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	description	Value Type	Interaction Map	Filtered	red	green	network_comparison

Results: HTML CSV LaTeX

Showing element 1130 to 1179 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	Network Comparison Type	Hugo	description	Value Type	red	green	network_comparison
142	Divided	PITRM1	metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889]	Measured	9276.47	7090.37	1.30832
		PRMT1	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873]	Rooted	55.6161	66.7332	1.19989
		RRAGB	ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]	Ranked	59	49	1.20408
	Subtracted	CHMP2A	putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]	Rooted	105.205	92.2415	12.9635
		JUND	transcription factor jun-d. [swissprot;acc:p17535]	Measured	5638.2	7523.39	1885.19
		PPIB	peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [swissprot;acc:p23284]	Squared	86600.9	65229.9	21371
		THBS3	thrombospondin 3 precursor. [swissprot;acc:p49746]	Ranked	239.99	269.234	29.244
143	Divided	ALG1	beta-1,4 mannosyltransferase. [refseq;acc:nm_019109]	Measured	9275.1	7089.65	1.30826
		ANLN	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]	Ranked	59	49	1.20408
		PPP1R13B	protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316]	Squared	124319	86848.2	1.43145
		PRMT8	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22]	Rooted	55.6161	66.7332	1.19989
	Subtracted	CSTF2	cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240]	Measured	15427.2	13572.8	1854.4
		OGT	udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294]	Squared	86600.9	65229.9	21371
		SF4	splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164]	Ranked	240.133	211.382	28.751
		STAMBP	associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]	Rooted	105.205	92.2415	12.9635
144	Divided	KCNIP1	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592]	Ranked	265.686	319.651	1.20312
		SNRP70	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621]	Rooted	55.6161	66.7332	1.19989
		TP53BP2	tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625]	Squared	123324	86277.9	1.42938
		UNC84A	sad1/unc-84 protein-like 1. [swissprot;acc:o94901]	Measured	3349.9	4362.61	1.30231
	Subtracted	COX4I1	cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [swissprot;acc:p13073]	Squared	86600.9	65229.9	21371
		CSRP1	cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291]	Ranked	239.35	267.915	28.565
		TIA1	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]	Measured	4133.47	5945.32	1811.85
		VPS24	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]	Rooted	105.205	92.2415	12.9635
145	Divided	no value	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]		55.6161	66.7332	1.19989
			nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Squared	310840	442993	1.42515
			ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	Measured	16771.5	12889.1	1.30122
		KCNIP4	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183]	Ranked	265.639	319.546	1.20293
	Subtracted	CHMP4A	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Rooted	105.205	92.2415	12.9635
		COX4I2	cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [swissprot;acc:q96kj9]	Squared	86600.9	65229.9	21371
		SHCBP1	likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	Ranked	239.336	267.881	28.545
		TIAL1	nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085]	Measured	4136.36	5943.56	1807.2
146	Divided	KCNIP2	kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193]	Ranked	265.632	319.531	1.20291
		PRPF40B	huntingtin interacting protein c. [refseq;acc:nm_012272]	Rooted	55.0737	66.0298	1.19894
		RRAGA	ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	Squared	103496	146848	1.41888
		STAMBPL1	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	Measured	11068	8508.5	1.30082
	Subtracted	CSRP2	smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527]	Ranked	239.336	267.879	28.543
		KCND2	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	Rooted	41.6734	28.9323	12.7411
		STAM2	signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [refseq;acc:nm_005843]	Squared	86281	65058.3	21222.7
		XAB1	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Measured	2671	871	1800
147	Divided	no value	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Ranked	50.7983	42.3003	1.2009
		CHMP2A	putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]	Measured	11068	8508.5	1.30082
		FOXP4	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457]	Rooted	42.0574	50.4237	1.19893
		RRAGC	ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]	Squared	103496	146848	1.41888
	Subtracted	ATPBD1C	protein x 0004. [refseq;acc:nm_016301]	Measured	2671	871	1800
		CSRP3	lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461]	Ranked	239.32	267.842	28.522
		CTH	cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929]	Rooted	41.6851	28.9509	12.7342
		NFU1	hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0]	Squared	55630.4	76083.7	20453.3
148	Divided	FOXP1	forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]	Rooted	42.0577	50.424	1.19892
		RRAGB	ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]	Squared	103496	146848	1.41888
		STAMBP	associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]	Measured	11068	8508.5	1.30082

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.