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 3051 to 3100 of 6456 in total

Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
1526	adamts-9 precursor (ec 3.4.24.-) (a disintegrin and metalloproteinase with thrombospondin motifs 9) (adam-ts 9) (adam-ts9). [swissprot;acc:q9p2n4]	Subtracted	5916.05	6350.53	434.48
	calreticulin precursor (crp55) (calregulin) (hacbp) (erp60). [swissprot;acc:p27797]	Divided	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
	dna fragmentation factor alpha subunit (dna fragmentation factor 45 kda subunit) (dff-45) (inhibitor of cad) (icad). [swissprot;acc:o00273]	Subtracted	5916.05	6350.53	434.48
1528	ankyrin 3 (ank-3) (ankyrin g). [swissprot;acc:q12955]
	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]	Divided	5869.97	6301.24	1.07347
1529	ankyrin 2 (brain ankyrin) (ankyrin b) (ankyrin, nonerythroid). [swissprot;acc:q01484]	Subtracted	5916.05	6350.53	434.48
	dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075]	Divided			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]
	adp-ribosylation factor-like protein 3. [swissprot;acc:p36405]	Subtracted			434.48
1531	dna fragmentation factor alpha subunit (dna fragmentation factor 45 kda subunit) (dff-45) (inhibitor of cad) (icad). [swissprot;acc:o00273]	Divided			1.07344
	unc-119 protein homolog (retinal protein 4) (hrg4). [swissprot;acc:q13432]	Subtracted			434.48
1532	26s proteasome non-atpase regulatory subunit 8 (26s proteasome regulatory subunit s14) (p31). [swissprot;acc:p48556]
	ankyrin 3 (ank-3) (ankyrin g). [swissprot;acc:q12955]	Divided			1.07344
1533	ankyrin 2 (brain ankyrin) (ankyrin b) (ankyrin, nonerythroid). [swissprot;acc:q01484]
	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902]	Subtracted	4713.58	4279.17	434.41
1534	adp-ribosylation factor-like protein 3. [swissprot;acc:p36405]	Divided	5916.05	6350.53	1.07344
	phospholipase d2 (ec 3.1.4.4) (pld 2) (choline phosphatase 2) (phosphatidylcholine-hydrolyzing phospholipase d2) (pld1c) (hpld2). [swissprot;acc:o14939]	Subtracted	6157.13	6591.53	434.4
1535	aminomethyltransferase, mitochondrial precursor (ec 2.1.2.10) (glycine cleavage system t protein) (gcvt). [swissprot;acc:p48728]		5945.96	6380.28	434.32
	unc-119 protein homolog (retinal protein 4) (hrg4). [swissprot;acc:q13432]	Divided	5916.05	6350.53	1.07344
1536	26s proteasome non-atpase regulatory subunit 8 (26s proteasome regulatory subunit s14) (p31). [swissprot;acc:p48556]
	adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123]	Subtracted	5984.88	6419.11	434.23
1537	evolutionarily conserved signaling intermediate in toll pathway; ecsit. [refseq;acc:nm_016581]	Divided	6184.27	6637.44	1.07328
	p29ing4; candidate tumor suppressor p33 ing1 homolog. [refseq;acc:nm_016162]	Subtracted	5696.65	6130.26	433.61
1538	brachyury protein (t protein). [swissprot;acc:o15178]		6179.59	6613.15	433.56
	tumor endothelial marker 6; thyroid specific ptb domain protein; tensin 3. [refseq;acc:nm_022748]	Divided	5870.72	6300.83	1.07326
1539	26s protease regulatory subunit 7 (mss1 protein). [swissprot;acc:p35998]		5783.97	6207.5	1.07322
	t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806]	Subtracted	6179.59	6613.15	433.56
1540	mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362]	Divided	6360.13	6825.36	1.07315
	pxr2b protein. [refseq;acc:nm_016559]	Subtracted	6996.51	7429.18	432.67
1541	adenylyl cyclase-associated protein 1 (cap 1). [swissprot;acc:q01518]	Divided	5989.3	6427.17	1.07311
	dimeric dihydrodiol dehydrogenase; 3-deoxyglucosone reductase. [refseq;acc:nm_014475]	Subtracted	6158.32	6590.99	432.67
1542	glycerol-3-phosphate dehydrogenase [nad+], cytoplasmic (ec 1.1.1.8) (gpd-c) (gpdh-c). [swissprot;acc:p21695]		5686.74	6119.36	432.62
	inositol polyphosphate multikinase. [refseq;acc:nm_152230]	Divided	5466	5865.33	1.07306
1543	3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362]	Subtracted	6885.11	7317.48	432.37
	afg3-like protein 2 (ec 3.4.24.-) (paraplegin-like protein). [swissprot;acc:q9y4w6]	Divided	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). [swissprot;acc:q9byc5]
	hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261]	Subtracted	5798.31	6230.55	432.24
1545	aminomethyltransferase, mitochondrial precursor (ec 2.1.2.10) (glycine cleavage system t protein) (gcvt). [swissprot;acc:p48728]	Divided	5945.96	6380.28	1.07304
	lim protein (similar to rat protein kinase c-binding enigma); enigma homolog. [refseq;acc:nm_006457]	Subtracted	5672.68	6104.68	432
1546	26s proteasome non-atpase regulatory subunit 3 (26s proteasome regulatory subunit s3) (proteasome subunit p58). [swissprot;acc:o43242]	Divided	5819.39	6244.37	1.07303
	e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409]	Subtracted	5672.25	6104.01	431.76
1547	cytidine deaminase (ec 3.5.4.5) (cytidine aminohydrolase). [swissprot;acc:p32320]	Divided	5397.21	5790.45	1.07286
	mitochondrial ribosomal protein l24. [refseq;acc:nm_024540]	Subtracted	5672.25	6104.01	431.76
1548	60s ribosomal protein l28. [swissprot;acc:p46779]	Divided	5987.29	6423.52	1.07286
	65 kda yes-associated protein (yap65). [swissprot;acc:p46937]	Subtracted	5672.25	6104.01	431.76
1549	9 kda protein. [swissprot;acc:p13994]
	glucose-6-phosphate 1-dehydrogenase (ec 1.1.1.49) (g6pd). [swissprot;acc:p11413]	Divided	6025.86	6464.16	1.07274
1550	collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400]	Subtracted	5672.23	6103.98	431.75
	dna-repair protein xrcc3 (x-ray repair cross-complementing protein 3). [swissprot;acc:o43542]	Divided	6025.86	6464.16	1.07274

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.