MK5 Microarray Data

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

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Showing element 1325 to 1374 of 3228 in total

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

Rank	green	red	description	network_comparison
1325	212.289	217.133	werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135]	1.02282
1326	213.648	218.509	dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2]	1.02275
1327			zinc finger protein zic 4 (zinc finger protein of the cerebellum 4) (fragment). [swissprot;acc:q8n9l1]
1328	213.649		calcipressin 2 (thyroid hormone-responsive protein zaki-4) (down syndrome candidate region 1-like 1) (myocyte-enriched calcineurin interacting protein 2) (mcip2). [swissprot;acc:q14206]
1329	213.648		dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7]
1330		218.508	calcipressin 1 (down syndrome critical region protein 1) (myocyte- enriched calcineurin interacting protein 1) (mcip1) (adapt78). [swissprot;acc:p53805]
1331	213.649	218.509	calcipressin 3 (down syndrome candidate region 1-like protein 2) (myocyte-enriched calcineurin interacting protein 3) (mcip3). [swissprot;acc:q9uka8]
1332	215.78	220.681	cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [swissprot;acc:q15070]	1.02271
1333			60s ribosomal protein l34, mitochondrial precursor (l34mt). [swissprot;acc:q9bq48]
1334	204.163	199.643	jm4 protein. [refseq;acc:nm_007213]	1.02264
1335	204.287	199.771	cytoskeleton related vitamin a responsive protein; glutamate transporter eeac1-associated protein; dermal papilla derived protein 11; putative mapk activating protein pm27. [refseq;acc:nm_006407]	1.02261
1336	210.412	215.162	n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [swissprot;acc:q01415]	1.02257
1337			galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [swissprot;acc:p07902]
1338			udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376]
1339	200.71	205.204	epididymal secretory protein e1 precursor (niemann-pick disease type c2 protein) (epi-1) (he1) (epididymal secretory protein 14.6) (esp14.6). [swissprot;acc:q15668]	1.02239
1340	231.491	226.433	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). [swissprot;acc:q9h5i1]	1.02234
1341			eukaryotic translation initiation factor 2 subunit 1 (eukaryotic translation initiation factor 2 alpha subunit) (eif-2-alpha) (eif- 2alpha) (eif-2a). [swissprot;acc:p05198]
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). [swissprot;acc:o43463]
1343	252.916	258.558	m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [swissprot;acc:p30304]	1.02231
1344	221.594	216.772	exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [refseq;acc:nm_006027]	1.02224
1345			phd finger protein 9. [refseq;acc:nm_018062]
1346			small optic lobes homolog; small optic lobes, drosophila, homolog of. [refseq;acc:nm_005632]
1347	209.517	204.961	lipoic acid synthetase, mitochondrial (lip-syn) (lipoate synthase) (hussy-01) (fragment). [swissprot;acc:o43766]	1.02223
1348	213.832	218.569	zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [swissprot;acc:q15915]	1.02215
1349	213.841	218.572	zinc finger protein zic 3 (zinc finger protein of the cerebellum 3). [swissprot;acc:o60481]	1.02212
1350	213.847	218.574	zinc finger protein zic 2 (zinc finger protein of the cerebellum 2). [swissprot;acc:o95409]	1.0221
1351	206.941	211.513	prohibitin. [swissprot;acc:p35232]	1.02209
1352			repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273]
1353	223.475	228.409	heparin sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.-) (n- hsst) (n-heparin sulfate sulfotransferase) (glucosaminyl n- deacetylase/n-sulfotransferase). [swissprot;acc:p52849]	1.02208
1354			n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [refseq;acc:nm_004784]
1355			n-deacetylase/n-sulfotransferase 4. [refseq;acc:nm_022569]
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). [swissprot;acc:p52848]
1357			protein cdc27hs (cell division cycle protein 27 homolog) (h-nuc). [swissprot;acc:p30260]
1358	210.359	214.987	upstream stimulatory factor 1 (major late transcription factor 1). [swissprot;acc:p22415]	1.022
1359	223.726	228.642	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712]	1.02197
1360	228.805	223.89	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). [swissprot;acc:p36897]	1.02195
1361	210.354	214.971	upstream stimulatory factor 2 (upstream transcription factor 2) (fos-interacting protein) (fip) (major late transcription factor 2). [swissprot;acc:q15853]
1362	223.736	228.644	peroxisomal n1-acetyl-spermine/spermidine oxidase. [refseq;acc:nm_152911]	1.02194
1363	213.899	218.591	camp response element-binding protein cre-bpa. [refseq;acc:nm_004904]
1364	228.797	223.885	serine/threonine-protein kinase receptor r2 precursor (ec 2.7.1.37) (skr2) (activin receptor-like kinase 4) (alk-4) (actr-ib). [swissprot;acc:p36896]
1365	223.736	228.644	atpase inhibitor, mitochondrial precursor. [swissprot;acc:q9uii2]
1366	228.795	223.884	activin a receptor, type ic; activin receptor-like kinase 7. [refseq;acc:nm_145259]
1367	228.799	223.887	neuronal calcium sensor 1 (ncs-1) (frequenin homolog) (frequenin-like protein) (frequenin-like ubiquitous protein). [swissprot;acc:p36610]
1368	223.736	228.644	polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [refseq;acc:nm_019025]
1369			cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [swissprot;acc:p53701]
1370	200.784	205.185	cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [swissprot;acc:p16333]	1.02192
1371	223.744	228.646	glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [swissprot;acc:p30711]	1.02191
1372	211.908	216.542	suppressor of cytokine signaling 1 (socs-1) (jak-binding protein) (jab) (stat induced stat inhibitor 1) (ssi-1) (tec-interacting protein 3) (tip-3). [swissprot;acc:o15524]	1.02187
1373			glia maturation factor gamma (gmf-gamma). [swissprot;acc:o60234]
1374			asc-1 complex subunit p100. [refseq;acc:nm_032204]

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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.