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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 1313 to 1362 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	green	red	network_comparison	
1313	signal transducer and activator of transcription 3 (acute-phase response factor). [source:swissprot;acc:p40763]	227.75	222.573	1.02326	
1314	signal transducer and activator of transcription 4. [source:swissprot;acc:q14765]	227.751	222.573	1.02326	
1315	signal transducer and activator of transcription 1-alpha/beta (transcription factor isgf-3 components p91/p84). [source:swissprot;acc:p42224]	227.752	222.574	1.02326	
1316	signal transducer and activator of transcription 6 (il-4 stat). [source:swissprot;acc:p42226]	227.739	222.569	1.02323	
1317	centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [source:refseq;acc:nm_018451]	202.105	206.773	1.0231	
1318	signal transducer and activator of transcription 5a. [source:swissprot;acc:p42229]	227.673	222.546	1.02304	
1319	glycogen [starch] synthase, muscle (ec 2.4.1.11). [source:swissprot;acc:p13807]	156.153	159.75	1.02304	
1320	signal transducer and activator of transcription 5b. [source:swissprot;acc:p51692]	227.667	222.544	1.02302	
1321	probable dimethyladenosine transferase (ec 2.1.1.-) (s- adenosylmethionine-6-n',n'-adenosyl(rrna) dimethyltransferase) (18s rrna dimethylase). [source:swissprot;acc:q9unq2]	221.259	226.347	1.023	
1322	endo-beta-n-acetylglucosaminidase. [source:refseq;acc:nm_022759]	156.275	159.86	1.02294	
1323	cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [source:swissprot;acc:o43639]	200.625	205.225	1.02293	
1324	glycogen [starch] synthase, liver (ec 2.4.1.11). [source:swissprot;acc:p54840]	156.421	159.993	1.02284	
1325	werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [source:refseq;acc:nm_020135]	212.289	217.133	1.02282	
1326	dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [source:sptrembl;acc:q9h4w2]	213.648	218.509	1.02275	
1327	zinc finger protein zic 4 (zinc finger protein of the cerebellum 4) (fragment). [source:swissprot;acc:q8n9l1]	213.648	218.509	1.02275	
1328	calcipressin 2 (thyroid hormone-responsive protein zaki-4) (down syndrome candidate region 1-like 1) (myocyte-enriched calcineurin interacting protein 2) (mcip2). [source:swissprot;acc:q14206]	213.649	218.509	1.02275	
1329	dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [source:sptrembl;acc:q9h4v7]	213.648	218.509	1.02275	
1330	calcipressin 1 (down syndrome critical region protein 1) (myocyte- enriched calcineurin interacting protein 1) (mcip1) (adapt78). [source:swissprot;acc:p53805]	213.648	218.508	1.02275	
1331	calcipressin 3 (down syndrome candidate region 1-like protein 2) (myocyte-enriched calcineurin interacting protein 3) (mcip3). [source:swissprot;acc:q9uka8]	213.649	218.509	1.02275	
1332	cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [source:swissprot;acc:q15070]	215.78	220.681	1.02271	
1333	60s ribosomal protein l34, mitochondrial precursor (l34mt). [source:swissprot;acc:q9bq48]	215.78	220.681	1.02271	
1334	jm4 protein. [source:refseq;acc:nm_007213]	204.163	199.643	1.02264	
1335	cytoskeleton related vitamin a responsive protein; glutamate transporter eeac1-associated protein; dermal papilla derived protein 11; putative mapk activating protein pm27. [source:refseq;acc:nm_006407]	204.287	199.771	1.02261	
1336	n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [source:swissprot;acc:q01415]	210.412	215.162	1.02257	
1337	galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [source:swissprot;acc:p07902]	210.412	215.162	1.02257	
1338	udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [source:swissprot;acc:q14376]	210.412	215.162	1.02257	
1339	epididymal secretory protein e1 precursor (niemann-pick disease type c2 protein) (epi-1) (he1) (epididymal secretory protein 14.6) (esp14.6). [source:swissprot;acc:q15668]	200.71	205.204	1.02239	
1340	histone-lysine n-methyltransferase, h3 lysine-9 specific 2 (ec 2.1.1.43) (histone h3-k9 methyltransferase 2) (h3-k9-hmtase 2) (suppressor of variegation 3-9 homolog 2) (su(var)3-9 homolog 2). [source:swissprot;acc:q9h5i1]	231.491	226.433	1.02234	
1341	eukaryotic translation initiation factor 2 subunit 1 (eukaryotic translation initiation factor 2 alpha subunit) (eif-2-alpha) (eif- 2alpha) (eif-2a). [source:swissprot;acc:p05198]	231.491	226.433	1.02234	
1342	histone-lysine n-methyltransferase, h3 lysine-9 specific 1 (ec 2.1.1.43) (histone h3-k9 methyltransferase 1) (h3-k9-hmtase 1) (suppressor of variegation 3-9 homolog 1) (su(var)3-9 homolog 1). [source:swissprot;acc:o43463]	231.491	226.433	1.02234	
1343	m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [source:swissprot;acc:p30304]	252.916	258.558	1.02231	
1344	exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [source:refseq;acc:nm_006027]	221.594	216.772	1.02224	
1345	phd finger protein 9. [source:refseq;acc:nm_018062]	221.594	216.772	1.02224	
1346	small optic lobes homolog; small optic lobes, drosophila, homolog of. [source:refseq;acc:nm_005632]	221.594	216.772	1.02224	
1347	lipoic acid synthetase, mitochondrial (lip-syn) (lipoate synthase) (hussy-01) (fragment). [source:swissprot;acc:o43766]	209.517	204.961	1.02223	
1348	zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [source:swissprot;acc:q15915]	213.832	218.569	1.02215	
1349	zinc finger protein zic 3 (zinc finger protein of the cerebellum 3). [source:swissprot;acc:o60481]	213.841	218.572	1.02212	
1350	zinc finger protein zic 2 (zinc finger protein of the cerebellum 2). [source:swissprot;acc:o95409]	213.847	218.574	1.0221	
1351	prohibitin. [source:swissprot;acc:p35232]	206.941	211.513	1.02209	
1352	repressor of estrogen receptor activity; b-cell associated protein. [source:refseq;acc:nm_007273]	206.941	211.513	1.02209	
1353	heparin sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.-) (n- hsst) (n-heparin sulfate sulfotransferase) (glucosaminyl n- deacetylase/n-sulfotransferase). [source:swissprot;acc:p52849]	223.475	228.409	1.02208	
1354	n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [source:refseq;acc:nm_004784]	223.475	228.409	1.02208	
1355	n-deacetylase/n-sulfotransferase 4. [source:refseq;acc:nm_022569]	223.475	228.409	1.02208	
1356	heparan sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.8) (n-hsst) (hsnst) ([heparan sulfate]-glucosamine n-sulfotransferase) (n-heparan sulfate sulfotransferase) (glucosaminyl n-deacetylase/n- sulfotransferase). [source:swissprot;acc:p52848]	223.475	228.409	1.02208	
1357	protein cdc27hs (cell division cycle protein 27 homolog) (h-nuc). [source:swissprot;acc:p30260]	223.475	228.409	1.02208	
1358	upstream stimulatory factor 1 (major late transcription factor 1). [source:swissprot;acc:p22415]	210.359	214.987	1.022	
1359	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [source:swissprot;acc:p30712]	223.726	228.642	1.02197	
1360	tgf-beta receptor type i precursor (ec 2.7.1.37) (tgfr-1) (tgf-beta type i receptor) (serine/threonine-protein kinase receptor r4) (skr4) (activin receptor-like kinase 5) (alk-5). [source:swissprot;acc:p36897]	228.805	223.89	1.02195	
1361	upstream stimulatory factor 2 (upstream transcription factor 2) (fos-interacting protein) (fip) (major late transcription factor 2). [source:swissprot;acc:q15853]	210.354	214.971	1.02195	
1362	peroxisomal n1-acetyl-spermine/spermidine oxidase. [source:refseq;acc:nm_152911]	223.736	228.644	1.02194	

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/