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 description Value Type 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

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