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 description Value Type Gene Network Comparison Type Filtered Interaction Map green network_comparison red
Results: HTML CSV LaTeX Showing element 1030 to 1079 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Filtered	1
Interaction Map	High confidence

Rank	description	green	network_comparison	red	
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]	215.535	1.03168	222.364	
1031	probable ribosome biogenesis protein nep1 (c2f protein). [source:swissprot;acc:q92979]	235.518	1.03167	242.978	
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]	180.943	1.03162	186.664	
1033	tyrosinase precursor (ec 1.14.18.1) (monophenol monooxygenase) (tumor rejection antigen ab) (sk29-ab) (lb24-ab). [source:swissprot;acc:p14679]	214.406	1.03161	221.183	
1034	steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [source:swissprot;acc:o95718]	180.837	1.0316	186.551	
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]	228.68	1.03157	221.682	
1036	coatomer beta subunit (beta-coat protein) (beta-cop). [source:swissprot;acc:p53618]	176.746	1.03155	171.341	
1037	thioredoxin-like; pkc-interacting cousin of thioredoxin. [source:refseq;acc:nm_006541]	235.609	1.03151	228.412	
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]	181.041	1.03148	186.741	
1039	dihydrolipoamide dehydrogenase, mitochondrial precursor (ec 1.8.1.4) (glycine cleavage system l protein). [source:swissprot;acc:p09622]	214.236	1.03137	207.719	
1040	t-complex protein 1, epsilon subunit (tcp-1-epsilon) (cct-epsilon). [source:swissprot;acc:p48643]	168.359	1.03136	163.24	
1041	heterogeneous nuclear ribonucleoprotein l (hnrnp l). [source:swissprot;acc:p14866]	181.099	1.03134	186.774	
1042	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [source:swissprot;acc:o75454]	181.127	1.03132	186.799	
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]	182.137	1.03128	187.834	
1044	t-complex associated-testis-expressed 1-like (protein 91/23). [source:swissprot;acc:p51808]	178.889	1.03121	173.475	
1045	fip1-like 1; rearranged in hypereosinophilia. [source:refseq;acc:nm_030917]	119.432	1.03121	115.817	
1046	double-strand break repair protein mre11a (mre11 homolog 1). [source:swissprot;acc:p49959]	178.889	1.03121	173.475	
1047	steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [source:swissprot;acc:p11474]	181.391	1.03104	187.022	
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]	182.308	1.031	187.96	
1049	adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [source:swissprot;acc:p07741]	217.998	1.03097	211.449	
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]	217.998	1.03097	211.449	
1051	17 beta-hydroxysteroid dehydrogenase. [source:sptrembl;acc:q13034]	217.998	1.03097	211.449	
1052	retinol dehydrogenase 8 (all-trans); photoreceptor outer segment all-trans retinol dehydrogenase. [source:refseq;acc:nm_015725]	217.998	1.03097	211.449	
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]	200.84	1.03087	207.04	
1054	60s ribosomal protein l21. [source:swissprot;acc:p46778]	217.263	1.03082	223.958	
1055	hcv ns3-transactivated protein 1. [source:refseq;acc:nm_019048]	212.468	1.03079	219.01	
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]	212.468	1.03079	219.01	
1057	asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [source:swissprot;acc:p08243]	212.468	1.03079	219.01	
1058	ataxin 2 related protein isoform a; ataxin-2 domain protein. [source:refseq;acc:nm_007245]	221.293	1.03078	228.105	
1059	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [source:refseq;acc:nm_002973]	221.293	1.03078	228.105	
1060	nemo-like kinase; likely ortholog of mouse nemo like kinase. [source:refseq;acc:nm_016231]	211.648	1.03078	218.162	
1061	elks protein. [source:refseq;acc:nm_015064]	211.648	1.03078	218.162	
1062	zinc finger protein 174 (aw-1). [source:swissprot;acc:q15697]	278.239	1.03066	269.963	
1063	zinc finger imprinted 2. [source:swissprot;acc:q9nzv7]	278.232	1.03064	269.96	
1064	zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [source:swissprot;acc:p17028]	278.221	1.03062	269.955	
1065	zinc finger protein 305. [source:swissprot;acc:o43309]	278.219	1.03062	269.954	
1066	zinc finger protein 18 (zinc finger protein kox11) (fragment). [source:swissprot;acc:p17022]	278.223	1.03062	269.956	
1067	zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [source:swissprot;acc:q9ul58]	278.223	1.03062	269.956	
1068	zinc finger protein 274 (zinc finger protein sp2114) (zinc finger protein hfb101) (zinc finger protein zfp2) (zf2). [source:swissprot;acc:q96gc6]	278.215	1.03061	269.953	
1069	zinc finger protein 232. [source:swissprot;acc:q9uny5]	278.218	1.03061	269.954	
1070	zinc finger protein 99. [source:refseq;acc:nm_032164]	278.218	1.03061	269.954	
1071	dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [source:swissprot;acc:q9y2s0]	238.356	1.03061	231.277	
1072	zinc finger protein 213 (putative transcription factor cr53). [source:swissprot;acc:o14771]	278.217	1.03061	269.954	
1073	ww domain binding protein 2 (wbp-2). [source:swissprot;acc:q969t9]	210.485	1.03048	216.901	
1074	coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [source:swissprot;acc:p35606]	179.697	1.03045	174.387	
1075	coatomer gamma subunit (gamma-coat protein) (gamma-cop). [source:swissprot;acc:q9y678]	179.697	1.03045	174.387	
1076	coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [source:swissprot;acc:q9y3c3]	179.697	1.03045	174.387	
1077	coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [source:swissprot;acc:p48444]	179.697	1.03045	174.387	
1078	peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [source:swissprot;acc:q9unp9]	179.697	1.03045	174.387	
1079	coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [source:swissprot;acc:q9p299]	179.697	1.03045	174.387	

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/