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.

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 38536 in total

Filtered  : 0
green  : 0.00001
Network Comparison Type  : Divided

Rank	description	Interaction Map	Value Type	network_comparison	red
1	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	High confidence	Measured	36400000	364
			Rooted	1907880	19.0788
		Low confidence	Measured	36400000	364
			Rooted	1907880	19.0788
2	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	High confidence	Squared	561325	5.61325
			Rooted	1240970	12.4097
3	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]		Squared	561325	5.61325
			Rooted	1240970	12.4097
5	carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615]	Low confidence	Squared	32402.4	0.324024
6			Rooted	608276	6.08276
	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]		Squared	32402.4	0.324024
	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]		Measured	1300000	13
7	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]		Rooted	608276	6.08276
	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]		Measured	231962	2.31962
8	ero1-like. [refseq;acc:nm_014584]	High confidence	Squared	159148	1.59148
			Rooted	905539	9.05539
	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	Low confidence		360555	3.60555
9			Squared	4000	0.04
	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	High confidence		85207.1	0.852071
			Rooted	774597	7.74597
10	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]	Low confidence		115981	1.15981
13	dok-like protein. [refseq;acc:nm_024872]	High confidence	Squared	28994.1	0.289941
			Rooted	591608	5.91608
	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]	Low confidence	Squared	219.609	0.00219609
15	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]	High confidence	Rooted	424264	4.24264
17			Squared	7668.64	0.0766864
20	ero1-like. [refseq;acc:nm_014584]		Measured	8200000	82
22	carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615]	Low confidence		3700000	37
	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	High confidence		6000000	60
23	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]	Low confidence		3700000	37
31	dok-like protein. [refseq;acc:nm_024872]	High confidence		3500000	35
44	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	Low confidence		28600000	286
45	neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]
49	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]		Rooted	1691150	16.9115
50	neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]
65	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]	High confidence	Measured	1800000	18
68	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]		Squared	3136000	31.36
73		Low confidence
95	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	High confidence	Measured	15400000	154
96	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]
111	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	Low confidence	Squared	1936000	19.36
112	neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]
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]	High confidence	Measured	1	0.00001
			Squared
			Rooted
495	histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]		Measured
			Squared
			Rooted
496	mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932]		Measured
			Squared

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.