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 2258 to 2307 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
283	60s ribosomal protein l23a. [swissprot;acc:p29316]	Squared	0	2784.77	3420.27	1.22821
	deltex 2. [refseq;acc:nm_020892]	Squared	1	6627.24	8484.19	1.2802
	krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887]	Rooted	1	57.9819	64.9302	1.11984
	lifeguard; kiaa0950 protein. [refseq;acc:nm_012306]	Ranked	0	11107.1	11959.2	1.07672
	lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776]	Measured	0	841.301	753.849	1.11601
	polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195]	Measured	1	5221.28	6314.35	1.20935
	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921]	Rooted	0	41.5652	38.2237	1.08742
284	60s ribosomal protein l23 (l17). [swissprot;acc:p23131]	Measured		1753.85	1956.36	1.11547
	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]	Rooted		21.8814	23.792	1.08732
	c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596]	Squared	1	59464	76120.8	1.28012
	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	Squared	0	2785.55	3421.01	1.22813
	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945]	Ranked	1	224.657	203.235	1.10541
	cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291]	Rooted		51.8647	46.3161	1.1198
	paxillin. [swissprot;acc:p49023]	Measured		5221.28	6314.35	1.20935
	tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677]	Ranked	0	14898.9	16041.6	1.0767
285	40s ribosomal protein s28. [swissprot;acc:p25112]	Rooted	0	13.5612	12.5026	1.08467
	atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072]	Rooted	1	48.4278	54.2262	1.11973
	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	Squared	1	6680.89	8549.44	1.27969
	dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9]	Measured	0	2698.62	3010.22	1.11547
		Ranked	0	10686	9925.58	1.07661
	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003]	Measured	1	23326.5	19296.4	1.20885
	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991]	Ranked	1	224.647	203.242	1.10532
	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

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/