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.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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

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Showing element 4858 to 4907 of 8289 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1

Rank	description	Interaction Map	red	green	network_comparison
2429	sphingosine-1-phosphate lyase 1; sphingosine-1-phosphate lyase. [refseq;acc:nm_003901]	Low confidence	198.047	194.468	1.0184
2430	epsin 1; eh domain-binding mitotic phosphoprotein. [refseq;acc:nm_013333]	High confidence	217.873	218.644	1.00354
	transmembrane 9 superfamily protein member 3 precursor (sm-11044 binding protein) (ep70-p-iso). [swissprot;acc:q9hd45]	Low confidence	201.516	197.878	1.01839
2431	dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9]		201.946	198.301	1.01838
	proteasome subunit alpha type 2 (ec 3.4.25.1) (proteasome component c3) (macropain subunit c3) (multicatalytic endopeptidase complex subunit c3). [swissprot;acc:p25787]	High confidence	213.048	212.3	1.00352
2432	26s proteasome non-atpase regulatory subunit 6 (26s proteasome regulatory subunit s10) (p42a) (proteasome regulatory particle subunit p44s10). [swissprot;acc:q15008]		215.807	216.556	1.00347
	hexaprenyldihydroxybenzoate methyltransferase, mitochondrial precursor (ec 2.1.1.114) (dihydroxyhexaprenylbenzoate methyltransferase) (3,4- dihydroxy-5-hexaprenylbenzoate methyltransferase) (dhhb methyltransferase) (dhhb-mt) (dhhb-mtase). [swissprot;acc:q9nzj6]	Low confidence	198.399	194.819	1.01838
2433	elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720]	High confidence	217.366	218.117	1.00346
	putative sialoglycoprotease type 2. [refseq;acc:nm_022353]	Low confidence	200.495	196.876	1.01838
2434	cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941]		200.752	197.128
	methylenetetrahydrofolate reductase (ec 1.5.1.20). [swissprot;acc:p42898]	High confidence	213.021	212.286	1.00346
2435	serine/threonine protein kinase 23 (ec 2.7.1.37) (muscle-specific serine kinase 1) (mssk-1). [swissprot;acc:q9upe1]	Low confidence	202.421	198.77	1.01837
	zinc-finger protein zpr1 (zinc finger protein 259). [swissprot;acc:o75312]	High confidence	217.366	218.117	1.00346
2436	elongation factor 1-alpha 2 (ef-1-alpha-2) (elongation factor 1 a-2) (eef1a-2) (statin s1). [swissprot;acc:q05639]
	inositol hexaphosphate kinase 1. [refseq;acc:nm_153273]	Low confidence	199.117	195.526	1.01837
2437	guanylate kinase (ec 2.7.4.8) (gmp kinase). [swissprot;acc:q16774]	High confidence	219.361	220.116	1.00344
	programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737]	Low confidence	202.072	198.428	1.01836
2438	proteasome subunit alpha type 4 (ec 3.4.25.1) (proteasome component c9) (macropain subunit c9) (multicatalytic endopeptidase complex subunit c9) (proteasome subunit l). [swissprot;acc:p25789]	High confidence	214.049	213.323	1.0034
	sex comb on midleg homolog 1. [refseq;acc:nm_012236]	Low confidence	203.896	200.219	1.01836
2439	14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [swissprot;acc:p31946]	High confidence	220.681	221.425	1.00337
	j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330]	Low confidence	198.685	195.104	1.01835
2440	26s proteasome non-atpase regulatory subunit 3 (26s proteasome regulatory subunit s3) (proteasome subunit p58). [swissprot;acc:o43242]	High confidence	217.645	218.376	1.00336
	synaptosomal-associated protein 25 (snap-25) (super protein) (sup). [swissprot;acc:p13795]	Low confidence	198.68	195.1	1.01835
2441	dgcr8 protein (digeorge syndrome critical region 8). [swissprot;acc:q8wyq5]		198.685	195.104
	electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [swissprot;acc:p13804]	High confidence	180.137	180.732	1.0033
2442	ribonuclease iii (ec 3.1.26.3) (rnase iii) (p241). [swissprot;acc:q9nrr4]	Low confidence	198.685	195.104	1.01835
	transcription initiation factor tfiid 70 kda subunit (tafii-70) (tafii-80) (tafii80). [swissprot;acc:p49848]	High confidence	204.419	203.748	1.00329
2443	nadh-ubiquinone oxidoreductase b18 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b18) (ci-b18) (cell adhesion protein sqm1). [swissprot;acc:p17568]	Low confidence	198.685	195.104	1.01835
	ubiquitin-like protein sumo-1 conjugating enzyme (ec 6.3.2.19) (sumo- 1-protein ligase) (ubiquitin carrier protein) (ubiquitin-conjugating enzyme ubce2a) (p18). [swissprot;acc:p50550]	High confidence	217.073	216.364	1.00328
2444	zinc finger protein 288 (dendritic-derived btb/poz zinc finger protein). [swissprot;acc:q9hc78]		206.086	206.753	1.00324
	zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [swissprot;acc:p15822]	Low confidence	198.685	195.104	1.01835
2445	kruppel-related zinc finger protein hckrox. [refseq;acc:nm_015872]	High confidence	206.088	206.756	1.00324
	synaptosomal-associated protein 23 (snap-23) (vesicle-membrane fusion protein snap-23). [swissprot;acc:o00161]	Low confidence	198.68	195.1	1.01835
2446	epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [swissprot;acc:p07099]	High confidence	182.272	181.683	1.00324
	g protein-coupled receptor 142. [refseq;acc:nm_181790]	Low confidence	200.512	196.901	1.01834
2447	peroxisomal targeting signal 2 receptor (pts2 receptor) (peroxin-7). [swissprot;acc:o00628]	High confidence	206.084	206.752	1.00324
	ras gtpase-activating-like protein iqgap2. [swissprot;acc:q13576]	Low confidence	199.294	195.705	1.01834
2448	glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378]	High confidence	212.446	211.766	1.00321
	translation initiation factor eif-2b epsilon subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q13144]	Low confidence	200.578	196.965	1.01834
2449	histone-lysine n-methyltransferase, h3 lysine-9 specific 4 (ec 2.1.1.43) (histone h3-k9 methyltransferase 4) (h3-k9-hmtase 4) (set domain bifurcated 1) (erg-associated protein with set domain) (eset). [swissprot;acc:q15047]		203.547	199.882
	phosphatidate cytidylyltransferase 2 (ec 2.7.7.41) (cdp-diglyceride synthetase 2) (cdp-diglyceride pyrophosphorylase 2) (cdp- diacylglycerol synthase 2) (cds 2) (ctp:phosphatidate cytidylyltransferase 2) (cdp-dag synthase 2) (cdp-dg synthetase 2). [swissprot;acc:o95674]	High confidence	204.717	205.371	1.00319
2450	proteasome subunit beta type 6 precursor (ec 3.4.25.1) (proteasome delta chain) (macropain delta chain) (multicatalytic endopeptidase complex delta chain) (proteasome subunit y). [swissprot;acc:p28072]		213.85	213.177	1.00316
	quaking isoform 6. [sptrembl;acc:q9p0x9]	Low confidence	203.547	199.882	1.01834
2451	60s ribosomal protein l35a. [swissprot;acc:p18077]		200.987	197.369	1.01833
	secretory carrier-associated membrane protein 2. [swissprot;acc:o15127]	High confidence	204.688	205.333	1.00315
2452	ras gtpase-activating-like protein iqgap1 (p195). [swissprot;acc:p46940]	Low confidence	199.295	195.707	1.01833
	secretory carrier-associated membrane protein 3. [swissprot;acc:o14828]	High confidence	204.688	205.333	1.00315
2453	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Low confidence	197.86	201.487	1.01833
	secretory carrier-associated membrane protein 1. [swissprot;acc:o15126]	High confidence	204.688	205.332	1.00315
2454	ruvb-like 1 (ec 3.6.1.-) (49-kda tata box-binding protein-interacting protein) (49 kda tbp-interacting protein) (tip49a) (pontin 52) (nuclear matrix protein 238) (nmp 238) (54 kda erythrocyte cytosolic protein) (ecp-54) (tip60-associated protein 54-alpha) (tap54-alpha). [swissprot;acc:q9y265]	Low confidence	198.737	195.161	1.01832

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.