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

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Showing element 501 to 550 of 77072 in total

Value Type  : Measured

Rank	description	Network Comparison Type	Interaction Map	Filtered	red	network_comparison	green
63	ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]	Subtracted	Low confidence	1	10618.8	1062.5	11681.3
	spermatogenesis associated 6. [refseq;acc:nm_019073]		High confidence		6475.5	3832	10307.5
	spir-2 protein (fragment). [sptrembl;acc:q8wwl2]	Divided		0	31.1429	1.80709	56.278
	zinc finger protein 8 (zinc finger protein hf.18) (fragment). [swissprot;acc:p17098]	Subtracted	Low confidence		2355.41	383.22	1972.19
64	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]		High confidence	1	6475.5	3832	10307.5
	b-lymphocyte activation-related protein. [sptrembl;acc:q96pn3]		Low confidence	0	2355.24	383.2	1972.04
	dna helicase homolog (fragment). [sptrembl;acc:q9y645]	Divided			48.2534	2.03615	23.6984
	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]		High confidence	1	4489.19	1.6231	2765.82
	importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292]	Subtracted		0	607	461	1068
	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]	Divided			0.00001	1800000	18
	ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	Subtracted	Low confidence	1	10585.5	1053.1	11638.6
	retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]	Divided			15464.1	1.13635	17572.7
65	bet5 homolog (multiple myeloma protein 2) (mum-2). [swissprot;acc:q9y5r8]			0	465.658	1.98228	923.065
	cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326]	Subtracted	High confidence	1	22515.5	3812.9	18702.6
	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]			0	420.365	441.449	861.814
	neuralized-like. [refseq;acc:nm_004210]	Divided		1	1657.68	1.6229	2690.25
	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]			0	18	1800000	0.00001
	septin 6. [swissprot;acc:q14141]		Low confidence	1	13005.8	1.13593	14773.7
	thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652]	Subtracted			1917.64	1032.86	2950.5
	zinc finger protein 169 (fragment). [swissprot;acc:q14929]			0	2355	383.18	1971.82
66	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398]		High confidence	1	17757.5	3749.5	14008
	fibrillin 3. [refseq;acc:nm_032447]			0	14246	437	13809
	gbp protein isoform a. [refseq;acc:nm_017870]		Low confidence	1	1921.96	1032.28	2954.24
	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]	Divided	High confidence		1991.03	1.61795	3221.38
	soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825]			0	688.436	1.78524	385.626
	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]		Low confidence	1	4900.7	1.13368	5555.81
	tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677]			0	271.484	1.89874	142.981
	zinc finger protein 350; zinc-finger protein zbrk1. [refseq;acc:nm_021632]	Subtracted			2354.46	383.14	1971.32
67	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]	Divided			270.264	1.89769	142.417
	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]		High confidence	1	6475.5	1.59177	10307.5
	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]			0	1603	1.78508	898
	hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0]		Low confidence	1	12176.9	1.1318	13781.8
	jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433]	Subtracted			1927.68	1031.51	2959.19
	purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491]		High confidence	0	4755.32	435.23	4320.09
	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049]			1	17756.5	3749.2	14007.3
	similar to zinc finger protein 20 (zinc finger protein kox13) (dkfzp572p0920). [refseq;acc:nm_145233]		Low confidence	0	2354.39	383.14	1971.25
68	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	Divided	High confidence	1	6475.5	1.59177	10307.5
	cyclin g2. [swissprot;acc:q16589]	Subtracted			17738.6	3742.9	13995.7
	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932]			0	6452.66	432.87	6019.79
	nadh-ubiquinone oxidoreductase mlrq subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-mlrq) (ci-mlrq). [swissprot;acc:o00483]	Divided	Low confidence		394	1.86294	734
	protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981]		High confidence		198.964	1.76802	351.772
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]		Low confidence	1	19498.1	1.12932	17265.4
	trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030]	Subtracted			1972.65	1025.45	2998.1
	zinc finger protein 222. [swissprot;acc:q9uk12]			0	2354.39	383.14	1971.25
69	amino acid transporter xat2; likely ortholog of mouse aspartate/glutamate transporter 1 (agt1). [refseq;acc:nm_138817]	Divided		1	6991.78	1.12253	7848.45
	cyclin g1 (cyclin g). [swissprot;acc:p51959]	Subtracted	High confidence		17738.5	3742.9	13995.6
	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	Divided		0	1593	1.7602	2804
	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]	Subtracted			570	431	139
	spermatogenesis associated 6. [refseq;acc:nm_019073]	Divided		1	6475.5	1.59177	10307.5
	trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477]	Subtracted	Low confidence		1983.91	1023.94	3007.85

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.