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

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Showing element 1318 to 1367 of 3228 in total

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

Rank	description	green	network_comparison	red
1318	signal transducer and activator of transcription 5a. [swissprot;acc:p42229]	227.673	1.02304	222.546
1319	glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807]	156.153		159.75
1320	signal transducer and activator of transcription 5b. [swissprot;acc:p51692]	227.667	1.02302	222.544
1321	probable dimethyladenosine transferase (ec 2.1.1.-) (s- adenosylmethionine-6-n',n'-adenosyl(rrna) dimethyltransferase) (18s rrna dimethylase). [swissprot;acc:q9unq2]	221.259	1.023	226.347
1322	endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759]	156.275	1.02294	159.86
1323	cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [swissprot;acc:o43639]	200.625	1.02293	205.225
1324	glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840]	156.421	1.02284	159.993
1325	werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135]	212.289	1.02282	217.133
1326	dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2]	213.648	1.02275	218.509
1327	zinc finger protein zic 4 (zinc finger protein of the cerebellum 4) (fragment). [swissprot;acc:q8n9l1]
1328	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]	213.649
1329	dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7]	213.648
1330	calcipressin 1 (down syndrome critical region protein 1) (myocyte- enriched calcineurin interacting protein 1) (mcip1) (adapt78). [swissprot;acc:p53805]			218.508
1331	calcipressin 3 (down syndrome candidate region 1-like protein 2) (myocyte-enriched calcineurin interacting protein 3) (mcip3). [swissprot;acc:q9uka8]	213.649		218.509
1332	cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [swissprot;acc:q15070]	215.78	1.02271	220.681
1333	60s ribosomal protein l34, mitochondrial precursor (l34mt). [swissprot;acc:q9bq48]
1334	jm4 protein. [refseq;acc:nm_007213]	204.163	1.02264	199.643
1335	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]	204.287	1.02261	199.771
1336	n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [swissprot;acc:q01415]	210.412	1.02257	215.162
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	epididymal secretory protein e1 precursor (niemann-pick disease type c2 protein) (epi-1) (he1) (epididymal secretory protein 14.6) (esp14.6). [swissprot;acc:q15668]	200.71	1.02239	205.204
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). [swissprot;acc:q9h5i1]	231.491	1.02234	226.433
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	m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [swissprot;acc:p30304]	252.916	1.02231	258.558
1344	exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [refseq;acc:nm_006027]	221.594	1.02224	216.772
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	lipoic acid synthetase, mitochondrial (lip-syn) (lipoate synthase) (hussy-01) (fragment). [swissprot;acc:o43766]	209.517	1.02223	204.961
1348	zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [swissprot;acc:q15915]	213.832	1.02215	218.569
1349	zinc finger protein zic 3 (zinc finger protein of the cerebellum 3). [swissprot;acc:o60481]	213.841	1.02212	218.572
1350	zinc finger protein zic 2 (zinc finger protein of the cerebellum 2). [swissprot;acc:o95409]	213.847	1.0221	218.574
1351	prohibitin. [swissprot;acc:p35232]	206.941	1.02209	211.513
1352	repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273]
1353	heparin sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.-) (n- hsst) (n-heparin sulfate sulfotransferase) (glucosaminyl n- deacetylase/n-sulfotransferase). [swissprot;acc:p52849]	223.475	1.02208	228.409
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	upstream stimulatory factor 1 (major late transcription factor 1). [swissprot;acc:p22415]	210.359	1.022	214.987
1359	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712]	223.726	1.02197	228.642
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). [swissprot;acc:p36897]	228.805	1.02195	223.89
1361	upstream stimulatory factor 2 (upstream transcription factor 2) (fos-interacting protein) (fip) (major late transcription factor 2). [swissprot;acc:q15853]	210.354		214.971
1362	peroxisomal n1-acetyl-spermine/spermidine oxidase. [refseq;acc:nm_152911]	223.736	1.02194	228.644
1363	camp response element-binding protein cre-bpa. [refseq;acc:nm_004904]	213.899		218.591
1364	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]	228.797		223.885
1365	atpase inhibitor, mitochondrial precursor. [swissprot;acc:q9uii2]	223.736		228.644
1366	activin a receptor, type ic; activin receptor-like kinase 7. [refseq;acc:nm_145259]	228.795		223.884
1367	neuronal calcium sensor 1 (ncs-1) (frequenin homolog) (frequenin-like protein) (frequenin-like ubiquitous protein). [swissprot;acc:p36610]	228.799		223.887

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.