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

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Showing element 501 to 550 of 77072 in total

Value Type  : Measured

Rank	Interaction Map	Network Comparison Type	description	Filtered	green	red	network_comparison
63	Low confidence	Divided	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	1	17572.7	15464.1	1.13635
			laminin beta-1 chain precursor (laminin b1 chain). [swissprot;acc:p07942]	0	75.6508	154.208	2.03842
		Subtracted	ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]	1	11681.3	10618.8	1062.5
			zinc finger protein 8 (zinc finger protein hf.18) (fragment). [swissprot;acc:p17098]	0	1972.19	2355.41	383.22
64	High confidence	Divided	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]	1	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
		Subtracted	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]	1	10307.5	6475.5	3832
			importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292]	0	1068	607	461
	Low confidence	Divided	dna helicase homolog (fragment). [sptrembl;acc:q9y645]		23.6984	48.2534	2.03615
			retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]	1	17572.7	15464.1	1.13635
		Subtracted	b-lymphocyte activation-related protein. [sptrembl;acc:q96pn3]	0	1972.04	2355.24	383.2
			ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	1	11638.6	10585.5	1053.1
65	High confidence	Divided	neuralized-like. [refseq;acc:nm_004210]		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
		Subtracted	cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326]	1	18702.6	22515.5	3812.9
			muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]	0	861.814	420.365	441.449
	Low confidence	Divided	bet5 homolog (multiple myeloma protein 2) (mum-2). [swissprot;acc:q9y5r8]		923.065	465.658	1.98228
			septin 6. [swissprot;acc:q14141]	1	14773.7	13005.8	1.13593
		Subtracted	thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652]		2950.5	1917.64	1032.86
			zinc finger protein 169 (fragment). [swissprot;acc:q14929]	0	1971.82	2355	383.18
66	High confidence	Divided	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]	1	3221.38	1991.03	1.61795
			soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825]	0	385.626	688.436	1.78524
		Subtracted	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398]	1	14008	17757.5	3749.5
			fibrillin 3. [refseq;acc:nm_032447]	0	13809	14246	437
	Low confidence	Divided	son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583]	1	5555.81	4900.7	1.13368
			tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677]	0	142.981	271.484	1.89874
		Subtracted	gbp protein isoform a. [refseq;acc:nm_017870]	1	2954.24	1921.96	1032.28
			zinc finger protein 350; zinc-finger protein zbrk1. [refseq;acc:nm_021632]	0	1971.32	2354.46	383.14
67	High confidence	Divided	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
		Subtracted	purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491]		4320.09	4755.32	435.23
			raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049]	1	14007.3	17756.5	3749.2
	Low confidence	Divided	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	142.417	270.264	1.89769
			hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0]	1	13781.8	12176.9	1.1318
		Subtracted	jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433]		2959.19	1927.68	1031.51
			similar to zinc finger protein 20 (zinc finger protein kox13) (dkfzp572p0920). [refseq;acc:nm_145233]	0	1971.25	2354.39	383.14
68	High confidence	Divided	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	1	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
		Subtracted	cyclin g2. [swissprot;acc:q16589]	1	13995.7	17738.6	3742.9
			folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932]	0	6019.79	6452.66	432.87
	Low confidence	Divided	nadh-ubiquinone oxidoreductase mlrq subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-mlrq) (ci-mlrq). [swissprot;acc:o00483]		734	394	1.86294
			putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	1	17265.4	19498.1	1.12932
		Subtracted	trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030]		2998.1	1972.65	1025.45
			zinc finger protein 222. [swissprot;acc:q9uk12]	0	1971.25	2354.39	383.14
69	High confidence	Divided	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]		2804	1593	1.7602
			spermatogenesis associated 6. [refseq;acc:nm_019073]	1	10307.5	6475.5	1.59177
		Subtracted	cyclin g1 (cyclin g). [swissprot;acc:p51959]		13995.6	17738.5	3742.9
			phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]	0	139	570	431
	Low confidence	Divided	amino acid transporter xat2; likely ortholog of mouse aspartate/glutamate transporter 1 (agt1). [refseq;acc:nm_138817]	1	7848.45	6991.78	1.12253
			tubulointerstitial nephritis antigen. [refseq;acc:nm_014464]	0	70.5	129	1.82979

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.