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	Value Type	Hugo	description	Interaction Map	network_comparison	Filtered	red	green

Results: HTML CSV LaTeX

Showing element 2858 to 2907 of 33156 in total

Network Comparison Type  : Divided
Filtered  : 1

Rank	Value Type	Hugo	description	Interaction Map	network_comparison	red	green
358	Measured	CAPN1	calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384]	Low confidence	1.05472	6822.26	7195.59
	Ranked	MOCS2	molybdenum cofactor synthesis protein 2 large subunit (molybdopterin synthase large subunit) (mpt synthase large subunit) (mocs2b) (moco1- b). [swissprot;acc:o96007]		1.03798	207.531	199.938
		RPL10L	ribosomal protein l10-like protein. [refseq;acc:nm_080746]	High confidence	1.09683	243.12	266.662
	Squared	no value	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007]		1.24071	9811.73	7908.13
		EPS15L1	epidermal growth factor receptor substrate eps15r. [refseq;acc:nm_021235]	Low confidence	1.07307	49917.8	46518.7
	Rooted	HOMER1	homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272]		1.05067	67.9062	71.347
		NEK2	serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [swissprot;acc:p51955]	High confidence	1.10587	61.2684	67.755
359	Measured	CDK3	cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]		1.17559	12798.9	10887.2
		DNPEP	aspartyl aminopeptidase (ec 3.4.11.21). [swissprot;acc:q9ula0]	Low confidence	1.0546	8966.11	9455.62
	Ranked	MOCS3	molybdenum cofactor synthesis protein 3 (molybdopterin synthase sulfurylase) (mpt synthase sulfurylase). [swissprot;acc:o95396]		1.03798	207.531	199.938
		RPL4	60s ribosomal protein l4 (l1). [swissprot;acc:p36578]	High confidence	1.09678	239.277	262.434
	Squared	EIF2S2	eukaryotic translation initiation factor 2 subunit 2 (eukaryotic translation initiation factor 2 beta subunit) (eif-2-beta). [swissprot;acc:p20042]	Low confidence	1.07302	49885.6	46490.8
		PPP2R2B	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005]	High confidence	1.24068	9812.34	7908.87
	Rooted	no value	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	Low confidence	1.05065	71.2795	74.8896
		PES1	pescadillo homolog 1. [swissprot;acc:o00541]	High confidence	1.10582	49.2488	54.4603
360	Measured	CCNB2	g2/mitotic-specific cyclin b2. [swissprot;acc:o95067]		1.17553	12796.8	10886
		OSBPL5	oxysterol binding protein-related protein 5 (osbp-related protein 5) (orp-5). [swissprot;acc:q9h0x9]	Low confidence	1.05443	8576.28	9043.11
	Ranked	no value	secreted modular calcium-binding protein 1. [refseq;acc:nm_022137]		1.0379	204.231	196.773
		SEC61G	protein transport protein sec61 gamma subunit. [swissprot;acc:p38384]	High confidence	1.09663	243.072	266.559
	Squared	PPP2R2C	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4]		1.24054	9814.47	7911.48
		TBX1	t-box transcription factor tbx1 (t-box protein 1) (testis-specific t-box protein). [swissprot;acc:o43435]	Low confidence	1.07214	50110.9	46739.1
	Rooted	DDX39	dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804]		1.05064	72.4449	76.1137
		GNL3	nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366]	High confidence	1.10558	49.3771	54.5905
361	Measured	CDK2	cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941]		1.17528	12787.6	10880.5
		SNRPD3	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]	Low confidence	1.05437	7773.85	8196.54
	Ranked	MRPL17	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061]	High confidence	1.09644	242.83	266.248
		PFDN1	prefoldin subunit 1. [swissprot;acc:o60925]	Low confidence	1.0379	204.231	196.773
	Squared	SFPQ	splicing factor, proline-and glutamine-rich (polypyrimidine tract- binding protein-associated splicing factor) (ptb-associated splicing factor) (psf) (dna-binding p52/p100 complex, 100 kda subunit). [swissprot;acc:p23246]	High confidence	1.24047	70694.1	56989.9
		UBE2S	ubiquitin-conjugating enzyme e2-24 kda (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2-epf5). [swissprot;acc:q16763]	Low confidence	1.07214	50110.9	46739.1
	Rooted	no value	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]		1.05056	71.2844	74.8882
		RPS4Y2	40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47]	High confidence	1.10518	50.7801	45.9472
362	Measured	CCNB1	g2/mitotic-specific cyclin b1. [swissprot;acc:p14635]		1.17525	12786.6	10879.9
		NEURL	neuralized-like. [refseq;acc:nm_004210]	Low confidence	1.05435	6456.59	6807.5
	Ranked	SHROOM2	apical-like protein (apxl protein). [swissprot;acc:q13796]	High confidence	1.09641	231.492	211.136
		SMOC2	secreted modular calcium-binding protein 2; smooth muscle associated protein 2. [refseq;acc:nm_022138]	Low confidence	1.0379	204.231	196.773
	Squared	SNAI2	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]		1.07186	46359.3	43251.4
		TAF7	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545]	High confidence	1.23973	57808.9	46630.3
	Rooted	no value	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]		1.10518	50.7803	45.9477
		HOMER2	homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839]	Low confidence	1.05045	67.9142	71.3405
363	Measured	CDC2	cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493]	High confidence	1.17509	12780.7	10876.4
		PARL	presenilins associated rhomboid-like protein. [refseq;acc:nm_018622]	Low confidence	1.05433	9099.15	9593.54
	Ranked	CHDH	choline dehydrogenase. [refseq;acc:nm_018397]		1.0379	204.231	196.773
		SHROOM3	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859]	High confidence	1.09639	231.481	211.131
	Squared	IPO13	importin 13; ran binding protein 13. [refseq;acc:nm_014652]	Low confidence	1.07149	47602.7	44426.5
		TAF7L	tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885]	High confidence	1.23834	57579.2	46497.2
	Rooted	BOP1	block of proliferation 1. [swissprot;acc:q14137]		1.10477	49.4884	54.6735
		PRPF19	nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502]	Low confidence	1.05019	71.4038	74.9877
364	Measured	GULP1	ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315]	High confidence	1.17334	5189	6088.47
		LUC7L2	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]	Low confidence	1.05423	7711.11	8129.27
	Ranked	DGCR14	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]		1.03785	212.235	204.495

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.