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 536 to 585 of 3730 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence

Rank	description	Filtered	red	green	network_comparison
268	maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168]	0	14257.4	13134.5	1.08549
269	cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585]	1	241.373	267.352	1.10763
	ischemia/reperfusion inducible protein. [refseq;acc:nm_024640]	0	12463.5	11482.6	1.08542
270	ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447]		10735.1	9891.37	1.0853
	fad synthetase. [refseq;acc:nm_025207]	1	241.373	267.352	1.10763
271	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340]
	myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829]	0	10735.1	9891.37	1.0853
272	ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214]	1	241.373	267.352	1.10763
	sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772]	0	7163.55	7759.61	1.08321
273	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252]	1	241.373	267.352	1.10763
	wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6]	0	12748.1	11770.9	1.08302
274	disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6]		10432.4	11298.4	1.08301
	nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435]	1	241.373	267.352	1.10763
275	cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3]
	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]	0	10783	11674.1	1.08264
276	60s ribosomal protein l32. [swissprot;acc:p02433]	1	241.13	266.969	1.10716
	60s ribosomal protein l9. [swissprot;acc:p32969]	0	10741.6	9922.33	1.08257
277	40s ribosomal protein s29. [swissprot;acc:p30054]	1	241.849	267.642	1.10665
	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	0	11096.8	10251.6	1.08245
278	40s ribosomal protein s11. [swissprot;acc:p04643]	1	241.399	267.088	1.10642
	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	0	11644	10763.4	1.08181
279	anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5]		10614.2	9812.39	1.08171
	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576]	1	252.644	228.42	1.10605
280	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]	0	10620.1	11471.2	1.08014
	metastasis-associated protein mta1. [swissprot;acc:q13330]	1	252.512	228.356	1.10578
281	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]		241.808	267.335	1.10557
	phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6]	0	12522.7	13514.5	1.0792
282	chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028]	1	252.39	228.297	1.10553
	sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961]	0	8095.69	8732.68	1.07868
283	60s ribosomal protein l11. [swissprot;acc:p39026]	1	241.828	267.346	1.10552
	lifeguard; kiaa0950 protein. [refseq;acc:nm_012306]	0	11107.1	11959.2	1.07672
284	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945]	1	224.657	203.235	1.10541
	tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677]	0	14898.9	16041.6	1.0767
285	dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9]		10686	9925.58	1.07661
	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991]	1	224.647	203.242	1.10532
286	dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832]	0	12228.2	11367.3	1.07573
	enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511]	1	224.633	203.251	1.1052
287	40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47]		240.758	266.079	1.10517
	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]	0	17842.7	16590.3	1.07549
288	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]	1	240.758	266.078	1.10517
	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]	0	14930.6	16053	1.07517
289	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488]		15147.2	14091.9	1.07489
	hpaii tiny fragments locus 9c. [refseq;acc:nm_022727]	1	272.781	246.892	1.10486
290	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123]	0	15147.2	14091.9	1.07489
	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350]	1	231.969	210.064	1.10428
291	far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [refseq;acc:nm_003902]	0	10922.9	11731.8	1.07406
	nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208]	1	251.679	228.037	1.10368
292	40s ribosomal protein s15a. [swissprot;acc:p39027]		241.411	266.414	1.10357
	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260]	0	10280.5	9574.98	1.07368
293	60s ribosomal protein l23 (l17). [swissprot;acc:p23131]	1	240.782	265.717	1.10356

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.