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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

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

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Showing element 3408 to 3457 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Hugo	Network Comparison Type	red	green	network_comparison
1704	myosin light chain 1, slow-twitch muscle b/ventricular isoform (mlc1sb) (alkali). [swissprot;acc:p08590]	MYL3	Subtracted	233.45	230.595	2.855
1705	nadh-ubiquinone oxidoreductase 13 kda-a subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-a) (ci-13kd-a). [swissprot;acc:o75380]	NDUFS6
	serine/threonine protein phosphatase 4 (ec 3.1.3.16) (pp4) (protein phosphatase x) (pp-x). [swissprot;acc:p33172]	PPP4C	Divided	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]	IGBP1
	myosin light chain 1, slow-twitch muscle a isoform (mlc1sa) (alkali). [swissprot;acc:p14649]	MYL6	Subtracted	233.45	230.595	2.855
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]	BUB1B	Divided	221.283	218.334	1.01351
	myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829]	no value	Subtracted	233.45	230.595	2.855
1708	inositol polyphosphate multikinase. [refseq;acc:nm_152230]	IPMK		217.676	220.53	2.854
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	PNPO	Divided	221.283	218.334	1.01351
1709	afg3-like protein 2 (ec 3.4.24.-) (paraplegin-like protein). [swissprot;acc:q9y4w6]	AFG3L2	Subtracted	217.676	220.53	2.854
	homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [swissprot;acc:q03014]	HHEX	Divided	198.014	195.385	1.01346
1710	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]	FUT8	Subtracted	217.676	220.53	2.854
	casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [swissprot;acc:p49674]	no value	Divided	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]	HLCS		218.436	215.553	1.01337
	yl-1 protein (transcription factor-like 1). [swissprot;acc:q15906]	VPS72	Subtracted	194.516	197.364	2.848
1712	hydroxyacylglutathione hydrolase (ec 3.1.2.6) (glyoxalase ii) (glx ii). [swissprot;acc:q16775]	HAGH
	transcription initiation factor tfiid 28 kda subunit (tafii-28) (tafii28) (tfiid subunit p30-beta). [swissprot;acc:q15544]	TAF11	Divided	208.598	211.375	1.01331
1713	nucleolar protein family a, member 2; component of the h/aca snornp. [refseq;acc:nm_017838]	NOLA2	Subtracted	221.921	219.081	2.84
	sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963]	SH3GL3	Divided	206.823	204.111	1.01329
1714	armet protein precursor (arginine-rich protein). [swissprot;acc:p55145]	ARMET		206.549	203.844	1.01327
	transcription initiation factor iif, alpha subunit (tfiif-alpha) (transcription initiation factor rap74). [swissprot;acc:p35269]	GTF2F1	Subtracted	221.921	219.081	2.84
1715	histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113]	HDC	Divided	206.549	203.844	1.01327
	myofibrillogenesis regulator 1; trans-activated by hepatitis c virus core protein 2; likely ortholog of mouse brain protein 17. [refseq;acc:nm_022572]	PNKD	Subtracted	194.476	197.305	2.829
1716	leucyl-trna synthetase. [refseq;acc:nm_020117]	LARS		218.99	216.189	2.801
	sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962]	SH3GL2	Divided	206.522	203.818	1.01327
1717	o-sialoglycoprotein endopeptidase. [refseq;acc:nm_017807]	OSGEP		221.058	218.164
	probable leucyl-trna synthetase, mitochondrial precursor (ec 6.1.1.4) (leucine--trna ligase) (leurs). [swissprot;acc:q15031]	LARS2	Subtracted	218.99	216.189	2.801
1718	c-1-tetrahydrofolate synthase, cytoplasmic (c1-thf synthase) [includes: methylenetetrahydrofolate dehydrogenase (ec 1.5.1.5); methenyltetrahydrofolate cyclohydrolase (ec 3.5.4.9); formyltetrahydrofolate synthetase (ec 6.3.4.3)]. [swissprot;acc:p11586]	MTHFD1		228.932	231.732	2.8
	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]	SH3GL1	Divided	206.251	203.553	1.01325
1719	helicase (fragment). [sptrembl;acc:q92771]	no value		187.204	189.679	1.01322
	sphingosine-1-phosphate lyase 1; sphingosine-1-phosphate lyase. [refseq;acc:nm_003901]	SGPL1	Subtracted	219.423	222.215	2.792
1720	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]	no value
	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]	DDX12	Divided	187.205	189.679	1.01322
1721	casein kinase i, delta isoform (ec 2.7.1.-) (cki-delta) (ckid). [swissprot;acc:p48730]	CSNK1D		227.125	224.164	1.01321
	ornithine aminotransferase, mitochondrial precursor (ec 2.6.1.13) (ornithine--oxo-acid aminotransferase). [swissprot;acc:p04181]	OAT	Subtracted	219.423	222.215	2.792
1722	40s ribosomal protein s13. [swissprot;acc:q02546]	RPS13	Divided	220.899	223.813	1.01319
	putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544]	NADK	Subtracted	212.36	215.147	2.787
1723	adaptor-related protein complex 1, mu 2 subunit (mu-adaptin 2) (adaptor protein complex ap-1 mu-2 subunit) (golgi adaptor ha1/ap1 adaptin mu-2 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 2) (ap-mu chain family member mu1b). [swissprot;acc:q9y6q5]	AP1M2		221.185	223.97	2.785
	putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544]	NADK	Divided	212.36	215.147	1.01312
1724	inositol polyphosphate multikinase. [refseq;acc:nm_152230]	IPMK		217.676	220.53	1.01311
	transcription initiation factor tfiid 28 kda subunit (tafii-28) (tafii28) (tfiid subunit p30-beta). [swissprot;acc:q15544]	TAF11	Subtracted	208.598	211.375	2.777
1725	afg3-like protein 2 (ec 3.4.24.-) (paraplegin-like protein). [swissprot;acc:q9y4w6]	AFG3L2	Divided	217.676	220.53	1.01311
	pre-mrna cleavage factor i, 59 kda subunit. [refseq;acc:nm_024811]	no value	Subtracted	218.176	215.402	2.774
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]	FUT8	Divided	217.676	220.53	1.01311
	chaperone-activity of bc1 complex-like, mitochondrial precursor (chaperone-abc1-like). [swissprot;acc:q8ni60]	CABC1	Subtracted	215.336	212.567	2.769
1727	aarf domain containing kinase 2; putative ubiquinone biosynthesis protein aarf. [refseq;acc:nm_052853]	ADCK2
	inositol-1(or 4)-monophosphatase (ec 3.1.3.25) (impase) (imp) (inositol monophosphatase) (lithium-sensitive myo-inositol monophosphatase a1). [swissprot;acc:p29218]	IMPA1	Divided	210.366	213.118	1.01308
1728	aarf domain containing kinase 4. [refseq;acc:nm_024876]	ADCK4	Subtracted	215.336	212.567	2.769
	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]	IMPA2	Divided	210.358	213.103	1.01305
1729	aarf domain containing kinase 1. [refseq;acc:nm_020421]	ADCK1	Subtracted	215.336	212.567	2.769

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
- Hugo is the HGNC identifier if it exists
- 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.