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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1333 to 1382 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
1333	60s ribosomal protein l34, mitochondrial precursor (l34mt). [source:swissprot;acc:q9bq48]	220.681	215.78	1.02271	
1334	jm4 protein. [source:refseq;acc:nm_007213]	199.643	204.163	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]	199.771	204.287	1.02261	
1336	n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [source:swissprot;acc:q01415]	215.162	210.412	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]	215.162	210.412	1.02257	
1338	udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [source:swissprot;acc:q14376]	215.162	210.412	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]	205.204	200.71	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]	226.433	231.491	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]	226.433	231.491	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]	226.433	231.491	1.02234	
1343	m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [source:swissprot;acc:p30304]	258.558	252.916	1.02231	
1344	exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [source:refseq;acc:nm_006027]	216.772	221.594	1.02224	
1345	phd finger protein 9. [source:refseq;acc:nm_018062]	216.772	221.594	1.02224	
1346	small optic lobes homolog; small optic lobes, drosophila, homolog of. [source:refseq;acc:nm_005632]	216.772	221.594	1.02224	
1347	lipoic acid synthetase, mitochondrial (lip-syn) (lipoate synthase) (hussy-01) (fragment). [source:swissprot;acc:o43766]	204.961	209.517	1.02223	
1348	zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [source:swissprot;acc:q15915]	218.569	213.832	1.02215	
1349	zinc finger protein zic 3 (zinc finger protein of the cerebellum 3). [source:swissprot;acc:o60481]	218.572	213.841	1.02212	
1350	zinc finger protein zic 2 (zinc finger protein of the cerebellum 2). [source:swissprot;acc:o95409]	218.574	213.847	1.0221	
1351	prohibitin. [source:swissprot;acc:p35232]	211.513	206.941	1.02209	
1352	repressor of estrogen receptor activity; b-cell associated protein. [source:refseq;acc:nm_007273]	211.513	206.941	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]	228.409	223.475	1.02208	
1354	n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [source:refseq;acc:nm_004784]	228.409	223.475	1.02208	
1355	n-deacetylase/n-sulfotransferase 4. [source:refseq;acc:nm_022569]	228.409	223.475	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]	228.409	223.475	1.02208	
1357	protein cdc27hs (cell division cycle protein 27 homolog) (h-nuc). [source:swissprot;acc:p30260]	228.409	223.475	1.02208	
1358	upstream stimulatory factor 1 (major late transcription factor 1). [source:swissprot;acc:p22415]	214.987	210.359	1.022	
1359	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [source:swissprot;acc:p30712]	228.642	223.726	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]	223.89	228.805	1.02195	
1361	upstream stimulatory factor 2 (upstream transcription factor 2) (fos-interacting protein) (fip) (major late transcription factor 2). [source:swissprot;acc:q15853]	214.971	210.354	1.02195	
1362	peroxisomal n1-acetyl-spermine/spermidine oxidase. [source:refseq;acc:nm_152911]	228.644	223.736	1.02194	
1363	camp response element-binding protein cre-bpa. [source:refseq;acc:nm_004904]	218.591	213.899	1.02194	
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	228.797	1.02194	
1365	atpase inhibitor, mitochondrial precursor. [source:swissprot;acc:q9uii2]	228.644	223.736	1.02194	
1366	activin a receptor, type ic; activin receptor-like kinase 7. [source:refseq;acc:nm_145259]	223.884	228.795	1.02194	
1367	neuronal calcium sensor 1 (ncs-1) (frequenin homolog) (frequenin-like protein) (frequenin-like ubiquitous protein). [source:swissprot;acc:p36610]	223.887	228.799	1.02194	
1368	polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [source:refseq;acc:nm_019025]	228.644	223.736	1.02194	
1369	cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [source:swissprot;acc:p53701]	228.644	223.736	1.02194	
1370	cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [source:swissprot;acc:p16333]	205.185	200.784	1.02192	
1371	glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [source:swissprot;acc:p30711]	228.646	223.744	1.02191	
1372	suppressor of cytokine signaling 1 (socs-1) (jak-binding protein) (jab) (stat induced stat inhibitor 1) (ssi-1) (tec-interacting protein 3) (tip-3). [source:swissprot;acc:o15524]	216.542	211.908	1.02187	
1373	glia maturation factor gamma (gmf-gamma). [source:swissprot;acc:o60234]	216.542	211.908	1.02187	
1374	asc-1 complex subunit p100. [source:refseq;acc:nm_032204]	216.542	211.908	1.02187	
1375	fk506-binding protein 1a (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (12 kda fkbp) (fkbp-12) (immunophilin fkbp12). [source:swissprot;acc:p20071]	216.542	211.908	1.02187	
1376	eyes absent homolog 3. [source:swissprot;acc:q99504]	218.537	213.91	1.02163	
1377	sal-like protein 2 (zinc finger protein sall2) (hsal2). [source:swissprot;acc:q9y467]	218.471	213.876	1.02148	
1378	sal-like protein 3 (zinc finger protein sall3) (hsall3). [source:swissprot;acc:q9bxa9]	218.47	213.876	1.02148	
1379	arginine-glutamic acid dipeptide (re) repeats; atrophin 1-like; arginine glutamic acid dipeptide re repeats. [source:refseq;acc:nm_012102]	218.47	213.875	1.02148	
1380	ubiquitin carboxyl-terminal hydrolase 8 (ec 3.1.2.15) (ubiquitin thiolesterase 8) (ubiquitin-specific processing protease 8) (deubiquitinating enzyme 8). [source:swissprot;acc:p40818]	218.47	213.876	1.02148	
1381	rod1 regulator of differentiation 1; fission yeast differentiation regulator; regulator of differentiation (in s. pombi) 1; regulator of differentiation (in s. pombe) 1. [source:refseq;acc:nm_005156]	218.47	213.876	1.02148	
1382	polypyrimidine tract binding protein 2; neural polypyrimidine tract binding protein; ptb-like protein. [source:refseq;acc:nm_021190]	218.47	213.876	1.02148	

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/