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	Value Type	Gene	description	Network Comparison Type	Interaction Map	Filtered	green	red	network_comparison

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Showing element 501 to 550 of 14920 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence

Rank	Value Type	description	Filtered	green	red	network_comparison
63	Squared	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	1	129762	219048	1.68808
		protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	0	0.365145	1.24091	3.3984
	Rooted	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]		12.6095	18.1049	1.43581
		kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193]	1	31.7576	43.4554	1.36835
64	Measured	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]		2765.82	4489.19	1.6231
		phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750]	0	18	0.00001	1800000
	Ranked	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152]	1	336.159	266.868	1.25965
		similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	0	20387	15264	1.33563
	Squared	melanoma antigen, family b, 6. [refseq;acc:nm_173523]	1	129762	219048	1.68808
		tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677]	0	15.2519	50.8715	3.33542
	Rooted	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	1	47.2654	63.8686	1.35128
		muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]	0	22.5496	15.7225	1.43422
65	Measured	neuralized-like. [refseq;acc:nm_004210]	1	2690.25	1657.68	1.6229
		rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]	0	0.00001	18	1800000
	Ranked	e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409]		10406.3	7853.67	1.32502
		guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148]	1	336.077	267.136	1.25807
	Squared	5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643]	0	15.1833	50.642	3.33538
		melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	1	129762	219048	1.68808
	Rooted	60s ribosomal protein l21. [swissprot;acc:p46778]	0	29.2291	20.5734	1.42072
		glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]	1	47.2654	63.8686	1.35128
66	Measured	nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09]		3221.38	1991.03	1.61795
		soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825]	0	385.626	688.436	1.78524
	Ranked	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992]	1	336.077	267.136	1.25807
		heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174]	0	15180	11461	1.32449
	Squared	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]		558.241	1797.76	3.2204
		melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	1	129762	219048	1.68808
	Rooted	glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]		47.2654	63.8686	1.35128
		oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	0	21.9983	30.9855	1.40854
67	Measured	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	1	10307.5	6475.5	1.59177
		filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]	0	898	1603	1.78508
	Ranked	guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087]	1	336.075	267.14	1.25805
		presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341]	0	14291.5	10793.5	1.32408
	Squared	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]		190.865	608.191	3.1865
		melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]	1	129762	219048	1.68808
	Rooted	isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252]	0	15.3166	11.0051	1.39177
		myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]	1	47.2654	63.8686	1.35128
68	Measured	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]		10307.5	6475.5	1.59177
		protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981]	0	351.772	198.964	1.76802
	Ranked	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086]	1	336.075	267.139	1.25805
		purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491]	0	11823.3	8932.56	1.32362
	Squared	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	1	129762	219048	1.68808
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0	0.00001	31.36	3136000
	Rooted	alpha crystallin a chain. [swissprot;acc:p02489]		8.63381	6.22183	1.38766
		glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]	1	47.2654	63.8686	1.35128
69	Measured	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	0	2804	1593	1.7602
		spermatogenesis associated 6. [refseq;acc:nm_019073]	1	10307.5	6475.5	1.59177
	Ranked	collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400]	0	10174.1	7704.7	1.32051
		guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488]	1	336.075	267.14	1.25805
	Squared	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]		129762	219048	1.68808
		protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981]	0	50.7408	16.2406	3.12432

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.