MK5 Microarray Data

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

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Showing element 51 to 100 of 77072 in total

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green	Value Type	network_comparison	red	Network Comparison Type	Interaction Map	Rank	description
0	Squared	0	0	Subtracted	Low confidence	840	translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]
						841	gamma-glutamyltransferase. [sptrembl;acc:q14390]
						842	gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [swissprot;acc:p19440]
						843	gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [swissprot;acc:p36269]
		0.00219609	0.00219609			835	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]
		0.04	0.04			833	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
		0.0766864	0.0766864		High confidence	471	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]
		0.289941	0.289941			467	dok-like protein. [refseq;acc:nm_024872]
		0.324024	0.324024		Low confidence	826	carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615]
						827	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]
		0.852071	0.852071		High confidence	449	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]
		1.59148	1.59148			440	ero1-like. [refseq;acc:nm_014584]
		5.61325	5.61325			409	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]
						410	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]
		19.36	19.36		Low confidence	727	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]
						728	neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]
		31.36	31.36		High confidence	357	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]
					Low confidence	704
	Rooted	0	0		High confidence	494	histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]
						495	histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]
						496	mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932]
						497	histone h2a; h2a histone family, member r. [refseq;acc:nm_170745]
						498	translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]
						499	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
						500	rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952]
						501	h2a histone family, member j isoform 1. [refseq;acc:nm_018267]
						502	brca1 associated protein. [refseq;acc:nm_006768]
					Low confidence	837	gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]
						838	gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]
						839	cobw-like protein. [refseq;acc:nm_018491]
						840	translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]
						841	gamma-glutamyltransferase. [sptrembl;acc:q14390]
						842	gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [swissprot;acc:p19440]
						843	gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [swissprot;acc:p36269]
		1.15981	1.15981			538	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]
		3.60555	3.60555			231	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
		4.24264	4.24264		High confidence	117	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]
		5.91608	5.91608			74	dok-like protein. [refseq;acc:nm_024872]
		6.08276	6.08276		Low confidence	42	carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615]
						43	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]
		7.74597	7.74597		High confidence	50	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]
		9.05539	9.05539			38	ero1-like. [refseq;acc:nm_014584]
		12.4097	12.4097			17	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]
						18	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]
		16.9115	16.9115		Low confidence	6	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]
						7	neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]
		19.0788	19.0788		High confidence	5	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]
					Low confidence	4
0.00001	Measured	1	0.00001	Divided	High confidence	494	histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]
						495	histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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.