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	Filtered	description	Interaction Map	Network Comparison Type	network_comparison	red	green

Results: HTML CSV LaTeX

Showing element 501 to 550 of 77072 in total

Value Type  : Measured

Rank	Filtered	description	Interaction Map	Network Comparison Type	network_comparison	red	green
63	1	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Low confidence	Divided	1.13635	15464.1	17572.7
		myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]	High confidence		1.6231	4489.19	2765.82
		ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]	Low confidence	Subtracted	1062.5	10618.8	11681.3
		spermatogenesis associated 6. [refseq;acc:nm_019073]	High confidence		3832	6475.5	10307.5
64	0	b-lymphocyte activation-related protein. [sptrembl;acc:q96pn3]	Low confidence		383.2	2355.24	1972.04
		dna helicase homolog (fragment). [sptrembl;acc:q9y645]		Divided	2.03615	48.2534	23.6984
		importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292]	High confidence	Subtracted	461	607	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	1800000	0.00001	18
	1	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]		Subtracted	3832	6475.5	10307.5
		glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]		Divided	1.6231	4489.19	2765.82
		ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	Low confidence	Subtracted	1053.1	10585.5	11638.6
		retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]		Divided	1.13635	15464.1	17572.7
65	0	bet5 homolog (multiple myeloma protein 2) (mum-2). [swissprot;acc:q9y5r8]			1.98228	465.658	923.065
		muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]	High confidence	Subtracted	441.449	420.365	861.814
		rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]		Divided	1800000	18	0.00001
		zinc finger protein 169 (fragment). [swissprot;acc:q14929]	Low confidence	Subtracted	383.18	2355	1971.82
	1	cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326]	High confidence		3812.9	22515.5	18702.6
		neuralized-like. [refseq;acc:nm_004210]		Divided	1.6229	1657.68	2690.25
		septin 6. [swissprot;acc:q14141]	Low confidence		1.13593	13005.8	14773.7
		thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652]		Subtracted	1032.86	1917.64	2950.5
66	0	fibrillin 3. [refseq;acc:nm_032447]	High confidence		437	14246	13809
		soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825]		Divided	1.78524	688.436	385.626
		tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677]	Low confidence		1.89874	271.484	142.981
		zinc finger protein 350; zinc-finger protein zbrk1. [refseq;acc:nm_021632]		Subtracted	383.14	2354.46	1971.32
	1	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398]	High confidence		3749.5	17757.5	14008
		gbp protein isoform a. [refseq;acc:nm_017870]	Low confidence		1032.28	1921.96	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]	High confidence	Divided	1.61795	1991.03	3221.38
		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		1.13368	4900.7	5555.81
67	0	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]			1.89769	270.264	142.417
		filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]	High confidence		1.78508	1603	898
		purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491]		Subtracted	435.23	4755.32	4320.09
		similar to zinc finger protein 20 (zinc finger protein kox13) (dkfzp572p0920). [refseq;acc:nm_145233]	Low confidence		383.14	2354.39	1971.25
	1	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	High confidence	Divided	1.59177	6475.5	10307.5
		hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0]	Low confidence		1.1318	12176.9	13781.8
		jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433]		Subtracted	1031.51	1927.68	2959.19
		raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049]	High confidence		3749.2	17756.5	14007.3
68	0	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932]			432.87	6452.66	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]	Low confidence	Divided	1.86294	394	734
		protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981]	High confidence		1.76802	198.964	351.772
		zinc finger protein 222. [swissprot;acc:q9uk12]	Low confidence	Subtracted	383.14	2354.39	1971.25
	1	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	High confidence	Divided	1.59177	6475.5	10307.5
		cyclin g2. [swissprot;acc:q16589]		Subtracted	3742.9	17738.6	13995.7
		putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Low confidence	Divided	1.12932	19498.1	17265.4
		trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030]		Subtracted	1025.45	1972.65	2998.1
69	0	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	High confidence	Divided	1.7602	1593	2804
		phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]		Subtracted	431	570	139
		tubulointerstitial nephritis antigen. [refseq;acc:nm_014464]	Low confidence	Divided	1.82979	129	70.5
		zinc finger protein 223. [swissprot;acc:q9uk11]		Subtracted	383.13	2354.34	1971.21
	1	amino acid transporter xat2; likely ortholog of mouse aspartate/glutamate transporter 1 (agt1). [refseq;acc:nm_138817]		Divided	1.12253	6991.78	7848.45
		cyclin g1 (cyclin g). [swissprot;acc:p51959]	High confidence	Subtracted	3742.9	17738.5	13995.6

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.