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

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Showing element 1012 to 1061 of 3228 in total

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

Rank	Hugo	description	red	network_comparison	green
1012	RBL1	retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749]	217.021	1.03252	210.185
1013	HEATR1	protein bap28. [swissprot;acc:q9h583]	244.312	1.03239	236.647
1014	AATF	apoptosis antagonizing transcription factor. [refseq;acc:nm_012138]	243.045	1.03238	235.422
1015	MAGI1	bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742]	221.73	1.03236	228.906
1016	KPNA4	importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629]	217.369	1.03233	210.561
1017	TOE1	target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077]	217.365		210.558
1018	KPNA3	importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505]	217.361		210.554
1019	TYRL	tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677]	221.302	1.03215	214.409
1020	DCT	dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [swissprot;acc:p40126]	221.28	1.03205
1021	TYRP1	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]	221.278	1.03204
1022	CBS	cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520]	205.632	1.03195	199.266
1023	RHOC	transforming protein rhoc (h9). [swissprot;acc:p08134]
1024	TST	thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762]
1025	MPST	3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325]
1026	RHOA	transforming protein rhoa (h12). [swissprot;acc:p06749]
1027	SUCLG1	succinyl-coa ligase [gdp-forming] alpha-chain, mitochondrial precursor (ec 6.2.1.4) (succinyl-coa synthetase, alpha chain) (scs-alpha). [swissprot;acc:p53597]	211.908	1.03171	218.627
1028	SUCLA2	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	DDB1	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]	222.364	1.03168	215.535
1030	PCCB	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	EMG1	probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979]	242.978	1.03167	235.518
1032	AGPAT2	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]	186.664	1.03162	180.943
1033	TYR	tyrosinase precursor (ec 1.14.18.1) (monophenol monooxygenase) (tumor rejection antigen ab) (sk29-ab) (lb24-ab). [swissprot;acc:p14679]	221.183	1.03161	214.406
1034	ESRRB	steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718]	186.551	1.0316	180.837
1035	MAGI2	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]	221.682	1.03157	228.68
1036	COPB1	coatomer beta subunit (beta-coat protein) (beta-cop). [swissprot;acc:p53618]	171.341	1.03155	176.746
1037	GLRX3	thioredoxin-like; pkc-interacting cousin of thioredoxin. [refseq;acc:nm_006541]	228.412	1.03151	235.609
1038	no value	1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943]	186.741	1.03148	181.041
1039	DLD	dihydrolipoamide dehydrogenase, mitochondrial precursor (ec 1.8.1.4) (glycine cleavage system l protein). [swissprot;acc:p09622]	207.719	1.03137	214.236
1040	CCT5	t-complex protein 1, epsilon subunit (tcp-1-epsilon) (cct-epsilon). [swissprot;acc:p48643]	163.24	1.03136	168.359
1041	HNRNPL	heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866]	186.774	1.03134	181.099
1042	no value	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454]	186.799	1.03132	181.127
1043	AGPAT3	1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7]	187.834	1.03128	182.137
1044	DYNLT3	t-complex associated-testis-expressed 1-like (protein 91/23). [swissprot;acc:p51808]	173.475	1.03121	178.889
1045	FIP1L1	fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917]	115.817		119.432
1046	MRE11A	double-strand break repair protein mre11a (mre11 homolog 1). [swissprot;acc:p49959]	173.475		178.889
1047	ESRRA	steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474]	187.022	1.03104	181.391
1048	AGPAT4	1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5]	187.96	1.031	182.308
1049	no value	adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741]	211.449	1.03097	217.998
1050	HSD17B1	estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061]
1051	no value	17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034]
1052	RDH8	retinol dehydrogenase 8 (all-trans); photoreceptor outer segment all-trans retinol dehydrogenase. [refseq;acc:nm_015725]
1053	PSMA5	proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [swissprot;acc:p28066]	207.04	1.03087	200.84
1054	no value	60s ribosomal protein l21. [swissprot;acc:p46778]	223.958	1.03082	217.263
1055	ASNSD1	hcv ns3-transactivated protein 1. [refseq;acc:nm_019048]	219.01	1.03079	212.468
1056	ATP6V1A	vacuolar atp synthase catalytic subunit a, ubiquitous isoform (ec 3.6.3.14) (v-atpase a subunit 1) (vacuolar proton pump alpha subunit 1) (v-atpase 69 kda subunit 1) (isoform va68). [swissprot;acc:p38606]
1057	ASNS	asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243]
1058	ATXN2L	ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245]	228.105	1.03078	221.293
1059	no value	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]
1060	NLK	nemo-like kinase; likely ortholog of mouse nemo like kinase. [refseq;acc:nm_016231]	218.162		211.648
1061	ERC1	elks protein. [refseq;acc:nm_015064]

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
- Hugo is the HGNC identifier if it exists
- 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.