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

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Showing element 1 to 50 of 77072 in total

Filtered  : 0
green  : 0
Network Comparison Type  : Subtracted

Rank	Interaction Map	description	Value Type	red	network_comparison
4	Low confidence	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Rooted	19.0788	19.0788
5	High confidence
6	Low confidence	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]		16.9115	16.9115
7		neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]
17	High confidence	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]		12.4097	12.4097
18		transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]
38		ero1-like. [refseq;acc:nm_014584]		9.05539	9.05539
42	Low confidence	carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615]		6.08276	6.08276
43		carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]
50	High confidence	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]		7.74597	7.74597
74		dok-like protein. [refseq;acc:nm_024872]		5.91608	5.91608
88		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Measured	364	364
117		rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]	Rooted	4.24264	4.24264
170	Low confidence	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Measured	364	364
200		neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]		286	286
201		neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]
206	High confidence	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]		154	154
207		transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]
231	Low confidence	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	Rooted	3.60555	3.60555
316	High confidence	ero1-like. [refseq;acc:nm_014584]	Measured	82	82
338		similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]		60	60
357		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Squared	31.36	31.36
386		dok-like protein. [refseq;acc:nm_024872]	Measured	35	35
409		nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Squared	5.61325	5.61325
410		transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]
429		rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]	Measured	18	18
440		ero1-like. [refseq;acc:nm_014584]	Squared	1.59148	1.59148
449		similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]		0.852071	0.852071
467		dok-like protein. [refseq;acc:nm_024872]		0.289941	0.289941
471		rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]		0.0766864	0.0766864
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]	Measured	0	0
			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
			Rooted
497		histone h2a; h2a histone family, member r. [refseq;acc:nm_170745]	Measured
			Squared
			Rooted
498		translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]	Measured
			Squared
			Rooted
499		homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	Measured
			Squared
			Rooted
500		rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952]	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.