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 1700 to 1749 of 3228 in total

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

Rank	description	red	green	network_comparison
1700	polyadenylate-binding protein 1 (poly(a)-binding protein 1) (pabp 1). [swissprot;acc:p11940]	217.624	214.69	1.01367
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
1713	sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963]	206.823	204.111	1.01329
1714	armet protein precursor (arginine-rich protein). [swissprot;acc:p55145]	206.549	203.844	1.01327
1715	histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113]
1716	sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962]	206.522	203.818
1717	o-sialoglycoprotein endopeptidase. [refseq;acc:nm_017807]	221.058	218.164
1718	sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961]	206.251	203.553	1.01325
1719	helicase (fragment). [sptrembl;acc:q92771]	187.204	189.679	1.01322
1720	dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [refseq;acc:nm_030655]	187.205
1721	casein kinase i, delta isoform (ec 2.7.1.-) (cki-delta) (ckid). [swissprot;acc:p48730]	227.125	224.164	1.01321
1722	40s ribosomal protein s13. [swissprot;acc:q02546]	220.899	223.813	1.01319
1723	putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544]	212.36	215.147	1.01312
1724	inositol polyphosphate multikinase. [refseq;acc:nm_152230]	217.676	220.53	1.01311
1725	afg3-like protein 2 (ec 3.4.24.-) (paraplegin-like protein). [swissprot;acc:q9y4w6]
1726	alpha-(1,6)-fucosyltransferase (ec 2.4.1.68) (glycoprotein 6-alpha-l- fucosyltransferase) (gdp-fucose--glycoprotein fucosyltransferase) (gdp-l-fuc:n-acetyl-beta-d-glucosaminide alpha1,6-fucosyltransferase) (alpha1-6fuct) (fucosyltransferase 8). [swissprot;acc:q9byc5]
1727	inositol-1(or 4)-monophosphatase (ec 3.1.3.25) (impase) (imp) (inositol monophosphatase) (lithium-sensitive myo-inositol monophosphatase a1). [swissprot;acc:p29218]	210.366	213.118	1.01308
1728	inositol-1(or 4)-monophosphatase 2 (ec 3.1.3.25) (impase 2) (imp 2) (inositol monophosphatase 2) (myo-inositol monophosphatase a2). [swissprot;acc:o14732]	210.358	213.103	1.01305
1729	autophagy protein 12-like (apg12-like). [swissprot;acc:o94817]	187.582	190.028	1.01304
1730	chaperone-activity of bc1 complex-like, mitochondrial precursor (chaperone-abc1-like). [swissprot;acc:q8ni60]	215.336	212.567	1.01303
1731	aarf domain containing kinase 2; putative ubiquinone biosynthesis protein aarf. [refseq;acc:nm_052853]
1732	aarf domain containing kinase 4. [refseq;acc:nm_024876]
1733	aarf domain containing kinase 1. [refseq;acc:nm_020421]
1734	nucleolar protein family a, member 2; component of the h/aca snornp. [refseq;acc:nm_017838]	221.921	219.081	1.01296
1735	leucyl-trna synthetase. [refseq;acc:nm_020117]	218.99	216.189
1736	transcription initiation factor iif, alpha subunit (tfiif-alpha) (transcription initiation factor rap74). [swissprot;acc:p35269]	221.921	219.081
1737	probable leucyl-trna synthetase, mitochondrial precursor (ec 6.1.1.4) (leucine--trna ligase) (leurs). [swissprot;acc:q15031]	218.99	216.189
1738	lipoate-protein ligase, mitochondrial precursor (ec 6.-.-.-) (lipoate biosynthesis protein) (lipoyl ligase) (lipoyltransferase). [swissprot;acc:q9y234]	206.595	209.258	1.01289
1739	tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258]
1740	defender against cell death 1 (dad-1). [swissprot;acc:p46966]
1741	t-complex 11. [refseq;acc:nm_018679]
1742	tubulin gamma-2 chain (gamma-2 tubulin). [swissprot;acc:q9nrh3]
1743	pre-mrna cleavage factor i, 59 kda subunit. [refseq;acc:nm_024811]	218.176	215.402	1.01288
1744	sphingosine-1-phosphate lyase 1; sphingosine-1-phosphate lyase. [refseq;acc:nm_003901]	219.423	222.215	1.01272
1745	4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404]
1746	ornithine aminotransferase, mitochondrial precursor (ec 2.6.1.13) (ornithine--oxo-acid aminotransferase). [swissprot;acc:p04181]
1747	tfiih basal transcription factor complex helicase subunit (ec 3.6.1.-) (dna-repair protein complementing xp-d cells) (xeroderma pigmentosum group d complementing protein) (cxpd) (dna excision repair protein ercc-2). [swissprot;acc:p18074]	188.452	190.845	1.0127
1748	bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132]	215.673	212.971	1.01269
1749	dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1]	206.058	203.485	1.01264

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.