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

Results: HTML CSV LaTeX

Showing element 2008 to 2057 of 8289 in total

Network Comparison Type  : Divided
Value Type  : Ranked
Filtered  : 1

Rank	Hugo	description	Interaction Map	red	green	network_comparison
1004	TIA1	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]	Low confidence	200.403	195.612	1.02449
1005	DYNC1I1	dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576]	High confidence	225.448	218.232	1.03307
	USP5	ubiquitin carboxyl-terminal hydrolase 5 (ec 3.1.2.15) (ubiquitin thiolesterase 5) (ubiquitin-specific processing protease 5) (deubiquitinating enzyme 5) (isopeptidase t). [swissprot;acc:p45974]	Low confidence	204.271	199.392	1.02447
1006	CPSF3	cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6]	High confidence	116.524	120.375	1.03305
	GIT1	arf gtpase-activating protein git1 (g protein-coupled receptor kinase- interactor 1). [swissprot;acc:q9y2x7]	Low confidence	206.183	201.259	1.02447
1007	ETFDH	electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial precursor (ec 1.5.5.1) (etf-qo) (etf-ubiquinone oxidoreductase) (etf dehydrogenase) (electron-transferring- flavoprotein dehydrogenase). [swissprot;acc:q16134]		198.075	193.349	1.02444
	RALGDS	ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967]	High confidence	162.055	156.884	1.03296
1008	CTTN	src substrate cortactin (amplaxin) (oncogene ems1). [swissprot;acc:q14247]	Low confidence	199.992	195.221	1.02444
	WDR46	wd-repeat protein bing4. [swissprot;acc:o15213]	High confidence	243.227	235.475	1.03292
1009	no value	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882]		229.116	221.823	1.03288
	PDZD4	lu1 protein. [refseq;acc:nm_032512]	Low confidence	204.391	199.514	1.02444
1010	BRF1	transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994]		202.366	197.54	1.02443
	CROT	peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9]	High confidence	217.523	210.648	1.03264
1011	LGTN	ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214]	Low confidence	208.97	214.075	1.02443
	RBL2	retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999]	High confidence	217.026	210.189	1.03253
1012	RBL1	retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749]		217.021	210.185	1.03252
	SHROOM3	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859]	Low confidence	204.877	199.992	1.02443
1013	HEATR1	protein bap28. [swissprot;acc:q9h583]	High confidence	244.312	236.647	1.03239
	IMPDH2	inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268]	Low confidence	200.743	195.959	1.02441
1014	AATF	apoptosis antagonizing transcription factor. [refseq;acc:nm_012138]	High confidence	243.045	235.422	1.03238
	MTHFR	methylenetetrahydrofolate reductase (ec 1.5.1.20). [swissprot;acc:p42898]	Low confidence	182.56	178.211	1.0244
1015	KIFC3	kinesin family member c3. [refseq;acc:nm_005550]		205.25	200.362
	MAGI1	bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742]	High confidence	221.73	228.906	1.03236
1016	KPNA4	importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629]		217.369	210.561	1.03233
	TAF7	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545]	Low confidence	201.283	196.49	1.02439
1017	IMPDH1	inosine-5'-monophosphate dehydrogenase 1 (ec 1.1.1.205) (imp dehydrogenase 1) (impdh-i) (impd 1). [swissprot;acc:p20839]		200.745	195.966
	TOE1	target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077]	High confidence	217.365	210.558	1.03233
1018	KPNA3	importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505]		217.361	210.554
	PDZRN3	similar to semaf cytoplasmic domain associated protein 3. [sptrembl;acc:q96cc2]	Low confidence	204.339	199.475	1.02438
1019	HIPK3	homeodomain interacting protein kinase 3; homeodomain-interacting protein kinase 3. [refseq;acc:nm_005734]		202.352	197.536
	TYRL	tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677]	High confidence	221.302	214.409	1.03215
1020	DCT	dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [swissprot;acc:p40126]		221.28		1.03205
	TRPC4	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4]	Low confidence	200.421	205.306	1.02437
1021	HIPK2	homeodomain-interacting protein kinase 2 (ec 2.7.1.-). [swissprot;acc:q9h2x6]		202.351	197.537
	TYRP1	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]	High confidence	221.278	214.409	1.03204
1022	CBS	cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520]		205.632	199.266	1.03195
	HIPK1	homeodomain-interacting protein kinase 1; homeodomain interacting protein kinase 1-like protein; nuclear body associated kinase 2b. [refseq;acc:nm_152696]	Low confidence	202.351	197.538	1.02436
1023	RHOC	transforming protein rhoc (h9). [swissprot;acc:p08134]	High confidence	205.632	199.266	1.03195
	UNC50	geal-6 membrane-associated high-copy suppressor 1; unc-50 related. [refseq;acc:nm_014044]	Low confidence	203.215	208.165	1.02436
1024	TIMM9	mitochondrial import inner membrane translocase subunit tim9 a. [swissprot;acc:q9y5j7]		205.995	201.097
	TST	thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762]	High confidence	205.632	199.266	1.03195
1025	MPST	3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325]
	NAP1L2	nucleosome assembly protein 1-like 2 (brain-specific protein, x- linked). [swissprot;acc:q9ulw6]	Low confidence	201.047	196.275	1.02431
1026	RHOA	transforming protein rhoa (h12). [swissprot;acc:p06749]	High confidence	205.632	199.266	1.03195
	SGCG	gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326]	Low confidence	206.781	201.874	1.02431
1027	PTRH2	protein cgi-147. [swissprot;acc:q9y3e5]		203.643	198.811	1.0243
	SUCLG1	succinyl-coa ligase [gdp-forming] alpha-chain, mitochondrial precursor (ec 6.2.1.4) (succinyl-coa synthetase, alpha chain) (scs-alpha). [swissprot;acc:p53597]	High confidence	211.908	218.627	1.03171
1028	SFRS8	splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872]	Low confidence	203.574	198.744	1.0243
	SUCLA2	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]	High confidence	211.908	218.627	1.03171
1029	DDB1	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]		222.364	215.535	1.03168

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.