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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 14920 in total

Filtered	0
green	0.00001
Interaction Map	High confidence
Network Comparison Type	Divided

Value Type	description	Rank	network_comparison	red	
Measured	brca1 associated protein. [source:refseq;acc:nm_006768]	502	1	0.00001	
Measured	dok-like protein. [source:refseq;acc:nm_024872]	31	3500000	35	
Measured	ero1-like. [source:refseq;acc:nm_014584]	20	8200000	82	
Measured	h2a histone family, member j isoform 1. [source:refseq;acc:nm_018267]	501	1	0.00001	
Measured	histone h2a.a (h2a/a) (h2a.2). [source:swissprot;acc:p28001]	495	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	1	0.00001	
Measured	histone h2a; h2a histone family, member r. [source:refseq;acc:nm_170745]	497	1	0.00001	
Measured	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [source:swissprot;acc:q93099]	499	1	0.00001	
Measured	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	1	36400000	364	
Measured	mitochondrial 28s ribosomal protein s6 (mrp-s6). [source:swissprot;acc:p82932]	496	1	0.00001	
Measured	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	95	15400000	154	
Measured	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [source:refseq;acc:nm_007372]	65	1800000	18	
Measured	rwd domain containing 1; ptd013 protein; cgi-24 protein. [source:refseq;acc:nm_015952]	500	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	6000000	60	
Measured	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [source:swissprot;acc:q9bq87]	96	15400000	154	
Measured	translin-associated protein x (translin-associated factor x). [source:swissprot;acc:q99598]	498	1	0.00001	
Ranked	brca1 associated protein. [source:refseq;acc:nm_006768]	502	1	0.00001	
Ranked	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [source:swissprot;acc:q93099]	501	1	0.00001	
Squared	brca1 associated protein. [source:refseq;acc:nm_006768]	502	1	0.00001	
Squared	dok-like protein. [source:refseq;acc:nm_024872]	13	28994.1	0.289941	
Squared	ero1-like. [source:refseq;acc:nm_014584]	8	159148	1.59148	
Squared	h2a histone family, member j isoform 1. [source:refseq;acc:nm_018267]	501	1	0.00001	
Squared	histone h2a.a (h2a/a) (h2a.2). [source:swissprot;acc:p28001]	495	1	0.00001	
Squared	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	0.00001	
Squared	histone h2a; h2a histone family, member r. [source:refseq;acc:nm_170745]	497	1	0.00001	
Squared	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [source:swissprot;acc:q93099]	499	1	0.00001	
Squared	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	68	3136000	31.36	
Squared	mitochondrial 28s ribosomal protein s6 (mrp-s6). [source:swissprot;acc:p82932]	496	1	0.00001	
Squared	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	2	561325	5.61325	
Squared	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [source:refseq;acc:nm_007372]	17	7668.64	0.0766864	
Squared	rwd domain containing 1; ptd013 protein; cgi-24 protein. [source:refseq;acc:nm_015952]	500	1	0.00001	
Squared	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [source:refseq;acc:nm_032517]	9	85207.1	0.852071	
Squared	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [source:swissprot;acc:q9bq87]	3	561325	5.61325	
Squared	translin-associated protein x (translin-associated factor x). [source:swissprot;acc:q99598]	498	1	0.00001	
Rooted	brca1 associated protein. [source:refseq;acc:nm_006768]	502	1	0.00001	
Rooted	dok-like protein. [source:refseq;acc:nm_024872]	13	591608	5.91608	
Rooted	ero1-like. [source:refseq;acc:nm_014584]	8	905539	9.05539	
Rooted	h2a histone family, member j isoform 1. [source:refseq;acc:nm_018267]	501	1	0.00001	
Rooted	histone h2a.a (h2a/a) (h2a.2). [source:swissprot;acc:p28001]	495	1	0.00001	
Rooted	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	0.00001	
Rooted	histone h2a; h2a histone family, member r. [source:refseq;acc:nm_170745]	497	1	0.00001	
Rooted	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [source:swissprot;acc:q93099]	499	1	0.00001	
Rooted	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	1	1907880	19.0788	
Rooted	mitochondrial 28s ribosomal protein s6 (mrp-s6). [source:swissprot;acc:p82932]	496	1	0.00001	
Rooted	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	2	1240970	12.4097	
Rooted	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [source:refseq;acc:nm_007372]	15	424264	4.24264	
Rooted	rwd domain containing 1; ptd013 protein; cgi-24 protein. [source:refseq;acc:nm_015952]	500	1	0.00001	
Rooted	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [source:refseq;acc:nm_032517]	9	774597	7.74597	
Rooted	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [source:swissprot;acc:q9bq87]	3	1240970	12.4097	
Rooted	translin-associated protein x (translin-associated factor x). [source:swissprot;acc:q99598]	498	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/