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.

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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 description Value Type 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

description	Value Type	Rank	network_comparison	red	
brca1 associated protein. [source:refseq;acc:nm_006768]	Measured	502	1	0.00001	
brca1 associated protein. [source:refseq;acc:nm_006768]	Ranked	502	1	0.00001	
brca1 associated protein. [source:refseq;acc:nm_006768]	Squared	502	1	0.00001	
brca1 associated protein. [source:refseq;acc:nm_006768]	Rooted	502	1	0.00001	
dok-like protein. [source:refseq;acc:nm_024872]	Measured	31	3500000	35	
dok-like protein. [source:refseq;acc:nm_024872]	Squared	13	28994.1	0.289941	
dok-like protein. [source:refseq;acc:nm_024872]	Rooted	13	591608	5.91608	
ero1-like. [source:refseq;acc:nm_014584]	Measured	20	8200000	82	
ero1-like. [source:refseq;acc:nm_014584]	Squared	8	159148	1.59148	
ero1-like. [source:refseq;acc:nm_014584]	Rooted	8	905539	9.05539	
h2a histone family, member j isoform 1. [source:refseq;acc:nm_018267]	Measured	501	1	0.00001	
h2a histone family, member j isoform 1. [source:refseq;acc:nm_018267]	Squared	501	1	0.00001	
h2a histone family, member j isoform 1. [source:refseq;acc:nm_018267]	Rooted	501	1	0.00001	
histone h2a.a (h2a/a) (h2a.2). [source:swissprot;acc:p28001]	Measured	495	1	0.00001	
histone h2a.a (h2a/a) (h2a.2). [source:swissprot;acc:p28001]	Squared	495	1	0.00001	
histone h2a.a (h2a/a) (h2a.2). [source:swissprot;acc:p28001]	Rooted	495	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	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	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	1	0.00001	
histone h2a; h2a histone family, member r. [source:refseq;acc:nm_170745]	Measured	497	1	0.00001	
histone h2a; h2a histone family, member r. [source:refseq;acc:nm_170745]	Squared	497	1	0.00001	
histone h2a; h2a histone family, member r. [source:refseq;acc:nm_170745]	Rooted	497	1	0.00001	
homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [source:swissprot;acc:q93099]	Measured	499	1	0.00001	
homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [source:swissprot;acc:q93099]	Ranked	501	1	0.00001	
homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [source:swissprot;acc:q93099]	Squared	499	1	0.00001	
homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [source:swissprot;acc:q93099]	Rooted	499	1	0.00001	
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	Measured	1	36400000	364	
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	Squared	68	3136000	31.36	
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	Rooted	1	1907880	19.0788	
mitochondrial 28s ribosomal protein s6 (mrp-s6). [source:swissprot;acc:p82932]	Measured	496	1	0.00001	
mitochondrial 28s ribosomal protein s6 (mrp-s6). [source:swissprot;acc:p82932]	Squared	496	1	0.00001	
mitochondrial 28s ribosomal protein s6 (mrp-s6). [source:swissprot;acc:p82932]	Rooted	496	1	0.00001	
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	Measured	95	15400000	154	
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	Squared	2	561325	5.61325	
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	Rooted	2	1240970	12.4097	
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [source:refseq;acc:nm_007372]	Measured	65	1800000	18	
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [source:refseq;acc:nm_007372]	Squared	17	7668.64	0.0766864	
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [source:refseq;acc:nm_007372]	Rooted	15	424264	4.24264	
rwd domain containing 1; ptd013 protein; cgi-24 protein. [source:refseq;acc:nm_015952]	Measured	500	1	0.00001	
rwd domain containing 1; ptd013 protein; cgi-24 protein. [source:refseq;acc:nm_015952]	Squared	500	1	0.00001	
rwd domain containing 1; ptd013 protein; cgi-24 protein. [source:refseq;acc:nm_015952]	Rooted	500	1	0.00001	
similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [source:refseq;acc:nm_032517]	Measured	22	6000000	60	
similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [source:refseq;acc:nm_032517]	Squared	9	85207.1	0.852071	
similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [source:refseq;acc:nm_032517]	Rooted	9	774597	7.74597	
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [source:swissprot;acc:q9bq87]	Measured	96	15400000	154	
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [source:swissprot;acc:q9bq87]	Squared	3	561325	5.61325	
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [source:swissprot;acc:q9bq87]	Rooted	3	1240970	12.4097	
translin-associated protein x (translin-associated factor x). [source:swissprot;acc:q99598]	Measured	498	1	0.00001	
translin-associated protein x (translin-associated factor x). [source:swissprot;acc:q99598]	Squared	498	1	0.00001	
translin-associated protein x (translin-associated factor x). [source:swissprot;acc:q99598]	Rooted	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/