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

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Showing element 1 to 50 of 38536 in total

Filtered	0
green	0.00001
Network Comparison Type	Divided

description	Value Type	network_comparison	Rank	Interaction Map	red	
brca1 associated protein. [source:refseq;acc:nm_006768]	Measured	1	502	High confidence	0.00001	
brca1 associated protein. [source:refseq;acc:nm_006768]	Ranked	1	502	High confidence	0.00001	
brca1 associated protein. [source:refseq;acc:nm_006768]	Squared	1	502	High confidence	0.00001	
brca1 associated protein. [source:refseq;acc:nm_006768]	Rooted	1	502	High confidence	0.00001	
carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [source:refseq;acc:nm_021615]	Measured	3700000	22	Low confidence	37	
carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [source:refseq;acc:nm_021615]	Squared	32402.4	5	Low confidence	0.324024	
carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [source:refseq;acc:nm_021615]	Rooted	608276	6	Low confidence	6.08276	
carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [source:refseq;acc:nm_004267]	Measured	3700000	23	Low confidence	37	
carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [source:refseq;acc:nm_004267]	Squared	32402.4	6	Low confidence	0.324024	
carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [source:refseq;acc:nm_004267]	Rooted	608276	7	Low confidence	6.08276	
cobw-like protein. [source:refseq;acc:nm_018491]	Measured	1	839	Low confidence	0.00001	
cobw-like protein. [source:refseq;acc:nm_018491]	Ranked	1	839	Low confidence	0.00001	
cobw-like protein. [source:refseq;acc:nm_018491]	Squared	1	839	Low confidence	0.00001	
cobw-like protein. [source:refseq;acc:nm_018491]	Rooted	1	839	Low confidence	0.00001	
dok-like protein. [source:refseq;acc:nm_024872]	Measured	3500000	31	High confidence	35	
dok-like protein. [source:refseq;acc:nm_024872]	Squared	28994.1	13	High confidence	0.289941	
dok-like protein. [source:refseq;acc:nm_024872]	Rooted	591608	13	High confidence	5.91608	
ero1-like. [source:refseq;acc:nm_014584]	Measured	8200000	20	High confidence	82	
ero1-like. [source:refseq;acc:nm_014584]	Squared	159148	8	High confidence	1.59148	
ero1-like. [source:refseq;acc:nm_014584]	Rooted	905539	8	High confidence	9.05539	
gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [source:refseq;acc:nm_080920]	Measured	1	838	Low confidence	0.00001	
gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [source:refseq;acc:nm_080920]	Ranked	1	838	Low confidence	0.00001	
gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [source:refseq;acc:nm_080920]	Squared	1	838	Low confidence	0.00001	
gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [source:refseq;acc:nm_080920]	Rooted	1	838	Low confidence	0.00001	
gamma-glutamyltransferase. [source:sptrembl;acc:q14390]	Measured	1	841	Low confidence	0.00001	
gamma-glutamyltransferase. [source:sptrembl;acc:q14390]	Ranked	1	841	Low confidence	0.00001	
gamma-glutamyltransferase. [source:sptrembl;acc:q14390]	Squared	1	841	Low confidence	0.00001	
gamma-glutamyltransferase. [source:sptrembl;acc:q14390]	Rooted	1	841	Low confidence	0.00001	
gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [source:swissprot;acc:p19440]	Measured	1	842	Low confidence	0.00001	
gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [source:swissprot;acc:p19440]	Ranked	1	842	Low confidence	0.00001	
gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [source:swissprot;acc:p19440]	Squared	1	842	Low confidence	0.00001	
gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [source:swissprot;acc:p19440]	Rooted	1	842	Low confidence	0.00001	
gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [source:swissprot;acc:p36268]	Measured	1	837	Low confidence	0.00001	
gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [source:swissprot;acc:p36268]	Ranked	1	837	Low confidence	0.00001	
gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [source:swissprot;acc:p36268]	Squared	1	837	Low confidence	0.00001	
gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [source:swissprot;acc:p36268]	Rooted	1	837	Low confidence	0.00001	
gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [source:swissprot;acc:p36269]	Measured	1	843	Low confidence	0.00001	
gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [source:swissprot;acc:p36269]	Ranked	1	843	Low confidence	0.00001	
gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [source:swissprot;acc:p36269]	Squared	1	843	Low confidence	0.00001	
gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [source:swissprot;acc:p36269]	Rooted	1	843	Low confidence	0.00001	
h2a histone family, member j isoform 1. [source:refseq;acc:nm_018267]	Measured	1	501	High confidence	0.00001	
h2a histone family, member j isoform 1. [source:refseq;acc:nm_018267]	Squared	1	501	High confidence	0.00001	
h2a histone family, member j isoform 1. [source:refseq;acc:nm_018267]	Rooted	1	501	High confidence	0.00001	
histone h2a.a (h2a/a) (h2a.2). [source:swissprot;acc:p28001]	Measured	1	495	High confidence	0.00001	
histone h2a.a (h2a/a) (h2a.2). [source:swissprot;acc:p28001]	Squared	1	495	High confidence	0.00001	
histone h2a.a (h2a/a) (h2a.2). [source:swissprot;acc:p28001]	Rooted	1	495	High confidence	0.00001	
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]	Measured	1	494	High confidence	0.00001	
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]	Squared	1	494	High confidence	0.00001	
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]	Rooted	1	494	High confidence	0.00001	
histone h2a; h2a histone family, member r. [source:refseq;acc:nm_170745]	Measured	1	497	High confidence	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/