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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 2001 to 2050 of 12912 in total

Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
501	cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [source:swissprot;acc:p08574]	Ranked	238.704	255.68	1.07112	
501	dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [source:swissprot;acc:o95602]	Rooted	50.4253	46.1792	1.09195	
501	glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [source:swissprot;acc:q99259]	Measured	4682.87	4093.05	1.1441	
501	vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [source:swissprot;acc:q9ubq0]	Squared	30286.5	36362	1.2006	
502	60s ribosomal protein l30. [source:swissprot;acc:p04645]	Rooted	50.4616	46.2257	1.09164	
502	numb-like protein (numb-r). [source:swissprot;acc:q9y6r0]	Squared	30286.5	36362	1.2006	
502	oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [source:swissprot;acc:q9una1]	Ranked	238.704	255.68	1.07112	
502	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [source:swissprot;acc:p23921]	Measured	6913.6	7907.05	1.1437	
503	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [source:refseq;acc:nm_006333]	Rooted	177.987	194.29	1.0916	
503	senescence marker protein-30 (smp-30) (regucalcin) (rc). [source:swissprot;acc:q15493]	Ranked	238.704	255.68	1.07112	
503	tubby related protein 3 (tubby-like protein 3). [source:swissprot;acc:o75386]	Squared	30286.5	36362	1.2006	
503	tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [source:swissprot;acc:q13625]	Measured	15182.5	13277.9	1.14344	
504	enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [source:swissprot;acc:p30084]	Measured	10067.9	11511	1.14334	
504	oligophrenin 1. [source:swissprot;acc:o60890]	Ranked	238.704	255.68	1.07112	
504	ras-related gtp binding a; ras-related gtp-binding protein. [source:refseq;acc:nm_006570]	Rooted	144.606	157.824	1.09141	
504	vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [source:swissprot;acc:q96qk1]	Squared	30286.5	36362	1.2006	
505	ad24 protein. [source:refseq;acc:nm_022451]	Ranked	251.334	234.672	1.071	
505	protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [source:swissprot;acc:q05513]	Squared	30286.5	36362	1.2006	
505	ras-related gtp binding c; rag c protein. [source:refseq;acc:nm_022157]	Rooted	144.606	157.824	1.09141	
505	signal transduction protein cbl-b (sh3-binding protein cbl-b). [source:swissprot;acc:q13191]	Measured	6856.71	7838.3	1.14316	
506	eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [source:swissprot;acc:p56537]	Measured	3893.85	4450.98	1.14308	
506	inhibitor of growth family, member 1; inhibitor of growth 1. [source:refseq;acc:nm_005537]	Ranked	224.535	240.476	1.071	
506	ras-related gtp binding b short isoform; gtp-binding protein ragb. [source:refseq;acc:nm_006064]	Rooted	144.606	157.824	1.09141	
506	vav-2 protein. [source:swissprot;acc:p52735]	Squared	31377.3	37670.1	1.20055	
507	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [source:refseq;acc:nm_018685]	Rooted	144.606	157.824	1.09141	
507	cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [source:swissprot;acc:p22681]	Measured	6875.08	7858.38	1.14302	
507	puromycin-sensitive aminopeptidase (ec 3.4.11.-) (psa). [source:swissprot;acc:p55786]	Squared	23512.2	28206.2	1.19964	
507	wd-repeat protein 12 (ytm1 homolog). [source:swissprot;acc:q9gzl7]	Ranked	251.299	234.729	1.07059	
508	1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [source:swissprot;acc:o15120]	Measured	7556.75	8636.87	1.14293	
508	autoantigen ngp-1. [source:swissprot;acc:q13823]	Rooted	49.4756	53.9896	1.09124	
508	leukotriene a-4 hydrolase (ec 3.3.2.6) (lta-4 hydrolase) (leukotriene a(4) hydrolase). [source:swissprot;acc:p09960]	Squared	23512.2	28206.2	1.19964	
508	mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [source:swissprot;acc:p15088]	Ranked	177.698	190.24	1.07058	
509	1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [source:swissprot;acc:q99943]	Measured	7551.8	8630.06	1.14278	
509	60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [source:swissprot;acc:q9y3b7]	Rooted	50.2583	46.057	1.09122	
509	carboxypeptidase b precursor. [source:refseq;acc:nm_020361]	Ranked	177.698	190.239	1.07057	
509	dihydroorotate dehydrogenase, mitochondrial precursor (ec 1.3.3.1) (dihydroorotate oxidase) (dhodehase) (fragment). [source:swissprot;acc:q02127]	Squared	23512.2	28206.2	1.19964	
510	growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [source:swissprot;acc:p29354]	Measured	5975.11	6826.24	1.14245	
510	plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [source:refseq;acc:nm_001872]	Ranked	177.699	190.24	1.07057	
510	protein phosphatase 1, regulatory subunit 7; sds22. [source:refseq;acc:nm_002712]	Rooted	149.397	136.972	1.09071	
510	transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [source:swissprot;acc:q92994]	Squared	17281.7	20723	1.19913	
511	nucleolar protein family a, member 1; gar1 protein. [source:refseq;acc:nm_018983]	Squared	17281.7	20723	1.19913	
511	proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [source:swissprot;acc:p46087]	Ranked	250.053	233.725	1.06986	
511	serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [source:swissprot;acc:p51955]	Measured	5975.11	6826.24	1.14245	
511	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [source:refseq;acc:nm_003169]	Rooted	50.5979	46.392	1.09066	
512	block of proliferation 1. [source:swissprot;acc:q14137]	Ranked	250.794	234.433	1.06979	
512	cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [source:swissprot;acc:p35520]	Squared	19987.6	23960.7	1.19878	
512	protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [source:swissprot;acc:o75688]	Rooted	56.3798	61.4858	1.09056	
512	small glutamine rich protein with tetratricopeptide repeats 2. [source:refseq;acc:nm_019072]	Measured	10807.4	12338.5	1.14167	
513	1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [source:swissprot;acc:q9nrz7]	Measured	7485.08	8543.66	1.14143	
513	60s ribosomal protein l4 (l1). [source:swissprot;acc:p36578]	Rooted	51.5881	47.3127	1.09036	

Legend:
- Rank is the rank after comparing the two networks
- 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/