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

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Showing element 986 to 1035 of 3228 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Network Comparison Type  : Divided

Rank	green	description	network_comparison	red
986	120.707	exocyst complex component sec5. [swissprot;acc:q96kp1]	1.03371	116.771
987	211.338	serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464]	1.03369	218.459
988	211.343	probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105]	1.03368	218.461
989	211.345	probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110]	1.03367	218.462
990	235.373	atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010]		243.297
991	196.76	dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [swissprot;acc:o60762]	1.03365	203.381
992	211.357	serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743]	1.03364	218.468
993	204.205	pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687]	1.03362	211.071
994	120.772	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3]	1.03361	116.845
995	212.547	mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95]	1.03345	219.656
996		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]
997		nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567]
998	218.271	dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409]	1.03338	225.557
999	208.95	vinculin (metavinculin). [swissprot;acc:p18206]	1.03336	215.92
1000	217.922	sprouty homolog 4 (spry-4). [swissprot;acc:q9c004]	1.03325	225.167
1001		sprouty homolog 3 (spry-3). [swissprot;acc:o43610]
1002		sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609]
1003		sprouty homolog 2 (spry-2). [swissprot;acc:o43597]
1004	231.059	sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633]	1.03318	238.725
1005	218.232	dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576]	1.03307	225.448
1006	120.375	cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6]	1.03305	116.524
1007	156.884	ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967]	1.03296	162.055
1008	235.475	wd-repeat protein bing4. [swissprot;acc:o15213]	1.03292	243.227
1009	221.823	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882]	1.03288	229.116
1010	210.648	peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9]	1.03264	217.523
1011	210.189	retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999]	1.03253	217.026
1012	210.185	retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749]	1.03252	217.021
1013	236.647	protein bap28. [swissprot;acc:q9h583]	1.03239	244.312
1014	235.422	apoptosis antagonizing transcription factor. [refseq;acc:nm_012138]	1.03238	243.045
1015	228.906	bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742]	1.03236	221.73
1016	210.561	importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629]	1.03233	217.369
1017	210.558	target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077]		217.365
1018	210.554	importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505]		217.361
1019	214.409	tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677]	1.03215	221.302
1020		dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [swissprot;acc:p40126]	1.03205	221.28
1021		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]	1.03204	221.278
1022	199.266	cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520]	1.03195	205.632
1023		transforming protein rhoc (h9). [swissprot;acc:p08134]
1024		thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762]
1025		3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325]
1026		transforming protein rhoa (h12). [swissprot;acc:p06749]
1027	218.627	succinyl-coa ligase [gdp-forming] alpha-chain, mitochondrial precursor (ec 6.2.1.4) (succinyl-coa synthetase, alpha chain) (scs-alpha). [swissprot;acc:p53597]	1.03171	211.908
1028		succinyl-coa ligase [adp-forming] beta-chain, mitochondrial precursor (ec 6.2.1.5) (succinyl-coa synthetase, betaa chain) (scs-betaa) (atp- specific succinyl-coa synthetase beta subunit). [swissprot;acc:q9p2r7]
1029	215.535	dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [swissprot;acc:q16531]	1.03168	222.364
1030		propionyl-coa carboxylase beta chain, mitochondrial precursor (ec 6.4.1.3) (pccase beta subunit) (propanoyl-coa:carbon dioxide ligase beta subunit). [swissprot;acc:p05166]
1031	235.518	probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979]	1.03167	242.978
1032	180.943	1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120]	1.03162	186.664
1033	214.406	tyrosinase precursor (ec 1.14.18.1) (monophenol monooxygenase) (tumor rejection antigen ab) (sk29-ab) (lb24-ab). [swissprot;acc:p14679]	1.03161	221.183
1034	180.837	steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718]	1.0316	186.551
1035	228.68	atrophin-1 interacting protein 1; activin receptor interacting protein 1; likely ortholog of mouse activin receptor interacting protein 1; atrophin-1 interacting protein a; membrane associated guanylate kinase 2; activin receptor interacting p. [refseq;acc:nm_012301]	1.03157	221.682

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.