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

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Showing element 1001 to 1050 of 38536 in total

Network Comparison Type  : Divided

Rank	Value Type	description	Filtered	red	Interaction Map	network_comparison	green
63	Squared	core1 udp-galactose:n-acetylgalactosamine-alpha-r beta 1,3-galac. [refseq;acc:nm_020156]	1	73677.6	Low confidence	1.28138	57498.7
		melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]		219048	High confidence	1.68808	129762
		protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	0	1.24091		3.3984	0.365145
		synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]		44.2067	Low confidence	3.92038	173.307
	Rooted	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]		18.1049	High confidence	1.43581	12.6095
		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	43.4554		1.36835	31.7576
		selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	0	8.48528	Low confidence	1.44818	12.2882
		t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806]	1	61.4851		1.10801	68.1264
64	Measured	dna helicase homolog (fragment). [sptrembl;acc:q9y645]	0	48.2534		2.03615	23.6984
		glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]	1	4489.19	High confidence	1.6231	2765.82
		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	0.00001		1800000	18
		retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]	1	15464.1	Low confidence	1.13635	17572.7
	Ranked	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152]		266.868	High confidence	1.25965	336.159
		selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	0	14463	Low confidence	1.2736	11356
		similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]		15264	High confidence	1.33563	20387
		transcription factor jun-d. [swissprot;acc:p17535]	1	202.709	Low confidence	1.10552	183.361
	Squared	melanoma antigen, family b, 6. [refseq;acc:nm_173523]		219048	High confidence	1.68808	129762
		neurochondrin. [refseq;acc:nm_014284]		73677.6	Low confidence	1.28138	57498.7
		sedlin. [swissprot;acc:o14582]	0	44.5387		3.88974	173.244
		tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677]		50.8715	High confidence	3.33542	15.2519
	Rooted	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	1	63.8686		1.35128	47.2654
		anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801]	0	45.6289	Low confidence	1.44645	66
		muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]		15.7225	High confidence	1.43422	22.5496
		rab11-family interacting protein 4. [refseq;acc:nm_032932]	1	73.6221	Low confidence	1.10693	81.4944
65	Measured	bet5 homolog (multiple myeloma protein 2) (mum-2). [swissprot;acc:q9y5r8]	0	465.658		1.98228	923.065
		neuralized-like. [refseq;acc:nm_004210]	1	1657.68	High confidence	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]	1	13005.8	Low confidence	1.13593	14773.7
	Ranked	alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7]	0	10172.1		1.27245	12943.5
		e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409]		7853.67	High confidence	1.32502	10406.3
		guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148]	1	267.136		1.25807	336.077
		transcription factor jun-b. [swissprot;acc:p17275]		202.728	Low confidence	1.10546	183.388
	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	50.642	High confidence	3.33538	15.1833
		l-lactate dehydrogenase a chain (ec 1.1.1.27) (ldh-a) (ldh muscle subunit) (ldh-m). [swissprot;acc:p00338]		13.3089	Low confidence	3.55848	47.3595
		melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	1	219048	High confidence	1.68808	129762
		septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599]		75490.8	Low confidence	1.26497	95493.3
	Rooted	60s ribosomal protein l21. [swissprot;acc:p46778]	0	20.5734	High confidence	1.42072	29.2291
		eferin. [swissprot;acc:o75154]	1	73.6221	Low confidence	1.10693	81.4944
		glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]		63.8686	High confidence	1.35128	47.2654
		transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193]	0	7.33436	Low confidence	1.43105	10.4958
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]	1	1991.03	High confidence	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]	1	4900.7	Low confidence	1.13368	5555.81
		tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677]	0	271.484		1.89874	142.981
	Ranked	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992]	1	267.136	High confidence	1.25807	336.077
		heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174]	0	11461		1.32449	15180
		kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8]		7923.89	Low confidence	1.26584	10030.4
		mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [refseq;acc:nm_020749]	1	221.902		1.10518	200.783
	Squared	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	0	1797.76	High confidence	3.2204	558.241
		melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	1	219048		1.68808	129762

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.