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

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Showing element 958 to 1007 of 3228 in total

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

red	green	Rank	description	network_comparison
4579.34	5940.64	173	breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]	1.29727
4582.38	4649.17	2629	dna-directed rna polymerase ii 14.4 kda polypeptide (ec 2.7.7.6) (rpb6) (rpb14.4) (rpabc2). [swissprot;acc:p41584]	1.01458
4585.86	4753.26	2433	mitochondrial 60s ribosomal protein l27 (l27mt) (hspc250). [swissprot;acc:q9p0m9]	1.0365
4590.18	5575.52	269	u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777]	1.21466
4590.74	4879.11	1897	thioredoxin-like; pkc-interacting cousin of thioredoxin. [refseq;acc:nm_006541]	1.06282
4591.08	4621.88	2666	dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832]	1.00671
4598.21	5500.48	312	u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45]	1.19622
4599.26	3058.57	76	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154]	1.50373
4608.54	4576.35	2663	microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2]	1.00703
4608.91	4576.78	2664	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]	1.00702
4612.39	3093.6	77	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153]	1.49095
4619.81	4965.45	1492	dna replication licensing factor mcm3 (dna polymerase alpha holoenzyme-associated protein p1) (rlf beta subunit) (p102 protein) (p1-mcm3). [swissprot;acc:p25205]	1.07482
		1494	kelch-like ech-associated protein 1 (cytosolic inhibitor of nrf2). [swissprot;acc:q14145]
4620.76	5501.94	323	u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0]	1.1907
4632.65	4892.66	2069	dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0]	1.05613
4633.48	5084.24	948	caspase-7 precursor (ec 3.4.22.-) (ice-like apoptotic protease 3) (ice-lap3) (apoptotic protease mch-3) (cmh-1). [swissprot;acc:p55210]	1.09728
		949	apopain precursor (ec 3.4.22.-) (cysteine protease cpp32) (yama protein) (cpp-32) (caspase-3) (casp-3) (srebp cleavage activity 1) (sca-1). [swissprot;acc:p42574]
4633.92	5572.85	298	u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333]	1.20262
4638.1	5923.4	191	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533]	1.27712
4640.26	5704.87	242	max protein. [swissprot;acc:p25912]	1.22943
4641.09	5588.75	292	nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384]	1.20419
		293	nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2]
4644.04	4470.47	2412	dynactin 4. [refseq;acc:nm_032486]	1.03883
4644.58	4892.06	2148	deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [swissprot;acc:p32321]	1.05328
4651.88	5296.78	531	transcription initiation factor iib (general transcription factor tfiib) (s300-ii). [swissprot;acc:q00403]	1.13863
		532	thyroid receptor interacting protein 3 (trip-3) (fragment). [swissprot;acc:q15649]
		533	nhp2-like protein 1 (high mobility group-like nuclear protein 2 homolog 1) ([u4/u6.u5] tri-snrnp 15.5 kda protein) (otk27). [swissprot;acc:p55769]
		534	nuclear fragile x mental retardation protein interacting protein 1; nuclear fragile x mental retardation intercating protein 1; nuclear fragile x mental retardation protein-interacting protein 1. [refseq;acc:nm_012345]
4668.29	4868.52	2371	dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [swissprot;acc:p52435]	1.04289
4673.96	4876.71	2362	dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959]	1.04338
4674.38	4877.31	2361	dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325]	1.04341
4682.87	4093.05	496	nostrin. [refseq;acc:nm_052946]	1.1441
		497	eap30 subunit of ell complex. [refseq;acc:nm_007241]
		498	liv-1 protein, estrogen regulated. [refseq;acc:nm_012319]
		499	glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329]
		500	gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747]
		501	glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259]
4682.88	5646.19	289	u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8]	1.20571
4689.78	4973.44	1956	nin one binding protein; adenocarcinoma antigen recognized by t lymphocytes 4. [refseq;acc:nm_014062]	1.06048
4700.42	5492.63	375	u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116]	1.16854
4708.61	5226.71	805	60s ribosomal protein l39. [swissprot;acc:p02404]	1.11003
		806	60s ribosomal protein l18a. [swissprot;acc:q02543]
		807	40s ribosomal protein s19. [swissprot;acc:p39019]
		808	60s ribosomal protein l31. [swissprot;acc:p12947]
4708.68	4702.58	2747	putatative 28 kda protein. [refseq;acc:nm_020143]	1.0013
4708.98	4817.39	2542	osteoclast stimulating factor 1. [swissprot;acc:q92882]	1.02302
4713.58	4279.17	900	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902]	1.10152
4714.85	5554.38	349	putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143]	1.17806
4723.53	5828.46	236	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834]	1.23392
4725.28	5261.06	756	topoisomerase-related function protein 4-2. [refseq;acc:nm_022447]	1.11339

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.