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

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Showing element 1158 to 1207 of 3228 in total

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

red	Rank	green	description	network_comparison
5076.73	2205	5326.29	ww domain binding protein 11; npw38-binding protein npwbp; sh3 domain-binding protein snp70. [refseq;acc:nm_016312]	1.04916
	2206		elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [refseq;acc:nm_018127]
	2207		rna-binding protein 5 (rna binding motif protein 5) (putative tumor suppressor luca15) (g15 protein). [swissprot;acc:p52756]
5078.5	2402	5275.76	40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865]	1.03884
	2403		40s ribosomal protein s21. [swissprot;acc:p35265]
	2404		cytoplasmic antiproteinase 3 (cap3) (cap-3) (protease inhibitor 9) (serpin b9). [swissprot;acc:p50453]
	2405		maspin precursor (protease inhibitor 5). [swissprot;acc:p36952]
	2406		bomapin (protease inhibitor 10) (serpin b10). [swissprot;acc:p48595]
	2407		plasminogen activator inhibitor-2 precursor (pai-2) (placental plasminogen activator inhibitor) (monocyte arg-serpin) (urokinase inhibitor). [swissprot;acc:p05120]
	2408		serpin b11. [swissprot;acc:q96p15]
	2409		placental thrombin inhibitor (cytoplasmic antiproteinase) (cap) (protease inhibitor 6) (pi-6). [swissprot;acc:p35237]
	2410		cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452]
	2411		leukocyte elastase inhibitor (lei) (monocyte/neutrophil elastase inhibitor) (m/nei) (ei). [swissprot;acc:p30740]
5082.66	368	5959.99	pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508]	1.17261
5084.26	398	5904.1	xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7]	1.16125
5096.02	1797	5432.63	valyl-trna synthetase 2 (ec 6.1.1.9) (valine--trna ligase 2) (valrs 2) (g7a). [swissprot;acc:p26640]	1.06605
5106.13	1574	5472.96	atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031]	1.07184
	1575		dna polymerase delta p38 subunit. [refseq;acc:nm_015584]
5110.6	996	5596.73	methionyl-trna formyltransferase, mitochondrial precursor (ec 2.1.2.9) (mtfmt). [swissprot;acc:q96dp5]	1.09512
5114.15	2461	5272.92	phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [swissprot;acc:o15067]	1.03105
	2462		bifunctional purine biosynthesis protein purh [includes: phosphoribosylaminoimidazolecarboxamide formyltransferase (ec 2.1.2.3) (aicar transformylase); imp cyclohydrolase (ec 3.5.4.10) (inosinicase) (imp synthetase) (atic)]. [swissprot;acc:p31939]
	2463		multifunctional protein ade2 [includes: phosphoribosylaminoimidazole- succinocarboxamide synthase (ec 6.3.2.6) (saicar synthetase); phosphoribosylaminoimidazole carboxylase (ec 4.1.1.21) (air carboxylase) (airc)]. [swissprot;acc:p22234]
5117.85	1445	5510.45	cd109; gov system alloantigens on platelets. [refseq;acc:nm_133493]	1.07671
	1446		peptidyl-prolyl cis-trans isomerase nima-interacting 1 (ec 5.2.1.8) (rotamase pin1) (ppiase pin1). [swissprot;acc:q13526]
	1447		iroquois-class homeodomain protein irx-4 (iroquois homeobox protein 4). [swissprot;acc:p78413]
5123.89	2334	5350.78	lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428]	1.04428
	2335		microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [swissprot;acc:q15005]
	2336		uridine 5'-monophosphate synthase (ump synthase) [includes: orotate phosphoribosyltransferase (ec 2.4.2.10) (oprtase); orotidine 5'- phosphate decarboxylase (ec 4.1.1.23) (ompdecase)]. [swissprot;acc:p11172]
	2337		cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294]
	2338		bactericidal permeability-increasing protein precursor (bpi) (cap 57). [swissprot;acc:p17213]
	2339		phospholipid transfer protein precursor (lipid transfer protein ii). [swissprot;acc:p55058]
5132.68	1231	5569.54	probable dimethyladenosine transferase (ec 2.1.1.-) (s- adenosylmethionine-6-n',n'-adenosyl(rrna) dimethyltransferase) (18s rrna dimethylase). [swissprot;acc:q9unq2]	1.08511
5136.78	120	6895.98	high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339]	1.34247
5140.14	122	6893.53	high-mobility group 20a. [refseq;acc:nm_018200]	1.34112
5144.74	997	5634	nucleolar protein family a, member 2; component of the h/aca snornp. [refseq;acc:nm_017838]	1.0951
	998		transcription initiation factor iif, alpha subunit (tfiif-alpha) (transcription initiation factor rap74). [swissprot;acc:p35269]
5147.9	990	5641.25	dead-box protein 4 (vasa homolog). [swissprot;acc:q9nqi0]	1.09584
5148.71	611	5811.74	dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409]	1.12878
5148.88	2262	5386.34	similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9]	1.04612
5150.14	2260	5387.84	block 23. [sptrembl;acc:q8nhw5]	1.04615
5150.31	2258	5388.05	60s acidic ribosomal protein p0 (l10e). [swissprot;acc:p05388]	1.04616
5162.27	1570	5534.71	n-acetylglutamate synthase. [refseq;acc:nm_153006]	1.07215
5162.52	617	5822.47	dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576]	1.12783
5166.04	880	5694.55	peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	1.1023
5167.15	884	5695.44	mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352]	1.10224
5167.88	647	4594.43	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4]	1.12481
5168.01	885	5696.12	mitochondrial translational release factor 1-like. [refseq;acc:nm_019041]	1.10219
5168.43	651	4597.44	ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6]	1.1242
	652		short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62]
5171.45	1936	5486.96	williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645]	1.06101

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.