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	network_comparison	green

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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	network_comparison	green
1700	polyadenylate-binding protein 1 (poly(a)-binding protein 1) (pabp 1). [swissprot;acc:p11940]	217.624	1.01367	214.69
1701	glucose-6-phosphate 1-dehydrogenase (ec 1.1.1.49) (g6pd). [swissprot;acc:p11413]	216.079	1.01363	219.024
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	1.01362	215.577
1705	serine/threonine protein phosphatase 4 (ec 3.1.3.16) (pp4) (protein phosphatase x) (pp-x). [swissprot;acc:p33172]	223.846	1.01358	220.847
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	1.01351	218.334
1708	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]
1709	homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [swissprot;acc:q03014]	198.014	1.01346	195.385
1710	casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [swissprot;acc:p49674]	227.225	1.01345	224.21
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	1.01337	215.553
1712	transcription initiation factor tfiid 28 kda subunit (tafii-28) (tafii28) (tfiid subunit p30-beta). [swissprot;acc:q15544]	208.598	1.01331	211.375
1713	sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963]	206.823	1.01329	204.111
1714	armet protein precursor (arginine-rich protein). [swissprot;acc:p55145]	206.549	1.01327	203.844
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	1.01325	203.553
1719	helicase (fragment). [sptrembl;acc:q92771]	187.204	1.01322	189.679
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	1.01321	224.164
1722	40s ribosomal protein s13. [swissprot;acc:q02546]	220.899	1.01319	223.813
1723	putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544]	212.36	1.01312	215.147
1724	inositol polyphosphate multikinase. [refseq;acc:nm_152230]	217.676	1.01311	220.53
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	1.01308	213.118
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	1.01305	213.103
1729	autophagy protein 12-like (apg12-like). [swissprot;acc:o94817]	187.582	1.01304	190.028
1730	chaperone-activity of bc1 complex-like, mitochondrial precursor (chaperone-abc1-like). [swissprot;acc:q8ni60]	215.336	1.01303	212.567
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	1.01296	219.081
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	1.01289	209.258
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	1.01288	215.402
1744	sphingosine-1-phosphate lyase 1; sphingosine-1-phosphate lyase. [refseq;acc:nm_003901]	219.423	1.01272	222.215
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	1.0127	190.845
1748	bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132]	215.673	1.01269	212.971
1749	dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1]	206.058	1.01264	203.485

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.