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

Results: HTML CSV LaTeX

Showing element 1463 to 1512 of 33156 in total

Network Comparison Type  : Divided
Filtered  : 1

Rank	Hugo	Value Type	description	Interaction Map	network_comparison	red	green
183	NEDD9	Rooted	enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511]	High confidence	1.15446	57.4586	66.3336
	PBLD	Measured	mawd binding protein (unknown protein 32 from 2d-page of liver tissue). [swissprot;acc:p30039]	Low confidence	1.07763	10087.8	10870.9
184	no value		spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813]		1.07749	7764.08	8365.72
		Squared	small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072]	High confidence	1.35203	72886.3	98544.5
	ATG4A	Rooted	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]		1.15321	153.602	133.195
	OSR1	Ranked	odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260]		1.15239	274.027	237.79
	SNRPB2	Rooted	u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579]	Low confidence	1.06257	70.6712	75.0934
	SRM	Squared	spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [swissprot;acc:p19623]		1.11039	54936	49474.7
	SYNCRIP	Measured	ns1-associated protein 1. [refseq;acc:nm_006372]	High confidence	1.29051	4069.83	5252.17
	TSGA10	Ranked	testis specific, 10. [refseq;acc:nm_025244]	Low confidence	1.05384	196.373	206.946
185	no value	Measured	putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2]		1.07736	6852.7	6360.64
		Ranked	f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755]		1.0537	212.589	201.755
	ADIPOR2		adiponectin receptor 2. [refseq;acc:nm_024551]	High confidence	1.14292	281.582	246.371
	HNRNPR	Measured	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390]		1.29051	4069.83	5252.17
	HS3ST6	Squared	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5]		1.34589	41502.9	30836.8
	MAP1LC3B	Rooted	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]		1.1532	153.578	133.176
	PRKAG3	Squared	5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9]	Low confidence	1.11029	54659.6	49230.2
	TPM3	Rooted	tropomyosin alpha 3 chain (tropomyosin 3) (tropomyosin gamma). [swissprot;acc:p06753]		1.0625	70.7318	75.1524
186	AADAT	Squared	alpha-aminoadipate aminotransferase; l-kynurenine/alpha-aminoadipate aminotransferase; kynurenine aminotransferase ii. [refseq;acc:nm_016228]		1.11014	59947	66549.6
	EIF4G1	Measured	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637]	High confidence	1.29001	4071.1	5251.75
	FLNB	Ranked	filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457]		1.14179	226.582	198.444
	HPRT1	Measured	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492]	Low confidence	1.0762	9896.39	10650.5
	HS3ST3A1	Squared	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042]	High confidence	1.34589	41502.9	30836.8
	MAP1LC3A	Rooted	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]		1.1532	153.578	133.176
	STAMBP	Ranked	associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]	Low confidence	1.05367	196.381	206.921
	TPM1	Rooted	tropomyosin 1 alpha chain (alpha-tropomyosin). [swissprot;acc:p09493]		1.06231	70.7466	75.1547
187	no value	Ranked	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]		1.05307	189.373	179.829
	ALG1	Measured	beta-1,4 mannosyltransferase. [refseq;acc:nm_019109]		1.0759	9012.1	8376.35
	ATG4B	Rooted	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	High confidence	1.15317	153.548	133.153
	DUOX2		dual oxidase 2 precursor; dual oxidase-like domains 2; nicotinamide adenine dinucleotide phosphate oxidase; flavoprotein nadph oxidase; nadph thyroid oxidase 2; nadh/nadph thyroid oxidase p138-tox; nadph oxidase/peroxidase duox2. [refseq;acc:nm_014080]	Low confidence	1.06175	69.8853	74.201
	HS3ST3B1	Squared	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041]	High confidence	1.34589	41502.9	30836.8
	MAK		serine/threonine-protein kinase mak (ec 2.7.1.-) (male germ cell- associated kinase). [swissprot;acc:p20794]	Low confidence	1.10969	45399.1	50379.1
	REV1	Ranked	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316]	High confidence	1.14179	226.582	198.444
	SNRPD3	Measured	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]		1.28807	4569.48	5885.79
188	AADAT		alpha-aminoadipate aminotransferase; l-kynurenine/alpha-aminoadipate aminotransferase; kynurenine aminotransferase ii. [refseq;acc:nm_016228]	Low confidence	1.07558	9986.51	10741.3
	DUOX1	Rooted	dual oxidase 1 precursor; nadph thyroid oxidase 1; flavoprotein nadph oxidase; nicotinamide adenine dinucleotide phosphate oxidase. [refseq;acc:nm_017434]		1.06171	69.8912	74.2044
	E2F1		transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094]	High confidence	1.15171	46.0352	53.0192
	HS3ST2	Squared	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043]		1.34589	41502.9	30836.8
	KRAS		transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116]	Low confidence	1.10966	51551.5	46457.1
	PRMT1	Ranked	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873]	High confidence	1.14179	226.582	198.444
	RPS6KC1		ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424]	Low confidence	1.05283	189.45	179.944
	STT3B	Measured	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]	High confidence	1.28281	4571.89	5864.86
189	CENPJ	Squared	centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451]	Low confidence	1.10919	65169.1	58753.9
	DCPS		mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026]	High confidence	1.34589	41502.9	30836.8
	DGAT1	Rooted	diacylglycerol o-acyltransferase 1 (ec 2.3.1.20) (diglyceride acyltransferase) (acat related gene product 1). [swissprot;acc:o75907]	Low confidence	1.06161	69.9065	74.2132
	DNALI1	Ranked	axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645]		1.05264	214.779	204.039
	E2F2	Rooted	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]	High confidence	1.15171	46.0352	53.0192
	PRMT8	Ranked	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22]		1.14179	226.582	198.444
	SLC11A1	Measured	natural resistance-associated macrophage protein 1 (nramp 1). [swissprot;acc:p49279]	Low confidence	1.0754	6933.47	7456.24
	STT3A		oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	High confidence	1.28281	4571.89	5864.86

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.