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

Results: HTML CSV LaTeX

Showing element 2008 to 2057 of 6456 in total

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

Rank	description	Hugo	Network Comparison Type	red	green	network_comparison
1004	skeletal muscle lim-protein 2 (slim 2) (four and a half lim domains protein 3) (fhl-3). [swissprot;acc:q13643]	FHL3	Subtracted	269.59	276.454	6.864
1005	dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576]	DYNC1I1	Divided	225.448	218.232	1.03307
	dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832]	DKC1	Subtracted	231.007	237.864	6.857
1006	cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6]	CPSF3	Divided	116.524	120.375	1.03305
	retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999]	RBL2	Subtracted	217.026	210.189	6.837
1007	ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967]	RALGDS	Divided	162.055	156.884	1.03296
	retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749]	RBL1	Subtracted	217.021	210.185	6.836
1008	dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [swissprot;acc:q16531]	DDB1		222.364	215.535	6.829
	wd-repeat protein bing4. [swissprot;acc:o15213]	WDR46	Divided	243.227	235.475	1.03292
1009	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882]	no value		229.116	221.823	1.03288
	propionyl-coa carboxylase beta chain, mitochondrial precursor (ec 6.4.1.3) (pccase beta subunit) (propanoyl-coa:carbon dioxide ligase beta subunit). [swissprot;acc:p05166]	PCCB	Subtracted	222.364	215.535	6.829
1010	ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245]	ATXN2L		228.105	221.293	6.812
	peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9]	CROT	Divided	217.523	210.648	1.03264
1011	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]	no value	Subtracted	228.105	221.293	6.812
	retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999]	RBL2	Divided	217.026	210.189	1.03253
1012	importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629]	KPNA4	Subtracted	217.369	210.561	6.808
	retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749]	RBL1	Divided	217.021	210.185	1.03252
1013	protein bap28. [swissprot;acc:q9h583]	HEATR1		244.312	236.647	1.03239
	target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077]	TOE1	Subtracted	217.365	210.558	6.807
1014	apoptosis antagonizing transcription factor. [refseq;acc:nm_012138]	AATF	Divided	243.045	235.422	1.03238
	importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505]	KPNA3	Subtracted	217.361	210.554	6.807
1015	bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742]	MAGI1	Divided	221.73	228.906	1.03236
	exocyst complex component sec6. [swissprot;acc:o60645]	EXOC3	Subtracted	207.186	200.398	6.788
1016	importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629]	KPNA4	Divided	217.369	210.561	1.03233
	tyrosinase precursor (ec 1.14.18.1) (monophenol monooxygenase) (tumor rejection antigen ab) (sk29-ab) (lb24-ab). [swissprot;acc:p14679]	TYR	Subtracted	221.183	214.406	6.777
1017	succinyl-coa ligase [gdp-forming] alpha-chain, mitochondrial precursor (ec 6.2.1.4) (succinyl-coa synthetase, alpha chain) (scs-alpha). [swissprot;acc:p53597]	SUCLG1		211.908	218.627	6.719
	target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077]	TOE1	Divided	217.365	210.558	1.03233
1018	importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505]	KPNA3		217.361	210.554
	succinyl-coa ligase [adp-forming] beta-chain, mitochondrial precursor (ec 6.2.1.5) (succinyl-coa synthetase, betaa chain) (scs-betaa) (atp- specific succinyl-coa synthetase beta subunit). [swissprot;acc:q9p2r7]	SUCLA2	Subtracted	211.908	218.627	6.719
1019	60s ribosomal protein l21. [swissprot;acc:p46778]	no value		223.958	217.263	6.695
	tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677]	TYRL	Divided	221.302	214.409	1.03215
1020	dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [swissprot;acc:p40126]	DCT		221.28		1.03205
	similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9]	no value	Subtracted	226.218	232.88	6.662
1021	5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643]	TYRP1	Divided	221.278	214.409	1.03204
	block 23. [sptrembl;acc:q8nhw5]	no value	Subtracted	226.205	232.858	6.653
1022	60s acidic ribosomal protein p0 (l10e). [swissprot;acc:p05388]	RPLP0		226.203	232.855	6.652
	cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520]	CBS	Divided	205.632	199.266	1.03195
1023	gcn5-like protein 1 (rt14 protein). [swissprot;acc:p78537]	BLOC1S1	Subtracted	202.027	195.386	6.641
	transforming protein rhoc (h9). [swissprot;acc:p08134]	RHOC	Divided	205.632	199.266	1.03195
1024	dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [swissprot;acc:o60762]	DPM1	Subtracted	203.381	196.76	6.621
	thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762]	TST	Divided	205.632	199.266	1.03195
1025	3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325]	MPST
	40s ribosomal protein s30. [swissprot;acc:q05472]	FAU	Subtracted	223.44	216.875	6.565
1026	hydroxyacid oxidase 1 (ec 1.1.3.15) (haox1) (glycolate oxidase) (gox). [swissprot;acc:q9ujm8]	HAO1		231.922	238.486	6.564
	transforming protein rhoa (h12). [swissprot;acc:p06749]	RHOA	Divided	205.632	199.266	1.03195
1027	adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741]	no value	Subtracted	211.449	217.998	6.549
	succinyl-coa ligase [gdp-forming] alpha-chain, mitochondrial precursor (ec 6.2.1.4) (succinyl-coa synthetase, alpha chain) (scs-alpha). [swissprot;acc:p53597]	SUCLG1	Divided	211.908	218.627	1.03171
1028	estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061]	HSD17B1	Subtracted	211.449	217.998	6.549
	succinyl-coa ligase [adp-forming] beta-chain, mitochondrial precursor (ec 6.2.1.5) (succinyl-coa synthetase, betaa chain) (scs-betaa) (atp- specific succinyl-coa synthetase beta subunit). [swissprot;acc:q9p2r7]	SUCLA2	Divided	211.908	218.627	1.03171
1029	17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034]	no value	Subtracted	211.449	217.998	6.549

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.