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 1513 to 1562 of 3228 in total

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

Rank	description	red	green	network_comparison	
1513	proteasome subunit beta type 10 precursor (ec 3.4.25.1) (proteasome mecl-1) (macropain subunit mecl-1) (multicatalytic endopeptidase complex subunit mecl-1). [source:swissprot;acc:p40306]	6079.65	6530.82	1.07421	
1514	acetyl-coa carboxylase 1 (ec 6.4.1.2) (acc-alpha) [includes: biotin carboxylase (ec 6.3.4.14)]. [source:swissprot;acc:q13085]	7232.14	7768.35	1.07414	
1515	lanc lantibiotic synthetase component c-like 2; testis-specific adriamycin sensitivity protein; lanc (bacterial lantibiotic synthetase component c)-like 2; g protein-coupled receptor 69b. [source:refseq;acc:nm_018697]	5633.67	6050.69	1.07402	
1516	lanthionine synthetase c-like protein 1; g protein-coupled receptor 69a; lanc (bacterial lantibiotic synthetase component c)-like 1; lanc (bacterial lantibiotic synthetase component). [source:refseq;acc:nm_006055]	5633.67	6050.69	1.07402	
1517	26s proteasome non-atpase regulatory subunit 9 (26s proteasome regulatory subunit p27). [source:swissprot;acc:o00233]	5996.14	6439.46	1.07393	
1518	anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [source:refseq;acc:nm_013366]	10341.2	9630.35	1.07381	
1519	gdp-mannose pyrophosphorylase b isoform 1; mannose-1-phosphate guanylyltransferase; amphoterin induced gene 3. [source:refseq;acc:nm_013334]	5283.8	5673.81	1.07381	
1520	gdp-mannose pyrophosphorylase a; mannose-1-phosphate guanylyltransferase (gdp). [source:refseq;acc:nm_013335]	5283.8	5673.81	1.07381	
1521	26s protease regulatory subunit 4 (p26s4). [source:swissprot;acc:q03527]	5938.56	6376.76	1.07379	
1522	glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [source:swissprot;acc:q14409]	6137.24	6589.72	1.07373	
1523	glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [source:swissprot;acc:p32189]	6137.09	6589.57	1.07373	
1524	glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [source:swissprot;acc:q14410]	6137.53	6590.01	1.07372	
1525	tensin. [source:refseq;acc:nm_022648]	5871.89	6303.56	1.07351	
1526	calreticulin precursor (crp55) (calregulin) (hacbp) (erp60). [source:swissprot;acc:p27797]	5369.1	5763.72	1.0735	
1527	26s protease regulatory subunit 6a (tat-binding protein 1) (tbp-1) (proteasome subunit p50). [source:swissprot;acc:p17980]	5926.76	6362.33	1.07349	
1528	c1 domain-containing phosphatase and tensin-like protein isoform 2; putative protein tyrosine phosphatase; c1 domain-containing phosphatase and tensin-like protein; tensin 2. [source:refseq;acc:nm_015319]	5869.97	6301.24	1.07347	
1529	dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [source:swissprot;acc:o76075]	5916.05	6350.53	1.07344	
1530	adamts-9 precursor (ec 3.4.24.-) (a disintegrin and metalloproteinase with thrombospondin motifs 9) (adam-ts 9) (adam-ts9). [source:swissprot;acc:q9p2n4]	5916.05	6350.53	1.07344	
1531	dna fragmentation factor alpha subunit (dna fragmentation factor 45 kda subunit) (dff-45) (inhibitor of cad) (icad). [source:swissprot;acc:o00273]	5916.05	6350.53	1.07344	
1532	ankyrin 3 (ank-3) (ankyrin g). [source:swissprot;acc:q12955]	5916.05	6350.53	1.07344	
1533	ankyrin 2 (brain ankyrin) (ankyrin b) (ankyrin, nonerythroid). [source:swissprot;acc:q01484]	5916.05	6350.53	1.07344	
1534	adp-ribosylation factor-like protein 3. [source:swissprot;acc:p36405]	5916.05	6350.53	1.07344	
1535	unc-119 protein homolog (retinal protein 4) (hrg4). [source:swissprot;acc:q13432]	5916.05	6350.53	1.07344	
1536	26s proteasome non-atpase regulatory subunit 8 (26s proteasome regulatory subunit s14) (p31). [source:swissprot;acc:p48556]	5916.05	6350.53	1.07344	
1537	evolutionarily conserved signaling intermediate in toll pathway; ecsit. [source:refseq;acc:nm_016581]	6184.27	6637.44	1.07328	
1538	tumor endothelial marker 6; thyroid specific ptb domain protein; tensin 3. [source:refseq;acc:nm_022748]	5870.72	6300.83	1.07326	
1539	26s protease regulatory subunit 7 (mss1 protein). [source:swissprot;acc:p35998]	5783.97	6207.5	1.07322	
1540	mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [source:refseq;acc:nm_022362]	6360.13	6825.36	1.07315	
1541	adenylyl cyclase-associated protein 1 (cap 1). [source:swissprot;acc:q01518]	5989.3	6427.17	1.07311	
1542	inositol polyphosphate multikinase. [source:refseq;acc:nm_152230]	5466	5865.33	1.07306	
1543	afg3-like protein 2 (ec 3.4.24.-) (paraplegin-like protein). [source:swissprot;acc:q9y4w6]	5466	5865.33	1.07306	
1544	alpha-(1,6)-fucosyltransferase (ec 2.4.1.68) (glycoprotein 6-alpha-l- fucosyltransferase) (gdp-fucose--glycoprotein fucosyltransferase) (gdp-l-fuc:n-acetyl-beta-d-glucosaminide alpha1,6-fucosyltransferase) (alpha1-6fuct) (fucosyltransferase 8). [source:swissprot;acc:q9byc5]	5466	5865.33	1.07306	
1545	aminomethyltransferase, mitochondrial precursor (ec 2.1.2.10) (glycine cleavage system t protein) (gcvt). [source:swissprot;acc:p48728]	5945.96	6380.28	1.07304	
1546	26s proteasome non-atpase regulatory subunit 3 (26s proteasome regulatory subunit s3) (proteasome subunit p58). [source:swissprot;acc:o43242]	5819.39	6244.37	1.07303	
1547	cytidine deaminase (ec 3.5.4.5) (cytidine aminohydrolase). [source:swissprot;acc:p32320]	5397.21	5790.45	1.07286	
1548	60s ribosomal protein l28. [source:swissprot;acc:p46779]	5987.29	6423.52	1.07286	
1549	glucose-6-phosphate 1-dehydrogenase (ec 1.1.1.49) (g6pd). [source:swissprot;acc:p11413]	6025.86	6464.16	1.07274	
1550	dna-repair protein xrcc3 (x-ray repair cross-complementing protein 3). [source:swissprot;acc:o43542]	6025.86	6464.16	1.07274	
1551	cleavage and polyadenylation specific factor 6, 68 kd subunit; pre-mrna cleavage factor im (68kd); cleavage and polyadenylation specific factor 6, 68kd subunit; pre-mrna cleavage factor i, 68kd subunit. [source:refseq;acc:nm_007007]	5732.83	6149.86	1.07274	
1552	atp-dependent dna helicase q5 (recq protein-like 5) (recq5). [source:swissprot;acc:o94762]	6025.86	6464.16	1.07274	
1553	secreted modular calcium-binding protein 1. [source:refseq;acc:nm_022137]	5875.75	6302.76	1.07267	
1554	prefoldin subunit 1. [source:swissprot;acc:o60925]	5875.75	6302.76	1.07267	
1555	secreted modular calcium-binding protein 2; smooth muscle associated protein 2. [source:refseq;acc:nm_022138]	5875.75	6302.76	1.07267	
1556	choline dehydrogenase. [source:refseq;acc:nm_018397]	5875.75	6302.76	1.07267	
1557	vacuolar protein sorting 18 (hvps18). [source:swissprot;acc:q9p253]	6018.7	6455.7	1.07261	
1558	vacuolar protein sorting 33b (hvps33b). [source:swissprot;acc:q9h267]	6048.57	6487.65	1.07259	
1559	vacuolar protein sorting 11 (hvps11) (pp3476). [source:swissprot;acc:q9h270]	6048.57	6487.65	1.07259	
1560	vacuolar protein sorting 33a (hvps33a). [source:swissprot;acc:q96ax1]	6048.57	6487.65	1.07259	
1561	vacuolar protein sorting 16 (hvps16). [source:swissprot;acc:q9h269]	6078.43	6519.6	1.07258	
1562	adenylyl cyclase-associated protein 2 (cap 2). [source:swissprot;acc:p40123]	5984.88	6419.11	1.07255	

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/