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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

value_type as 'ranked' since this provides a very robust analysis method.

intercation map as 'high confidence'

network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins

filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 1018 to 1067 of 3228 in total

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

Rank	description	red	green	network_comparison	
1018	importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [source:swissprot;acc:o00505]	217.361	210.554	1.03233	
1019	tyrosinase-related gene segment, exon 5 (fragment). [source:sptrembl;acc:q15677]	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]	221.28	214.409	1.03205	
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	214.409	1.03204	
1022	cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [source:swissprot;acc:p35520]	205.632	199.266	1.03195	
1023	transforming protein rhoc (h9). [source:swissprot;acc:p08134]	205.632	199.266	1.03195	
1024	thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [source:swissprot;acc:q16762]	205.632	199.266	1.03195	
1025	3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [source:swissprot;acc:p25325]	205.632	199.266	1.03195	
1026	transforming protein rhoa (h12). [source:swissprot;acc:p06749]	205.632	199.266	1.03195	
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	218.627	1.03171	
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	218.627	1.03171	
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	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]	222.364	215.535	1.03168	
1031	probable ribosome biogenesis protein nep1 (c2f protein). [source:swissprot;acc:q92979]	242.978	235.518	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]	186.664	180.943	1.03162	
1033	tyrosinase precursor (ec 1.14.18.1) (monophenol monooxygenase) (tumor rejection antigen ab) (sk29-ab) (lb24-ab). [source:swissprot;acc:p14679]	221.183	214.406	1.03161	
1034	steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [source:swissprot;acc:o95718]	186.551	180.837	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]	221.682	228.68	1.03157	
1036	coatomer beta subunit (beta-coat protein) (beta-cop). [source:swissprot;acc:p53618]	171.341	176.746	1.03155	
1037	thioredoxin-like; pkc-interacting cousin of thioredoxin. [source:refseq;acc:nm_006541]	228.412	235.609	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]	186.741	181.041	1.03148	
1039	dihydrolipoamide dehydrogenase, mitochondrial precursor (ec 1.8.1.4) (glycine cleavage system l protein). [source:swissprot;acc:p09622]	207.719	214.236	1.03137	
1040	t-complex protein 1, epsilon subunit (tcp-1-epsilon) (cct-epsilon). [source:swissprot;acc:p48643]	163.24	168.359	1.03136	
1041	heterogeneous nuclear ribonucleoprotein l (hnrnp l). [source:swissprot;acc:p14866]	186.774	181.099	1.03134	
1042	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [source:swissprot;acc:o75454]	186.799	181.127	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]	187.834	182.137	1.03128	
1044	t-complex associated-testis-expressed 1-like (protein 91/23). [source:swissprot;acc:p51808]	173.475	178.889	1.03121	
1045	fip1-like 1; rearranged in hypereosinophilia. [source:refseq;acc:nm_030917]	115.817	119.432	1.03121	
1046	double-strand break repair protein mre11a (mre11 homolog 1). [source:swissprot;acc:p49959]	173.475	178.889	1.03121	
1047	steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [source:swissprot;acc:p11474]	187.022	181.391	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]	187.96	182.308	1.031	
1049	adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [source:swissprot;acc:p07741]	211.449	217.998	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]	211.449	217.998	1.03097	
1051	17 beta-hydroxysteroid dehydrogenase. [source:sptrembl;acc:q13034]	211.449	217.998	1.03097	
1052	retinol dehydrogenase 8 (all-trans); photoreceptor outer segment all-trans retinol dehydrogenase. [source:refseq;acc:nm_015725]	211.449	217.998	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]	207.04	200.84	1.03087	
1054	60s ribosomal protein l21. [source:swissprot;acc:p46778]	223.958	217.263	1.03082	
1055	hcv ns3-transactivated protein 1. [source:refseq;acc:nm_019048]	219.01	212.468	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]	219.01	212.468	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]	219.01	212.468	1.03079	
1058	ataxin 2 related protein isoform a; ataxin-2 domain protein. [source:refseq;acc:nm_007245]	228.105	221.293	1.03078	
1059	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [source:refseq;acc:nm_002973]	228.105	221.293	1.03078	
1060	nemo-like kinase; likely ortholog of mouse nemo like kinase. [source:refseq;acc:nm_016231]	218.162	211.648	1.03078	
1061	elks protein. [source:refseq;acc:nm_015064]	218.162	211.648	1.03078	
1062	zinc finger protein 174 (aw-1). [source:swissprot;acc:q15697]	269.963	278.239	1.03066	
1063	zinc finger imprinted 2. [source:swissprot;acc:q9nzv7]	269.96	278.232	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]	269.955	278.221	1.03062	
1065	zinc finger protein 305. [source:swissprot;acc:o43309]	269.954	278.219	1.03062	
1066	zinc finger protein 18 (zinc finger protein kox11) (fragment). [source:swissprot;acc:p17022]	269.956	278.223	1.03062	
1067	zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [source:swissprot;acc:q9ul58]	269.956	278.223	1.03062	

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/