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

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Showing element 1 to 50 of 38536 in total

green	0.00001
Filtered	0
Network Comparison Type	Divided

Value Type	description	Rank	Interaction Map	network_comparison	red	
Measured	brca1 associated protein. [source:refseq;acc:nm_006768]	502	High confidence	1	0.00001	
Measured	carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [source:refseq;acc:nm_021615]	22	Low confidence	3700000	37	
Measured	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [source:refseq;acc:nm_004267]	23	Low confidence	3700000	37	
Measured	cobw-like protein. [source:refseq;acc:nm_018491]	839	Low confidence	1	0.00001	
Measured	dok-like protein. [source:refseq;acc:nm_024872]	31	High confidence	3500000	35	
Measured	ero1-like. [source:refseq;acc:nm_014584]	20	High confidence	8200000	82	
Measured	gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [source:refseq;acc:nm_080920]	838	Low confidence	1	0.00001	
Measured	gamma-glutamyltransferase. [source:sptrembl;acc:q14390]	841	Low confidence	1	0.00001	
Measured	gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [source:swissprot;acc:p19440]	842	Low confidence	1	0.00001	
Measured	gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [source:swissprot;acc:p36268]	837	Low confidence	1	0.00001	
Measured	gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [source:swissprot;acc:p36269]	843	Low confidence	1	0.00001	
Measured	h2a histone family, member j isoform 1. [source:refseq;acc:nm_018267]	501	High confidence	1	0.00001	
Measured	histone h2a.a (h2a/a) (h2a.2). [source:swissprot;acc:p28001]	495	High confidence	1	0.00001	
Measured	histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [source:swissprot;acc:p02261]	494	High confidence	1	0.00001	
Measured	histone h2a; h2a histone family, member r. [source:refseq;acc:nm_170745]	497	High confidence	1	0.00001	
Measured	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [source:swissprot;acc:q93099]	6	Low confidence	1300000	13	
Measured	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [source:swissprot;acc:q93099]	499	High confidence	1	0.00001	
Measured	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	1	High confidence	36400000	364	
Measured	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	1	Low confidence	36400000	364	
Measured	mitochondrial 28s ribosomal protein s6 (mrp-s6). [source:swissprot;acc:p82932]	496	High confidence	1	0.00001	
Measured	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [source:swissprot;acc:p46531]	44	Low confidence	28600000	286	
Measured	neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [source:swissprot;acc:q04721]	45	Low confidence	28600000	286	
Measured	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	95	High confidence	15400000	154	
Measured	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [source:refseq;acc:nm_007372]	65	High confidence	1800000	18	
Measured	rwd domain containing 1; ptd013 protein; cgi-24 protein. [source:refseq;acc:nm_015952]	500	High confidence	1	0.00001	
Measured	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [source:refseq;acc:nm_032517]	22	High confidence	6000000	60	
Measured	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [source:refseq;acc:nm_007063]	7	Low confidence	231962	2.31962	
Measured	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [source:swissprot;acc:q9bq87]	96	High confidence	15400000	154	
Measured	translin-associated protein x (translin-associated factor x). [source:swissprot;acc:q99598]	498	High confidence	1	0.00001	
Measured	translin-associated protein x (translin-associated factor x). [source:swissprot;acc:q99598]	840	Low confidence	1	0.00001	
Ranked	brca1 associated protein. [source:refseq;acc:nm_006768]	502	High confidence	1	0.00001	
Ranked	cobw-like protein. [source:refseq;acc:nm_018491]	839	Low confidence	1	0.00001	
Ranked	gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [source:refseq;acc:nm_080920]	838	Low confidence	1	0.00001	
Ranked	gamma-glutamyltransferase. [source:sptrembl;acc:q14390]	841	Low confidence	1	0.00001	
Ranked	gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [source:swissprot;acc:p19440]	842	Low confidence	1	0.00001	
Ranked	gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [source:swissprot;acc:p36268]	837	Low confidence	1	0.00001	
Ranked	gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [source:swissprot;acc:p36269]	843	Low confidence	1	0.00001	
Ranked	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [source:swissprot;acc:q93099]	501	High confidence	1	0.00001	
Squared	brca1 associated protein. [source:refseq;acc:nm_006768]	502	High confidence	1	0.00001	
Squared	carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [source:refseq;acc:nm_021615]	5	Low confidence	32402.4	0.324024	
Squared	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [source:refseq;acc:nm_004267]	6	Low confidence	32402.4	0.324024	
Squared	cobw-like protein. [source:refseq;acc:nm_018491]	839	Low confidence	1	0.00001	
Squared	dok-like protein. [source:refseq;acc:nm_024872]	13	High confidence	28994.1	0.289941	
Squared	ero1-like. [source:refseq;acc:nm_014584]	8	High confidence	159148	1.59148	
Squared	gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [source:refseq;acc:nm_080920]	838	Low confidence	1	0.00001	
Squared	gamma-glutamyltransferase. [source:sptrembl;acc:q14390]	841	Low confidence	1	0.00001	
Squared	gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [source:swissprot;acc:p19440]	842	Low confidence	1	0.00001	
Squared	gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [source:swissprot;acc:p36268]	837	Low confidence	1	0.00001	
Squared	gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [source:swissprot;acc:p36269]	843	Low confidence	1	0.00001	
Squared	h2a histone family, member j isoform 1. [source:refseq;acc:nm_018267]	501	High confidence	1	0.00001	

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/