Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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 Network Comparison Type Value Type Interaction Map red Filtered network_comparison green
Results: HTML CSV LaTeX Showing element 1008 to 1057 of 3228 in total 
Network Comparison Type	Divided
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	red	network_comparison	green	
1008	wd-repeat protein bing4. [source:swissprot;acc:o15213]	243.227	1.03292	235.475	
1009	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [source:swissprot;acc:q12882]	229.116	1.03288	221.823	
1010	peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [source:swissprot;acc:q9ukg9]	217.523	1.03264	210.648	
1011	retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [source:swissprot;acc:q08999]	217.026	1.03253	210.189	
1012	retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [source:swissprot;acc:p28749]	217.021	1.03252	210.185	
1013	protein bap28. [source:swissprot;acc:q9h583]	244.312	1.03239	236.647	
1014	apoptosis antagonizing transcription factor. [source:refseq;acc:nm_012138]	243.045	1.03238	235.422	
1015	bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [source:refseq;acc:nm_004742]	221.73	1.03236	228.906	
1016	importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [source:swissprot;acc:o00629]	217.369	1.03233	210.561	
1017	target of egr1, member 1 (nuclear); target of egr1, member 1. [source:refseq;acc:nm_025077]	217.365	1.03233	210.558	
1018	importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [source:swissprot;acc:o00505]	217.361	1.03233	210.554	
1019	tyrosinase-related gene segment, exon 5 (fragment). [source:sptrembl;acc:q15677]	221.302	1.03215	214.409	
1020	dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [source:swissprot;acc:p40126]	221.28	1.03205	214.409	
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). [source:swissprot;acc:p17643]	221.278	1.03204	214.409	
1022	cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [source:swissprot;acc:p35520]	205.632	1.03195	199.266	
1023	transforming protein rhoc (h9). [source:swissprot;acc:p08134]	205.632	1.03195	199.266	
1024	thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [source:swissprot;acc:q16762]	205.632	1.03195	199.266	
1025	3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [source:swissprot;acc:p25325]	205.632	1.03195	199.266	
1026	transforming protein rhoa (h12). [source:swissprot;acc:p06749]	205.632	1.03195	199.266	
1027	succinyl-coa ligase [gdp-forming] alpha-chain, mitochondrial precursor (ec 6.2.1.4) (succinyl-coa synthetase, alpha chain) (scs-alpha). [source:swissprot;acc:p53597]	211.908	1.03171	218.627	
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). [source:swissprot;acc:q9p2r7]	211.908	1.03171	218.627	
1029	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). [source:swissprot;acc:q16531]	222.364	1.03168	215.535	
1030	propionyl-coa carboxylase beta chain, mitochondrial precursor (ec 6.4.1.3) (pccase beta subunit) (propanoyl-coa:carbon dioxide ligase beta subunit). [source:swissprot;acc:p05166]	222.364	1.03168	215.535	
1031	probable ribosome biogenesis protein nep1 (c2f protein). [source:swissprot;acc:q92979]	242.978	1.03167	235.518	
1032	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). [source:swissprot;acc:o15120]	186.664	1.03162	180.943	
1033	tyrosinase precursor (ec 1.14.18.1) (monophenol monooxygenase) (tumor rejection antigen ab) (sk29-ab) (lb24-ab). [source:swissprot;acc:p14679]	221.183	1.03161	214.406	
1034	steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [source:swissprot;acc:o95718]	186.551	1.0316	180.837	
1035	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. [source:refseq;acc:nm_012301]	221.682	1.03157	228.68	
1036	coatomer beta subunit (beta-coat protein) (beta-cop). [source:swissprot;acc:p53618]	171.341	1.03155	176.746	
1037	thioredoxin-like; pkc-interacting cousin of thioredoxin. [source:refseq;acc:nm_006541]	228.412	1.03151	235.609	
1038	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). [source:swissprot;acc:q99943]	186.741	1.03148	181.041	
1039	dihydrolipoamide dehydrogenase, mitochondrial precursor (ec 1.8.1.4) (glycine cleavage system l protein). [source:swissprot;acc:p09622]	207.719	1.03137	214.236	
1040	t-complex protein 1, epsilon subunit (tcp-1-epsilon) (cct-epsilon). [source:swissprot;acc:p48643]	163.24	1.03136	168.359	
1041	heterogeneous nuclear ribonucleoprotein l (hnrnp l). [source:swissprot;acc:p14866]	186.774	1.03134	181.099	
1042	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [source:swissprot;acc:o75454]	186.799	1.03132	181.127	
1043	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). [source:swissprot;acc:q9nrz7]	187.834	1.03128	182.137	
1044	t-complex associated-testis-expressed 1-like (protein 91/23). [source:swissprot;acc:p51808]	173.475	1.03121	178.889	
1045	fip1-like 1; rearranged in hypereosinophilia. [source:refseq;acc:nm_030917]	115.817	1.03121	119.432	
1046	double-strand break repair protein mre11a (mre11 homolog 1). [source:swissprot;acc:p49959]	173.475	1.03121	178.889	
1047	steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [source:swissprot;acc:p11474]	187.022	1.03104	181.391	
1048	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). [source:swissprot;acc:q9nrz5]	187.96	1.031	182.308	
1049	adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [source:swissprot;acc:p07741]	211.449	1.03097	217.998	
1050	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). [source:swissprot;acc:p14061]	211.449	1.03097	217.998	
1051	17 beta-hydroxysteroid dehydrogenase. [source:sptrembl;acc:q13034]	211.449	1.03097	217.998	
1052	retinol dehydrogenase 8 (all-trans); photoreceptor outer segment all-trans retinol dehydrogenase. [source:refseq;acc:nm_015725]	211.449	1.03097	217.998	
1053	proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [source:swissprot;acc:p28066]	207.04	1.03087	200.84	
1054	60s ribosomal protein l21. [source:swissprot;acc:p46778]	223.958	1.03082	217.263	
1055	hcv ns3-transactivated protein 1. [source:refseq;acc:nm_019048]	219.01	1.03079	212.468	
1056	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). [source:swissprot;acc:p38606]	219.01	1.03079	212.468	
1057	asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [source:swissprot;acc:p08243]	219.01	1.03079	212.468	

Legend:
- Rank is the rank after comparing the two networks
- 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.
- http://analysis.yellowcouch.org/