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

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Showing element 2080 to 2129 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
130	udp-glucuronosyltransferase 2b4 precursor, microsomal (ec 2.4.1.17) (udpgt) (hyodeoxycholic acid) (hlug25) (udpgth-1). [swissprot;acc:p06133]	Rooted	Subtracted	0	32.4121	28.377	4.0351
131	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	Squared			101.05	1034.13	933.08
	60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268]	Rooted	Divided		19.3128	16.0484	1.20341
	dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692]	Ranked			8375.43	9873.58	1.17887
	egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215]		Subtracted	1	242.718	276.018	33.3
	forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]	Measured	Divided		2234.73	2978.57	1.33285
	glutamyl aminopeptidase (ec 3.4.11.7) (eap) (aminopeptidase a) (apa) (differentiation antigen gp160). [swissprot;acc:q07075]	Rooted	Subtracted	0	32.4121	28.377	4.0351
	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]		Divided	1	55.1113	67.5537	1.22577
	integral membrane protein cii-3b. [sptrembl;acc:o75609]	Ranked	Subtracted	0	14951.6	13204.2	1747.4
	nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972]	Squared	Divided	1	148058	99628.4	1.4861
	protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031]	Measured	Subtracted	0	4912.01	4658.69	253.32
	ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]	Rooted		1	144.606	157.824	13.218
	serpin b11. [swissprot;acc:q96p15]	Measured	Divided	0	42	56	1.33333
	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]	Ranked		1	294.053	242.562	1.21228
	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]	Squared	Subtracted		71062.4	95488.9	24426.5
	transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699]	Measured			12839	10911.1	1927.9
	vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670]	Squared	Divided	0	451.156	817.981	1.81308
132	arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143]		Subtracted		5671.94	6590.82	918.88
	autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0]		Divided	1	36359.2	24466.8	1.48606
	creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532]	Rooted		0	23.9003	19.8655	1.20311
	cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452]	Measured			42	56	1.33333
	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	Ranked	Subtracted	1	229.406	196.695	32.711
	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1]	Measured	Divided		2236.61	2980.35	1.33253
	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929]	Rooted			44.963	55.0576	1.22451
	lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428]	Squared		0	1.75053	0.969467	1.80566
	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	Ranked	Subtracted		10883	12622.8	1739.8
	protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467]	Squared		1	71062.2	95488.6	24426.4
	ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]	Rooted			144.606	157.824	13.218
	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]	Ranked	Divided	0	19048	22389	1.1754
	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]			1	350	290	1.2069
	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735]	Measured	Subtracted		12839	10911.1	1927.9
	udp-glucuronosyltransferase 2b10 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:p36537]	Rooted		0	32.4121	28.377	4.0351
	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02]	Measured			1949.36	2202	252.64
133	alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7]	Ranked	Divided		6814	8009	1.17537
	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]	Rooted	Subtracted	1	144.606	157.824	13.218
	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340]	Measured	Divided	0	252	335	1.32937
	cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]		Subtracted	1	12798.9	10887.2	1911.7
	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	Ranked			226.887	194.72	32.167
	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	Measured	Divided		23421.5	17580.4	1.33225
	gbp protein isoform a. [refseq;acc:nm_017870]	Squared			1182.25	1726.55	1.46039
	histone deacetylase 2 (hd2). [swissprot;acc:q92769]		Subtracted	0	4748.4	5654.56	906.16
	metaxin 1. [swissprot;acc:q13505]		Divided		6149.89	3429.64	1.79316
	mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362]	Ranked	Subtracted		17144.8	15405.6	1739.2
	odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260]	Rooted	Divided	1	45.4558	55.5995	1.22316
	testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7]	Measured	Subtracted	0	3036.85	2784.59	252.26
	tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888]	Rooted	Divided		27.4578	22.8323	1.20259
	thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7]	Squared	Subtracted	1	71062.2	95488.6	24426.4
	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Ranked	Divided		350	290	1.2069
	udp-glucuronosyltransferase 2b15 precursor, microsomal (ec 2.4.1.17) (udpgt) (udpgth-3) (hlug4). [swissprot;acc:p54855]	Rooted	Subtracted	0	32.4121	28.377	4.0351
134	60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]	Squared			3438.01	4339.96	901.95

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.