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

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Showing element 501 to 550 of 29840 in total

Interaction Map  : High confidence

Rank	Value Type	description	Filtered	red	Network Comparison Type	green	network_comparison
32	Ranked	guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899]	1	267.142	Subtracted	336.074	68.932
		importin 9. [refseq;acc:nm_018085]	0	13292.2	Divided	8691.76	1.52929
		serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4]	1	187.462		243.673	1.29985
		syntaxin 10 (syn10). [swissprot;acc:o60499]	0	13884.4	Subtracted	19014.6	5130.2
	Squared	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	1	9924.76	Divided	25146.6	2.53372
		pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]		106226	Subtracted	192141	85915
		phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]	0	76.8994	Divided	4.57302	16.8159
		sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961]		19892.6	Subtracted	27221.2	7328.6
	Rooted	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]	1	26.0288	Divided	43.1914	1.65937
		gbp protein isoform a. [refseq;acc:nm_017870]		23.9771	Subtracted	42.4773	18.5002
		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	0	0		9.43398	9.43398
		ubiquitin protein ligase. [refseq;acc:nm_130466]		24.0391	Divided	11.258	2.13529
33	Measured	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152]	1	1835.3		896.972	2.04611
		lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	0	12.6208		39.8063	3.15402
		melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	1	23693.7	Subtracted	18263	5430.7
		protein cgi-147. [swissprot;acc:q9y3e5]	0	8396.12		9192.38	796.26
	Ranked	guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898]	1	267.144		336.073	68.929
		nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733]	0	13292.2	Divided	8691.76	1.52929
		serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154]	1	188.688		242.742	1.28647
		similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	0	15264	Subtracted	20387	5123
	Squared	ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9]		29812		36822.7	7010.7
		beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]		76.8994	Divided	4.57302	16.8159
		pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	1	106226	Subtracted	192141	85915
		spermatogenesis associated 6. [refseq;acc:nm_019073]		9924.76	Divided	25146.6	2.53372
	Rooted	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	0	12.3693		25.7294	2.0801
		nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]		61.6393	Subtracted	70.9983	9.359
		protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	1	25.6987		43.561	17.8623
		protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]		26.0288	Divided	43.1914	1.65937
34	Measured	acrc protein; putative nuclear protein. [refseq;acc:nm_052957]	0	4131.06	Subtracted	3340.03	791.03
		glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]		143	Divided	47	3.04255
		guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992]	1	1836.71		907.546	2.02382
		melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]		23693.7	Subtracted	18263	5430.7
	Ranked	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	0	11543		6812	4731
		guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754]	1	267.144		336.073	68.929
		microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]	0	11284	Divided	17173.8	1.52196
		serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153]	1	189.07		242.453	1.28235
	Squared	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]		9924.76		25146.6	2.53372
		coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606]	0	79383.4	Subtracted	72701	6682.4
		lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]		0.0435834	Divided	0.697197	15.9968
		pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	1	106226	Subtracted	192141	85915
	Rooted	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]		140.508		122.878	17.63
		guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992]		40.2812	Divided	24.3678	1.65305
		phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]	0	23.8747		11.7898	2.02503
		succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521]		3.16228	Subtracted	12.49	9.32772
35	Measured	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236]		459.5	Divided	1377	2.99674
		filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]		1603	Subtracted	898	705
		guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148]	1	1836.71	Divided	907.564	2.02378
		melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]		23693.7	Subtracted	18263	5430.7
	Ranked	guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775]		267.636		335.359	67.723
		importin 9. [refseq;acc:nm_018085]	0	13292.2		8691.76	4600.44

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.