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

Results: HTML CSV LaTeX

Showing element 3914 to 3963 of 12912 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Value Type	red	green	network_comparison
979	gcn5-like protein 1 (rt14 protein). [swissprot;acc:p78537]	Ranked	202.027	195.386	1.03399
	very long-chain acyl-coa synthetase homolog 1. [refseq;acc:nm_014031]	Squared	27403.4	31533.4	1.15071
	vesicle-associated membrane protein 1 (vamp-1) (synaptobrevin 1). [swissprot;acc:p23763]	Measured	6654.42	7296.51	1.09649
980	b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056]	Ranked	130.289	134.713	1.03396
	dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [swissprot;acc:p40126]	Rooted	61.9121	65.373	1.0559
	solute carrier family 27 (fatty acid transporter), member 5; very long-chain acyl-coa synthetase homolog 2; very long-chain acyl-coa synthetase-related protein; likely ortholog of mouse solute carrier family 27 (fatty acid transporter), member 5. [refseq;acc:nm_012254]	Squared	27403.6	31533.6	1.15071
	vesicule-associated membrane protein 4 (vamp-4). [swissprot;acc:o75379]	Measured	6654.42	7296.51	1.09649
981	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]	Rooted	61.9129	65.3733	1.05589
	cdp-diacylglycerol--inositol 3-phosphatidyltransferase (ec 2.7.8.11) (phosphatidylinositol synthase) (ptdins synthase) (pi synthase). [swissprot;acc:o14735]	Measured	6654.42	7296.51	1.09649
	exocyst complex component sec6. [swissprot;acc:o60645]	Ranked	207.186	200.398	1.03387
	similar to cg7020 gene product (fragment). [sptrembl;acc:q96ib4]	Squared	27403.1	31533	1.15071
982	adp-ribosylation factor gtpase activating protein 1 (adp-ribosylation factor 1 gtpase activating protein) (arf1 gap) (arf1-directed gtpase- activating protein) (gap protein). [swissprot;acc:q8n6t3]	Measured	6654.42	7296.51	1.09649
	bystin. [swissprot;acc:q13895]	Rooted	53.1515	56.1209	1.05587
	cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830]	Ranked	243.312	235.351	1.03383
	protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761]	Squared	30999.6	35666.3	1.15054
983	microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2]	Rooted	56.1832	53.2244	1.05559
	pbk1 protein. [sptrembl;acc:o76021]	Ranked	243.312	235.353	1.03382
	protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760]	Squared	31010.8	35677.6	1.15049
	vesicle-associated membrane protein 3 (vamp-3) (synaptobrevin 3) (cellubrevin) (ceb). [swissprot;acc:q15836]	Measured	6654.42	7296.51	1.09649
984	bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001]	Rooted	56.1854	53.2272	1.05558
	integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [swissprot;acc:q9y287]	Measured	6362.64	6976.1	1.09642
	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003]	Ranked	116.71	120.654	1.03379
	steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718]	Squared	59338.5	68268.3	1.15049
985	integral membrane protein 2c (transmembrane protein bri3) (npd018). [swissprot;acc:q9nqx7]	Measured	6362.64	6976.1	1.09642
	ketohexokinase (ec 2.7.1.3) (hepatic fructokinase). [swissprot;acc:p50053]	Squared	22569.9	25956.6	1.15005
	programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737]	Ranked	233.402	225.782	1.03375
	tyrosinase precursor (ec 1.14.18.1) (monophenol monooxygenase) (tumor rejection antigen ab) (sk29-ab) (lb24-ab). [swissprot;acc:p14679]	Rooted	61.9502	65.389	1.05551
986	adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559]		62.4582	65.9096	1.05526
	exocyst complex component sec5. [swissprot;acc:q96kp1]	Ranked	116.771	120.707	1.03371
	integral membrane protein 2a (e25 protein). [swissprot;acc:o43736]	Measured	6362.64	6976.1	1.09642
	purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491]	Squared	22569.9	25956.6	1.15005
987	maguk p55 subfamily member 3 (mpp3 protein) (discs, large homolog 3). [swissprot;acc:q13368]	Measured	6660.04	7301.81	1.09636
	methionyl-trna formyltransferase, mitochondrial precursor (ec 2.1.2.9) (mtfmt). [swissprot;acc:q96dp5]	Squared	20465.9	23535.3	1.14998
	serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464]	Ranked	218.459	211.338	1.03369
	vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase ac39 subunit) (v-atpase 40 kda accessory protein) (p39) (32 kda accessory protein). [swissprot;acc:p12953]	Rooted	62.4582	65.9096	1.05526
988	adp-ribosylation factor-like protein 4. [swissprot;acc:p40617]
	deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [swissprot;acc:p32321]	Squared	18082.5	20792.7	1.14988
	probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105]	Ranked	218.461	211.343	1.03368
	ubiquitin-conjugating enzyme e2 n (ec 6.3.2.19) (ubiquitin-protein ligase n) (ubiquitin carrier protein n) (ubc13) (bendless-like ubiquitin conjugating enzyme). [swissprot;acc:q16781]	Measured	6229.69	6829.58	1.0963
989	epididymal secretory protein e1 precursor (niemann-pick disease type c2 protein) (epi-1) (he1) (epididymal secretory protein 14.6) (esp14.6). [swissprot;acc:q15668]	Rooted	67.7394	71.4737	1.05513
	kccr13l. [refseq;acc:nm_139179]	Squared	23339.9	26834.1	1.14971
	probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110]	Ranked	218.462	211.345	1.03367
	signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [refseq;acc:nm_005843]	Measured	11743.3	10712.3	1.09624
990	atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010]	Ranked	243.297	235.373	1.03367
	dead-box protein 4 (vasa homolog). [swissprot;acc:q9nqi0]	Measured	5147.9	5641.25	1.09584
	dna repair protein rad51 homolog 1 (hrad51) (hsrad51). [swissprot;acc:q06609]	Squared	23339.9	26834.1	1.14971
	orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406]	Rooted	64.0581	67.5829	1.05503
991	aspartyl-trna synthetase (ec 6.1.1.12) (aspartate--trna ligase) (asprs). [swissprot;acc:p14868]	Squared	26705.9	30699	1.14952
	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]	Ranked	203.381	196.76	1.03365
	transformer-2 protein homolog (tra-2 alpha). [swissprot;acc:q13595]	Measured	6472.38	7092.65	1.09583

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
- 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.