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 51 to 100 of 38536 in total

green	0.00001
Network Comparison Type	Divided

Filtered	description	Value Type	Rank	Interaction Map	network_comparison	red	
0	histone h2a; h2a histone family, member r. [source:refseq;acc:nm_170745]	Squared	497	High confidence	1	0.00001	
0	histone h2a; h2a histone family, member r. [source:refseq;acc:nm_170745]	Rooted	497	High confidence	1	0.00001	
0	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [source:swissprot;acc:q93099]	Measured	6	Low confidence	1300000	13	
0	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [source:swissprot;acc:q93099]	Measured	499	High confidence	1	0.00001	
0	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [source:swissprot;acc:q93099]	Ranked	501	High confidence	1	0.00001	
0	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [source:swissprot;acc:q93099]	Squared	9	Low confidence	4000	0.04	
0	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [source:swissprot;acc:q93099]	Squared	499	High confidence	1	0.00001	
0	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [source:swissprot;acc:q93099]	Rooted	8	Low confidence	360555	3.60555	
0	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [source:swissprot;acc:q93099]	Rooted	499	High confidence	1	0.00001	
0	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	Measured	1	High confidence	36400000	364	
0	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	Measured	1	Low confidence	36400000	364	
0	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	Squared	68	High confidence	3136000	31.36	
0	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	Squared	73	Low confidence	3136000	31.36	
0	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	Rooted	1	High confidence	1907880	19.0788	
0	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	Rooted	1	Low confidence	1907880	19.0788	
0	mitochondrial 28s ribosomal protein s6 (mrp-s6). [source:swissprot;acc:p82932]	Measured	496	High confidence	1	0.00001	
0	mitochondrial 28s ribosomal protein s6 (mrp-s6). [source:swissprot;acc:p82932]	Squared	496	High confidence	1	0.00001	
0	mitochondrial 28s ribosomal protein s6 (mrp-s6). [source:swissprot;acc:p82932]	Rooted	496	High confidence	1	0.00001	
0	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [source:swissprot;acc:p46531]	Measured	44	Low confidence	28600000	286	
0	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [source:swissprot;acc:p46531]	Squared	111	Low confidence	1936000	19.36	
0	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [source:swissprot;acc:p46531]	Rooted	49	Low confidence	1691150	16.9115	
0	neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [source:swissprot;acc:q04721]	Measured	45	Low confidence	28600000	286	
0	neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [source:swissprot;acc:q04721]	Squared	112	Low confidence	1936000	19.36	
0	neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [source:swissprot;acc:q04721]	Rooted	50	Low confidence	1691150	16.9115	
0	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	Measured	95	High confidence	15400000	154	
0	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	Squared	2	High confidence	561325	5.61325	
0	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	Rooted	2	High confidence	1240970	12.4097	
0	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [source:refseq;acc:nm_007372]	Measured	65	High confidence	1800000	18	
0	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [source:refseq;acc:nm_007372]	Squared	17	High confidence	7668.64	0.0766864	
0	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [source:refseq;acc:nm_007372]	Rooted	15	High confidence	424264	4.24264	
0	rwd domain containing 1; ptd013 protein; cgi-24 protein. [source:refseq;acc:nm_015952]	Measured	500	High confidence	1	0.00001	
0	rwd domain containing 1; ptd013 protein; cgi-24 protein. [source:refseq;acc:nm_015952]	Squared	500	High confidence	1	0.00001	
0	rwd domain containing 1; ptd013 protein; cgi-24 protein. [source:refseq;acc:nm_015952]	Rooted	500	High confidence	1	0.00001	
0	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [source:refseq;acc:nm_032517]	Measured	22	High confidence	6000000	60	
0	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [source:refseq;acc:nm_032517]	Squared	9	High confidence	85207.1	0.852071	
0	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [source:refseq;acc:nm_032517]	Rooted	9	High confidence	774597	7.74597	
0	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [source:refseq;acc:nm_007063]	Measured	7	Low confidence	231962	2.31962	
0	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [source:refseq;acc:nm_007063]	Squared	13	Low confidence	219.609	0.00219609	
0	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [source:refseq;acc:nm_007063]	Rooted	10	Low confidence	115981	1.15981	
0	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [source:swissprot;acc:q9bq87]	Measured	96	High confidence	15400000	154	
0	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [source:swissprot;acc:q9bq87]	Squared	3	High confidence	561325	5.61325	
0	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [source:swissprot;acc:q9bq87]	Rooted	3	High confidence	1240970	12.4097	
0	translin-associated protein x (translin-associated factor x). [source:swissprot;acc:q99598]	Measured	498	High confidence	1	0.00001	
0	translin-associated protein x (translin-associated factor x). [source:swissprot;acc:q99598]	Measured	840	Low confidence	1	0.00001	
0	translin-associated protein x (translin-associated factor x). [source:swissprot;acc:q99598]	Squared	498	High confidence	1	0.00001	
0	translin-associated protein x (translin-associated factor x). [source:swissprot;acc:q99598]	Squared	840	Low confidence	1	0.00001	
0	translin-associated protein x (translin-associated factor x). [source:swissprot;acc:q99598]	Rooted	498	High confidence	1	0.00001	
0	translin-associated protein x (translin-associated factor x). [source:swissprot;acc:q99598]	Rooted	840	Low confidence	1	0.00001	
1	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 4 (ec 3.1.4.11) (phosphoinositide phospholipase c) (plc-beta-4) (phospholipase c-beta-4). [source:swissprot;acc:q15147]	Measured	3126	High confidence	1	0.00001	
1	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 4 (ec 3.1.4.11) (phosphoinositide phospholipase c) (plc-beta-4) (phospholipase c-beta-4). [source:swissprot;acc:q15147]	Ranked	3126	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/