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

Results: HTML CSV LaTeX

Showing element 1030 to 1079 of 3228 in total

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

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

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/