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 1008 to 1057 of 3228 in total

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

red	Rank	green	description	network_comparison
4725.79	2548	4824.4	60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403]	1.02087
	2549		splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [swissprot;acc:q07955]
	2550		amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [swissprot;acc:q06203]
	2551		sorting nexin 17. [swissprot;acc:q15036]
4726.38	765	5258.95	polymerase (dna directed) sigma; topoisomerase-related function protein 4-1; polymerase (dna-directed) sigma. [refseq;acc:nm_006999]	1.11268
4730.66	2440	4891.26	u3 snornp protein 4 homolog. [refseq;acc:nm_033416]	1.03395
4749.52	873	5237.77	programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737]	1.1028
4751.74	2458	4900.37	presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [swissprot;acc:q8tct8]	1.03128
	2459		gtp-binding nuclear protein ran (tc4) (ran gtpase) (androgen receptor- associated protein 24). [swissprot;acc:p17080]
	2460		presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7]
4757.46	1044	5198.91	mbd2 (methyl-cpg-binding protein)-interacting zinc finger protein. [refseq;acc:nm_015517]	1.09279
	1046		skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [swissprot;acc:q9nzq9]
	1047		ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9]
	1048		tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [swissprot;acc:p28289]
	1049		sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1]
	1050		neuronal tropomodulin (n-tmod) (tropomodulin 2). [swissprot;acc:q9nzr1]
	1051		homeobox protein dlx-2. [swissprot;acc:q07687]
	1052		homeobox protein dlx-5. [swissprot;acc:p56178]
	1053		fetal brain protein 239 (239fb). [swissprot;acc:q15777]
	1054		homeobox protein dlx-3. [swissprot;acc:o60479]
	1055		activated p21cdc42hs kinase. [refseq;acc:nm_005781]
	1056		mitogen-activated protein kinase kinase kinase 7 interacting protein 2 isoform 1; tak1-binding protein 2. [refseq;acc:nm_015093]
4763.99	2546	4868.66	dna-directed rna polymerase ii 14.5 kda polypeptide (ec 2.7.7.6) (rpb9) (rpb14.5). [swissprot;acc:p36954]	1.02197
4771.21	207	5961.43	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]	1.24946
4775.11	527	5438.18	protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688]	1.13886
4775.25	1332	5158.86	my016 protein. [sptrembl;acc:q9h3k6]	1.08033
4778.28	2646	4732.13	mct-1 protein. [refseq;acc:nm_014060]	1.00975
	2647		mitochondrial ribosomal protein l22. [refseq;acc:nm_014180]
4783.49	1806	5097.66	pyruvate kinase, m1 isozyme (ec 2.7.1.40) (pyruvate kinase muscle isozyme) (cytosolic thyroid hormone-binding protein) (cthbp) (thbp1). [swissprot;acc:p14618]	1.06568
4800.81	78	7132.71	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	1.48573
4806.33	2126	5066.92	40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677]	1.05422
4806.38	2125	5067	ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920]
4808.79	200	6074.21	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945]	1.26315
4810.22	201	6075.04	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991]	1.26294
4810.71	645	5413.89	glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [swissprot;acc:p30711]	1.12538
4810.85	641	5414.21	peroxisomal n1-acetyl-spermine/spermidine oxidase. [refseq;acc:nm_152911]	1.12542
	642	5414.23	atpase inhibitor, mitochondrial precursor. [swissprot;acc:q9uii2]
	643		polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [refseq;acc:nm_019025]
	644	5414.22	cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [swissprot;acc:p53701]
4811.02	640	5414.64	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712]	1.12547
4812.01	202	6076.09	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]	1.26269
4813.13	2025	5091.36	candidate tumor suppressor in ovarian cancer 2. [refseq;acc:nm_080822]	1.05781
4824.49	2743	4813.92	60s acidic ribosomal protein p2. [swissprot;acc:p05387]	1.0022
4835.55	1244	5243.23	sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538]	1.08431
	1245		casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862]
4846.16	1108	5283.08	rrp5 protein homolog (programmed cell death protein 11). [swissprot;acc:q14690]	1.09016
4855.46	304	5824.52	pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629]	1.19958
4857.03	2418	5039.78	60s acidic ribosomal protein p1. [swissprot;acc:p05386]	1.03763
	2419		thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [refseq;acc:nm_032243]
	2420		thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [swissprot;acc:p10599]

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.