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 Network Comparison Type Value Type Interaction Map red Filtered network_comparison green
Results: HTML CSV LaTeX Showing element 1318 to 1367 of 3228 in total 
Network Comparison Type	Divided
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	red	network_comparison	green	
1318	signal transducer and activator of transcription 5a. [source:swissprot;acc:p42229]	222.546	1.02304	227.673	
1319	glycogen [starch] synthase, muscle (ec 2.4.1.11). [source:swissprot;acc:p13807]	159.75	1.02304	156.153	
1320	signal transducer and activator of transcription 5b. [source:swissprot;acc:p51692]	222.544	1.02302	227.667	
1321	probable dimethyladenosine transferase (ec 2.1.1.-) (s- adenosylmethionine-6-n',n'-adenosyl(rrna) dimethyltransferase) (18s rrna dimethylase). [source:swissprot;acc:q9unq2]	226.347	1.023	221.259	
1322	endo-beta-n-acetylglucosaminidase. [source:refseq;acc:nm_022759]	159.86	1.02294	156.275	
1323	cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [source:swissprot;acc:o43639]	205.225	1.02293	200.625	
1324	glycogen [starch] synthase, liver (ec 2.4.1.11). [source:swissprot;acc:p54840]	159.993	1.02284	156.421	
1325	werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [source:refseq;acc:nm_020135]	217.133	1.02282	212.289	
1326	dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [source:sptrembl;acc:q9h4w2]	218.509	1.02275	213.648	
1327	zinc finger protein zic 4 (zinc finger protein of the cerebellum 4) (fragment). [source:swissprot;acc:q8n9l1]	218.509	1.02275	213.648	
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]	218.509	1.02275	213.649	
1329	dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [source:sptrembl;acc:q9h4v7]	218.509	1.02275	213.648	
1330	calcipressin 1 (down syndrome critical region protein 1) (myocyte- enriched calcineurin interacting protein 1) (mcip1) (adapt78). [source:swissprot;acc:p53805]	218.508	1.02275	213.648	
1331	calcipressin 3 (down syndrome candidate region 1-like protein 2) (myocyte-enriched calcineurin interacting protein 3) (mcip3). [source:swissprot;acc:q9uka8]	218.509	1.02275	213.649	
1332	cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [source:swissprot;acc:q15070]	220.681	1.02271	215.78	
1333	60s ribosomal protein l34, mitochondrial precursor (l34mt). [source:swissprot;acc:q9bq48]	220.681	1.02271	215.78	
1334	jm4 protein. [source:refseq;acc:nm_007213]	199.643	1.02264	204.163	
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]	199.771	1.02261	204.287	
1336	n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [source:swissprot;acc:q01415]	215.162	1.02257	210.412	
1337	galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [source:swissprot;acc:p07902]	215.162	1.02257	210.412	
1338	udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [source:swissprot;acc:q14376]	215.162	1.02257	210.412	
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]	205.204	1.02239	200.71	
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]	226.433	1.02234	231.491	
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]	226.433	1.02234	231.491	
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]	226.433	1.02234	231.491	
1343	m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [source:swissprot;acc:p30304]	258.558	1.02231	252.916	
1344	exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [source:refseq;acc:nm_006027]	216.772	1.02224	221.594	
1345	phd finger protein 9. [source:refseq;acc:nm_018062]	216.772	1.02224	221.594	
1346	small optic lobes homolog; small optic lobes, drosophila, homolog of. [source:refseq;acc:nm_005632]	216.772	1.02224	221.594	
1347	lipoic acid synthetase, mitochondrial (lip-syn) (lipoate synthase) (hussy-01) (fragment). [source:swissprot;acc:o43766]	204.961	1.02223	209.517	
1348	zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [source:swissprot;acc:q15915]	218.569	1.02215	213.832	
1349	zinc finger protein zic 3 (zinc finger protein of the cerebellum 3). [source:swissprot;acc:o60481]	218.572	1.02212	213.841	
1350	zinc finger protein zic 2 (zinc finger protein of the cerebellum 2). [source:swissprot;acc:o95409]	218.574	1.0221	213.847	
1351	prohibitin. [source:swissprot;acc:p35232]	211.513	1.02209	206.941	
1352	repressor of estrogen receptor activity; b-cell associated protein. [source:refseq;acc:nm_007273]	211.513	1.02209	206.941	
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]	228.409	1.02208	223.475	
1354	n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [source:refseq;acc:nm_004784]	228.409	1.02208	223.475	
1355	n-deacetylase/n-sulfotransferase 4. [source:refseq;acc:nm_022569]	228.409	1.02208	223.475	
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]	228.409	1.02208	223.475	
1357	protein cdc27hs (cell division cycle protein 27 homolog) (h-nuc). [source:swissprot;acc:p30260]	228.409	1.02208	223.475	
1358	upstream stimulatory factor 1 (major late transcription factor 1). [source:swissprot;acc:p22415]	214.987	1.022	210.359	
1359	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [source:swissprot;acc:p30712]	228.642	1.02197	223.726	
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]	223.89	1.02195	228.805	
1361	upstream stimulatory factor 2 (upstream transcription factor 2) (fos-interacting protein) (fip) (major late transcription factor 2). [source:swissprot;acc:q15853]	214.971	1.02195	210.354	
1362	peroxisomal n1-acetyl-spermine/spermidine oxidase. [source:refseq;acc:nm_152911]	228.644	1.02194	223.736	
1363	camp response element-binding protein cre-bpa. [source:refseq;acc:nm_004904]	218.591	1.02194	213.899	
1364	serine/threonine-protein kinase receptor r2 precursor (ec 2.7.1.37) (skr2) (activin receptor-like kinase 4) (alk-4) (actr-ib). [source:swissprot;acc:p36896]	223.885	1.02194	228.797	
1365	atpase inhibitor, mitochondrial precursor. [source:swissprot;acc:q9uii2]	228.644	1.02194	223.736	
1366	activin a receptor, type ic; activin receptor-like kinase 7. [source:refseq;acc:nm_145259]	223.884	1.02194	228.795	
1367	neuronal calcium sensor 1 (ncs-1) (frequenin homolog) (frequenin-like protein) (frequenin-like ubiquitous protein). [source:swissprot;acc:p36610]	223.887	1.02194	228.799	

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/