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 1525 to 1574 of 3228 in total

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

Rank	description	red	green	network_comparison
1525	tensin. [refseq;acc:nm_022648]	5871.89	6303.56	1.07351
1526	calreticulin precursor (crp55) (calregulin) (hacbp) (erp60). [swissprot;acc:p27797]	5369.1	5763.72	1.0735
1527	26s protease regulatory subunit 6a (tat-binding protein 1) (tbp-1) (proteasome subunit p50). [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. [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). [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). [swissprot;acc:q9p2n4]
1531	dna fragmentation factor alpha subunit (dna fragmentation factor 45 kda subunit) (dff-45) (inhibitor of cad) (icad). [swissprot;acc:o00273]
1532	ankyrin 3 (ank-3) (ankyrin g). [swissprot;acc:q12955]
1533	ankyrin 2 (brain ankyrin) (ankyrin b) (ankyrin, nonerythroid). [swissprot;acc:q01484]
1534	adp-ribosylation factor-like protein 3. [swissprot;acc:p36405]
1535	unc-119 protein homolog (retinal protein 4) (hrg4). [swissprot;acc:q13432]
1536	26s proteasome non-atpase regulatory subunit 8 (26s proteasome regulatory subunit s14) (p31). [swissprot;acc:p48556]
1537	evolutionarily conserved signaling intermediate in toll pathway; ecsit. [refseq;acc:nm_016581]	6184.27	6637.44	1.07328
1538	tumor endothelial marker 6; thyroid specific ptb domain protein; tensin 3. [refseq;acc:nm_022748]	5870.72	6300.83	1.07326
1539	26s protease regulatory subunit 7 (mss1 protein). [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. [refseq;acc:nm_022362]	6360.13	6825.36	1.07315
1541	adenylyl cyclase-associated protein 1 (cap 1). [swissprot;acc:q01518]	5989.3	6427.17	1.07311
1542	inositol polyphosphate multikinase. [refseq;acc:nm_152230]	5466	5865.33	1.07306
1543	afg3-like protein 2 (ec 3.4.24.-) (paraplegin-like protein). [swissprot;acc:q9y4w6]
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). [swissprot;acc:q9byc5]
1545	aminomethyltransferase, mitochondrial precursor (ec 2.1.2.10) (glycine cleavage system t protein) (gcvt). [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). [swissprot;acc:o43242]	5819.39	6244.37	1.07303
1547	cytidine deaminase (ec 3.5.4.5) (cytidine aminohydrolase). [swissprot;acc:p32320]	5397.21	5790.45	1.07286
1548	60s ribosomal protein l28. [swissprot;acc:p46779]	5987.29	6423.52
1549	glucose-6-phosphate 1-dehydrogenase (ec 1.1.1.49) (g6pd). [swissprot;acc:p11413]	6025.86	6464.16	1.07274
1550	dna-repair protein xrcc3 (x-ray repair cross-complementing protein 3). [swissprot;acc:o43542]
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. [refseq;acc:nm_007007]	5732.83	6149.86
1552	atp-dependent dna helicase q5 (recq protein-like 5) (recq5). [swissprot;acc:o94762]	6025.86	6464.16
1553	secreted modular calcium-binding protein 1. [refseq;acc:nm_022137]	5875.75	6302.76	1.07267
1554	prefoldin subunit 1. [swissprot;acc:o60925]
1555	secreted modular calcium-binding protein 2; smooth muscle associated protein 2. [refseq;acc:nm_022138]
1556	choline dehydrogenase. [refseq;acc:nm_018397]
1557	vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253]	6018.7	6455.7	1.07261
1558	vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267]	6048.57	6487.65	1.07259
1559	vacuolar protein sorting 11 (hvps11) (pp3476). [swissprot;acc:q9h270]
1560	vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1]
1561	vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269]	6078.43	6519.6	1.07258
1562	adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123]	5984.88	6419.11	1.07255
1563	proteasome subunit beta type 6 precursor (ec 3.4.25.1) (proteasome delta chain) (macropain delta chain) (multicatalytic endopeptidase complex delta chain) (proteasome subunit y). [swissprot;acc:p28072]	6221.35	6672.51	1.07252
1564	proteasome subunit beta type 9 precursor (ec 3.4.25.1) (proteasome chain 7) (macropain chain 7) (multicatalytic endopeptidase complex chain 7) (ring12 protein) (low molecular mass protein 2). [swissprot;acc:p28065]	6257.62	6711.4
1565	proteasome subunit alpha type 2 (ec 3.4.25.1) (proteasome component c3) (macropain subunit c3) (multicatalytic endopeptidase complex subunit c3). [swissprot;acc:p25787]	6343.76	6803.44	1.07246
1566	protein phosphatase 1, regulatory (inhibitor) subunit 12b isoform a; myosin phosphatase regulatory subunit; myosin phosphatase, target subunit 2. [refseq;acc:nm_002481]	5846.67	6269.41	1.0723
1567	26s protease regulatory subunit 6b (mip224) (mb67 interacting protein) (tat-binding protein-7) (tbp-7). [swissprot;acc:p43686]	5822.25	6242.94	1.07226
1568	protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [refseq;acc:nm_002480]	5845.22	6267.34	1.07222
1569	traf and tnf receptor-associated protein; ets1-associated protein 2. [refseq;acc:nm_016614]	5819.37	6239.55	1.0722
1570	n-acetylglutamate synthase. [refseq;acc:nm_153006]	5162.27	5534.71	1.07215
1571	26s proteasome non-atpase regulatory subunit 7 (26s proteasome regulatory subunit s12) (proteasome subunit p40) (mov34 protein homolog). [swissprot;acc:p51665]	5851.64	6273.4	1.07208
1572	proteasome subunit alpha type 1 (ec 3.4.25.1) (proteasome component c2) (macropain subunit c2) (multicatalytic endopeptidase complex subunit c2) (proteasome nu chain) (30 kda prosomal protein) (pros-30). [swissprot;acc:p25786]	6068.03	6504.59	1.07194
1573	epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [swissprot;acc:p07099]	11785.4	10995.3	1.07186
1574	atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031]	5106.13	5472.96	1.07184

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.