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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2012 to 2061 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
1006	retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [source:swissprot;acc:q08999]	Subtracted	217.026	210.189	6.837	
1007	ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [source:swissprot;acc:q12967]	Divided	162.055	156.884	1.03296	
1007	retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [source:swissprot;acc:p28749]	Subtracted	217.021	210.185	6.836	
1008	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]	Subtracted	222.364	215.535	6.829	
1008	wd-repeat protein bing4. [source:swissprot;acc:o15213]	Divided	243.227	235.475	1.03292	
1009	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [source:swissprot;acc:q12882]	Divided	229.116	221.823	1.03288	
1009	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]	Subtracted	222.364	215.535	6.829	
1010	ataxin 2 related protein isoform a; ataxin-2 domain protein. [source:refseq;acc:nm_007245]	Subtracted	228.105	221.293	6.812	
1010	peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [source:swissprot;acc:q9ukg9]	Divided	217.523	210.648	1.03264	
1011	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [source:refseq;acc:nm_002973]	Subtracted	228.105	221.293	6.812	
1011	retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [source:swissprot;acc:q08999]	Divided	217.026	210.189	1.03253	
1012	importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [source:swissprot;acc:o00629]	Subtracted	217.369	210.561	6.808	
1012	retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [source:swissprot;acc:p28749]	Divided	217.021	210.185	1.03252	
1013	protein bap28. [source:swissprot;acc:q9h583]	Divided	244.312	236.647	1.03239	
1013	target of egr1, member 1 (nuclear); target of egr1, member 1. [source:refseq;acc:nm_025077]	Subtracted	217.365	210.558	6.807	
1014	apoptosis antagonizing transcription factor. [source:refseq;acc:nm_012138]	Divided	243.045	235.422	1.03238	
1014	importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [source:swissprot;acc:o00505]	Subtracted	217.361	210.554	6.807	
1015	bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [source:refseq;acc:nm_004742]	Divided	221.73	228.906	1.03236	
1015	exocyst complex component sec6. [source:swissprot;acc:o60645]	Subtracted	207.186	200.398	6.788	
1016	importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [source:swissprot;acc:o00629]	Divided	217.369	210.561	1.03233	
1016	tyrosinase precursor (ec 1.14.18.1) (monophenol monooxygenase) (tumor rejection antigen ab) (sk29-ab) (lb24-ab). [source:swissprot;acc:p14679]	Subtracted	221.183	214.406	6.777	
1017	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]	Subtracted	211.908	218.627	6.719	
1017	target of egr1, member 1 (nuclear); target of egr1, member 1. [source:refseq;acc:nm_025077]	Divided	217.365	210.558	1.03233	
1018	importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [source:swissprot;acc:o00505]	Divided	217.361	210.554	1.03233	
1018	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]	Subtracted	211.908	218.627	6.719	
1019	60s ribosomal protein l21. [source:swissprot;acc:p46778]	Subtracted	223.958	217.263	6.695	
1019	tyrosinase-related gene segment, exon 5 (fragment). [source:sptrembl;acc:q15677]	Divided	221.302	214.409	1.03215	
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]	Divided	221.28	214.409	1.03205	
1020	similar to ribosomal protein, large, p0. [source:sptrembl;acc:q96fq9]	Subtracted	226.218	232.88	6.662	
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]	Divided	221.278	214.409	1.03204	
1021	block 23. [source:sptrembl;acc:q8nhw5]	Subtracted	226.205	232.858	6.653	
1022	60s acidic ribosomal protein p0 (l10e). [source:swissprot;acc:p05388]	Subtracted	226.203	232.855	6.652	
1022	cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [source:swissprot;acc:p35520]	Divided	205.632	199.266	1.03195	
1023	gcn5-like protein 1 (rt14 protein). [source:swissprot;acc:p78537]	Subtracted	202.027	195.386	6.641	
1023	transforming protein rhoc (h9). [source:swissprot;acc:p08134]	Divided	205.632	199.266	1.03195	
1024	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). [source:swissprot;acc:o60762]	Subtracted	203.381	196.76	6.621	
1024	thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [source:swissprot;acc:q16762]	Divided	205.632	199.266	1.03195	
1025	3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [source:swissprot;acc:p25325]	Divided	205.632	199.266	1.03195	
1025	40s ribosomal protein s30. [source:swissprot;acc:q05472]	Subtracted	223.44	216.875	6.565	
1026	hydroxyacid oxidase 1 (ec 1.1.3.15) (haox1) (glycolate oxidase) (gox). [source:swissprot;acc:q9ujm8]	Subtracted	231.922	238.486	6.564	
1026	transforming protein rhoa (h12). [source:swissprot;acc:p06749]	Divided	205.632	199.266	1.03195	
1027	adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [source:swissprot;acc:p07741]	Subtracted	211.449	217.998	6.549	
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]	Divided	211.908	218.627	1.03171	
1028	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]	Subtracted	211.449	217.998	6.549	
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]	Divided	211.908	218.627	1.03171	
1029	17 beta-hydroxysteroid dehydrogenase. [source:sptrembl;acc:q13034]	Subtracted	211.449	217.998	6.549	
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]	Divided	222.364	215.535	1.03168	
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]	Divided	222.364	215.535	1.03168	
1030	retinol dehydrogenase 8 (all-trans); photoreceptor outer segment all-trans retinol dehydrogenase. [source:refseq;acc:nm_015725]	Subtracted	211.449	217.998	6.549	
1031	hcv ns3-transactivated protein 1. [source:refseq;acc:nm_019048]	Subtracted	219.01	212.468	6.542	

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/