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

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Showing element 1663 to 1712 of 3228 in total

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

Rank	description	red	green	network_comparison
1663	tryptophan 2,3-dioxygenase (ec 1.13.11.11) (tryptophan pyrrolase) (tryptophanase) (tryptophan oxygenase) (tryptamin 2,3-dioxygenase) (trpo). [swissprot;acc:p48775]	218.335	215.26	1.01429
1664	transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690]	228.484	231.74	1.01425
1665	adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520]	204.433	201.564	1.01423
1666	karyopherin beta 2b, transportin; importin 3. [refseq;acc:nm_013433]	218.679	215.612	1.01422
1667	cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858]	214.898	211.898	1.01416
1668	survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637]	228.496	231.729	1.01415
1669	ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154]
1670	ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658]
1671	nucleoporin 54kda; nucleoporin p54. [refseq;acc:nm_017426]
1672	ras-related c3 botulinum toxin substrate 2 (p21-rac2) (small g protein) (gx). [swissprot;acc:p15153]
1673	dna replication licensing factor mcm5 (cdc46 homolog) (p1-cdc46). [swissprot;acc:p33992]
1674	survival of motor neuron protein-interacting protein 1 (smn- interacting protein 1) (component of gems 2) (gemin2). [swissprot;acc:o14893]
1675	probable atp-dependent rna helicase ddx20 (dead-box protein 20) (dead- box protein dp 103) (component of gems 3) (gemin3). [swissprot;acc:q9uhi6]
1676	importin beta-2 subunit (karyopherin beta-2 subunit) (transportin) (m9 region interaction protein) (mip). [swissprot;acc:q92973]	218.691	215.645	1.01413
1677	glutathione s-transferase p (ec 2.5.1.18) (gst class-pi) (gstp1-1). [swissprot;acc:p09211]	218.654	221.732	1.01408
1678	serine/threonine protein kinase 23 (ec 2.7.1.37) (muscle-specific serine kinase 1) (mssk-1). [swissprot;acc:q9upe1]	216.899	213.889	1.01407
1679	gtp binding protein 2. [refseq;acc:nm_019096]
1680	cyclic-amp-dependent transcription factor atf-6 beta (activating transcription factor 6 beta) (atf6-beta) (camp responsive element binding protein-like 1) (camp response element binding protein-related protein) (creb-rp) (g13 protein). [swissprot;acc:q99941]
1681	dna segment on chromosome 6(unique) 2654 expressed sequence; dna segment on chromosome x (unique) 2654 expressed sequence. [refseq;acc:nm_012135]
1682	sfrs protein kinase 2 isoform b. [refseq;acc:nm_182691]
1683	cyclic-amp-dependent transcription factor atf-6 alpha (activating transcription factor 6 alpha) (atf6-alpha). [swissprot;acc:p18850]
1684	sfrs protein kinase 1; sr protein kinase 1. [refseq;acc:nm_003137]
1685	xap-5 protein (hxc-26 protein). [swissprot;acc:q14320]
1686	putative sialoglycoprotease type 2. [refseq;acc:nm_022353]	220.75	217.704	1.01399
1687	atp synthase delta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p30049]	215.345	212.386	1.01393
1688	transcription factor-like protein mrg15 (morf-related gene 15 protein) (mortality factor 4-like 1) (msl3-1 protein) (hspc008/hspc061). [swissprot;acc:q9ubu8]	228.523	231.703	1.01392
1689	dead-box protein 4 (vasa homolog). [swissprot;acc:q9nqi0]	228.277	225.163	1.01383
1690	40s ribosomal protein s24 (s19). [swissprot;acc:p16632]	224.091	227.184	1.0138
1691	translation initiation factor if-2. [swissprot;acc:o60841]	217.263	214.315	1.01376
1692	rna-binding protein 9 (rna binding motif protein 9) (hexaribonucleotide binding protein 2) (repressor of tamoxifen transcriptional activity). [swissprot;acc:o43251]	218.515	215.551	1.01375
1693	inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268]	218.937	215.971	1.01373
1694	gmp synthase [glutamine-hydrolyzing] (ec 6.3.5.2) (glutamine amidotransferase) (gmp synthetase). [swissprot;acc:p49915]
1695	inosine-5'-monophosphate dehydrogenase 1 (ec 1.1.1.205) (imp dehydrogenase 1) (impdh-i) (impd 1). [swissprot;acc:p20839]
1696	polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361]	217.624	214.69	1.01367
1697	hskin17 protein. [refseq;acc:nm_012311]
1698	carnitine o-acetyltransferase (ec 2.3.1.7) (carnitine acetylase) (cat). [swissprot;acc:p43155]
1699	polyadenylate-binding protein 4 (poly(a)-binding protein 4) (pabp 4) (inducible poly(a)-binding protein) (ipabp) (activated-platelet protein-1) (app-1). [swissprot;acc:q13310]
1700	polyadenylate-binding protein 1 (poly(a)-binding protein 1) (pabp 1). [swissprot;acc:p11940]
1701	glucose-6-phosphate 1-dehydrogenase (ec 1.1.1.49) (g6pd). [swissprot;acc:p11413]	216.079	219.024	1.01363
1702	dna-repair protein xrcc3 (x-ray repair cross-complementing protein 3). [swissprot;acc:o43542]
1703	atp-dependent dna helicase q5 (recq protein-like 5) (recq5). [swissprot;acc:o94762]
1704	ataxin 2-binding protein. [swissprot;acc:q9nwb1]	218.514	215.577	1.01362
1705	serine/threonine protein phosphatase 4 (ec 3.1.3.16) (pp4) (protein phosphatase x) (pp-x). [swissprot;acc:p33172]	223.846	220.847	1.01358
1706	immunoglobulin-binding protein 1 (cd79a-binding protein 1) (b cell signal transduction molecule alpha 4) (alpha 4 protein). [swissprot;acc:p78318]
1707	mitotic checkpoint serine/threonine-protein kinase bub1 beta (ec 2.7.1.-) (hbubr1) (mad3/bub1-related protein kinase) (mitotic checkpoint kinase mad3l). [swissprot;acc:o60566]	221.283	218.334	1.01351
1708	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]
1709	homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [swissprot;acc:q03014]	198.014	195.385	1.01346
1710	casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [swissprot;acc:p49674]	227.225	224.21	1.01345
1711	biotin--protein ligase (ec 6.3.4.-) (biotin apo-protein ligase) [includes: biotin--[methylmalonyl-coa-carboxyltransferase] ligase (ec 6.3.4.9); biotin--[propionyl-coa-carboxylase [atp-hydrolyzing]] ligase (ec 6.3.4.10) (holocarboxylase synthetase) (hcs); biotin--[methylcrotonoyl-coa-carboxylase] ligase (ec 6.3.4.11); biotin--[acetyl-coa-carboxylase] ligase (ec 6.3.4.15)]. [swissprot;acc:p50747]	218.436	215.553	1.01337
1712	transcription initiation factor tfiid 28 kda subunit (tafii-28) (tafii28) (tfiid subunit p30-beta). [swissprot;acc:q15544]	208.598	211.375	1.01331

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.