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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

value_type as 'ranked' since this provides a very robust analysis method.

intercation map as 'high confidence'

network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins

filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 38536 in total

green	0.00001
Filtered	0
Network Comparison Type	Divided

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