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

Results: HTML CSV LaTeX

Showing element 1980 to 2029 of 6456 in total

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

Rank	description	Hugo	Network Comparison Type	red	network_comparison	green
990	atrophin-1 interacting protein 1; activin receptor interacting protein 1; likely ortholog of mouse activin receptor interacting protein 1; atrophin-1 interacting protein a; membrane associated guanylate kinase 2; activin receptor interacting p. [refseq;acc:nm_012301]	MAGI2	Subtracted	221.682	6.998	228.68
991	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	Divided	203.381	1.03365	196.76
	polymyositis/scleroderma autoantigen 2 (autoantigen pm/scl 2) (polymyositis/scleroderma autoantigen 100 kda) (pm/scl-100) (p100 polymyositis-scleroderma overlap syndrome associated autoantigen). [swissprot;acc:q01780]	EXOSC10	Subtracted	198.494	6.972	205.466
992	serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743]	HTRA1	Divided	218.468	1.03364	211.357
	vinculin (metavinculin). [swissprot;acc:p18206]	VCL	Subtracted	215.92	6.97	208.95
993	hepatocyte nuclear factor 4-gamma (hnf-4-gamma). [swissprot;acc:q14541]	HNF4G		251.863	6.966	258.829
	pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687]	PNN	Divided	211.071	1.03362	204.205
994	growth arrest and dna-damage-inducible protein gadd45 gamma (cytokine responsive protein cr6). [swissprot;acc:o95257]	GADD45G	Subtracted	251.863	6.966	258.829
	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3]	PAPOLG	Divided	116.845	1.03361	120.772
995	growth arrest and dna-damage-inducible protein gadd45 alpha (dna- damage inducible transcript 1) (ddit1). [swissprot;acc:p24522]	GADD45A	Subtracted	251.863	6.966	258.829
	mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95]	MAD2L2	Divided	219.656	1.03345	212.547
996	hepatocyte nuclear factor 4-alpha (hnf-4-alpha) (transcription factor hnf-4) (transcription factor 14). [swissprot;acc:p41235]	HNF4A	Subtracted	251.863	6.966	258.829
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	no value	Divided	219.656	1.03345	212.547
997	growth arrest and dna-damage-inducible protein gadd45 beta (negative growth-regulatory protein myd118) (myeloid differentiation primary response protein myd118). [swissprot;acc:o75293]	GADD45B	Subtracted	251.863	6.966	258.829
	nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567]	NUP88	Divided	219.656	1.03345	212.547
998	dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409]	DYNC1I2		225.557	1.03338	218.271
	tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677]	TYRL	Subtracted	221.302	6.893	214.409
999	skeletal muscle lim-protein 3 (slim 3) (lim-domain protein dral) (four and a half lim domains protein 2) (fhl-2). [swissprot;acc:q14192]	FHL2		269.608	6.885	276.493
	vinculin (metavinculin). [swissprot;acc:p18206]	VCL	Divided	215.92	1.03336	208.95
1000	peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9]	CROT	Subtracted	217.523	6.875	210.648
	sprouty homolog 4 (spry-4). [swissprot;acc:q9c004]	no value	Divided	225.167	1.03325	217.922
1001	dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [swissprot;acc:p40126]	DCT	Subtracted	221.28	6.871	214.409
	sprouty homolog 3 (spry-3). [swissprot;acc:o43610]	SPRY3	Divided	225.167	1.03325	217.922
1002	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	Subtracted	221.278	6.869	214.409
	sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609]	SPRY1	Divided	225.167	1.03325	217.922
1003	pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687]	PNN	Subtracted	211.071	6.866	204.205
	sprouty homolog 2 (spry-2). [swissprot;acc:o43597]	SPRY2	Divided	225.167	1.03325	217.922
1004	sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633]	no value		238.725	1.03318	231.059
	skeletal muscle lim-protein 2 (slim 2) (four and a half lim domains protein 3) (fhl-3). [swissprot;acc:q13643]	FHL3	Subtracted	269.59	6.864	276.454
1005	dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576]	DYNC1I1	Divided	225.448	1.03307	218.232
	dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832]	DKC1	Subtracted	231.007	6.857	237.864
1006	cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6]	CPSF3	Divided	116.524	1.03305	120.375
	retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999]	RBL2	Subtracted	217.026	6.837	210.189
1007	ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967]	RALGDS	Divided	162.055	1.03296	156.884
	retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749]	RBL1	Subtracted	217.021	6.836	210.185
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	6.829	215.535
	wd-repeat protein bing4. [swissprot;acc:o15213]	WDR46	Divided	243.227	1.03292	235.475
1009	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882]	no value		229.116	1.03288	221.823
	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	6.829	215.535
1010	ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245]	ATXN2L		228.105	6.812	221.293
	peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9]	CROT	Divided	217.523	1.03264	210.648
1011	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]	no value	Subtracted	228.105	6.812	221.293
	retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999]	RBL2	Divided	217.026	1.03253	210.189
1012	importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629]	KPNA4	Subtracted	217.369	6.808	210.561
	retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749]	RBL1	Divided	217.021	1.03252	210.185
1013	protein bap28. [swissprot;acc:q9h583]	HEATR1		244.312	1.03239	236.647
	target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077]	TOE1	Subtracted	217.365	6.807	210.558
1014	apoptosis antagonizing transcription factor. [refseq;acc:nm_012138]	AATF	Divided	243.045	1.03238	235.422
	importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505]	KPNA3	Subtracted	217.361	6.807	210.554
1015	bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742]	MAGI1	Divided	221.73	1.03236	228.906

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.