45	1.07571	
1470	ornithine aminotransferase, mitochondrial precursor (ec 2.6.1.13) (ornithine--oxo-acid aminotransferase). [source:swissprot;acc:p04181]	5473.09	5887.45	1.07571	
1471	40s ribosomal protein s8. [source: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). [source:swissprot;acc:q15008]	5984.47	6435.42	1.07535	
1473	calmegin precursor. [source:swissprot;acc:o14967]	5910.06	6355.08	1.0753	
1474	calnexin precursor (major histocompatibility complex class i antigen-binding protein p88) (p90) (ip90). [source:swissprot;acc:p27824]	5910.06	6355.08	1.0753	
1475	soluble liver antigen/liver pancreas antigen. [source:refseq;acc:nm_153825]	5910.06	6355.08	1.0753	
1476	rna (guanine-7-) methyltransferase. [source:refseq;acc:nm_003799]	5910.06	6355.08	1.0753	
1477	palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [source: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). [source:swissprot;acc:p17544]	5659.22	6084.68	1.07518	
1479	hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [source:swissprot;acc:p55317]	5787.03	6221.72	1.07511	
1480	cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [source:swissprot;acc:p15336]	5660.17	6085.22	1.07509	
1481	egf-like-domain, multiple 7; neu1 protein. [source:refseq;acc:nm_016215]	3688.8	3431.33	1.07504	
1482	leng5 protein. [source:refseq;acc:nm_024075]	5372.25	5775.21	1.07501	

Legend:
- Rank is the rank after comparing the two networks
- 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/