Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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

Results: HTML CSV LaTeX

Showing element 2280 to 2329 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
285	williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71]	Squared	0	208.691	170.202	1.22614
286	clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675]	Measured		5497.01	6127.24	1.11465
	dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832]	Ranked		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]	Ranked	1	224.633	203.251	1.1052
	exocyst complex component sec5. [swissprot;acc:q96kp1]	Measured	1	23316	19288.8	1.20878
	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932]	Rooted	0	54.8943	59.4407	1.08282
	glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [swissprot;acc:p32189]	Squared	0	188.588	231.109	1.22547
	smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527]	Rooted	1	51.8717	46.3287	1.11965
	t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492]	Squared		6693.64	8564.94	1.27956
287	40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47]	Ranked		240.758	266.079	1.10517
	5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196]	Measured	0	726.245	808.929	1.11385
	glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14409]	Squared	0	188.452	230.941	1.22546
	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]	Squared	1	6693.64	8564.94	1.27956
	likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	Rooted	1	51.8714	46.3281	1.11965
	peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521]	Rooted	0	34.7164	32.0874	1.08193
	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3]	Measured	1	23303.1	19279.5	1.2087
	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]	Ranked	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
	cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6]	Measured	1	23422.4	19380.3	1.20857
	glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410]	Squared	0	188.176	230.603	1.22546
	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559]	Squared	1	6693.64	8564.94	1.27956
	likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	Measured	0	1293.73	1161.64	1.11371
	lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461]	Rooted	1	51.8789	46.3416	1.11949
	my016 protein. [sptrembl;acc:q9h3k6]	Rooted	0	37.7009	34.862	1.08143
289	cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]	Squared		5868.74	4797.35	1.22333
	dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832]	Rooted		28.6008	30.8974	1.0803
	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488]	Ranked		15147.2	14091.9	1.07489
	hpaii tiny fragments locus 9c. [refseq;acc:nm_022727]	Ranked	1	272.781	246.892	1.10486
	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]	Squared		6693.64	8564.94	1.27956
	pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629]	Rooted		57.4274	64.2609	1.11899
	tubby protein homolog. [swissprot;acc:p50607]	Measured	0	3797.57	4228.27	1.11341
	u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8]	Measured	1	4682.88	5646.19	1.20571
290	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298]	Squared		15734.4	20126.8	1.27916
	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	Rooted		75.6323	67.6572	1.11788
	atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031]	Rooted	0	22.6917	24.5013	1.07975
	dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880]	Measured		1370.82	1525.56	1.11288
	integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [swissprot;acc:p05106]	Squared		6188.69	7568.12	1.2229
	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123]	Ranked		15147.2	14091.9	1.07489
	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350]	Ranked	1	231.969	210.064	1.10428
	tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9]	Measured	1	4991.48	6014.08	1.20487
291	far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [refseq;acc:nm_003902]	Ranked	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]	Ranked	1	251.679	228.037	1.10368
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Measured	1	44490.5	36927.5	1.20481
	similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9]	Measured	0	1961.09	2179.77	1.11151
	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	Rooted		136.763	147.411	1.07786
	swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [refseq;acc:nm_003075]	Squared		1021.12	1246	1.22023
	tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452]	Squared	1	59016.1	75486.9	1.27909
	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	Rooted		113.983	101.979	1.11771
292	40s ribosomal protein s15a. [swissprot;acc:p39027]	Ranked		241.411	266.414	1.10357

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.

- http://analysis.yellowcouch.org/