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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 1942 in total

Interaction Map  : High confidence
Filtered  : 0
Network Comparison Type  : Subtracted
green  : 0

Rank	Value Type	description	red	network_comparison
5	Rooted	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	19.0788	19.0788
17		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
50		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	Measured	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	364	364
117	Rooted	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]	4.24264	4.24264
206	Measured	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]
316		ero1-like. [refseq;acc:nm_014584]	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	Squared	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	31.36	31.36
386	Measured	dok-like protein. [refseq;acc:nm_024872]	35	35
409	Squared	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	5.61325	5.61325
410		transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]
429	Measured	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]	18	18
440	Squared	ero1-like. [refseq;acc:nm_014584]	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	Measured	histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]	0	0
	Squared
	Rooted
495	Measured	histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]
	Squared
	Rooted
496	Measured	mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932]
	Squared
	Rooted
497	Measured	histone h2a; h2a histone family, member r. [refseq;acc:nm_170745]
	Squared
	Rooted
498	Measured	translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]
	Squared
	Rooted
499	Measured	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
	Squared
	Rooted
500	Measured	rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952]
	Squared
	Rooted
501	Measured	h2a histone family, member j isoform 1. [refseq;acc:nm_018267]
	Ranked	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
	Squared	h2a histone family, member j isoform 1. [refseq;acc:nm_018267]
	Rooted
502	Measured	brca1 associated protein. [refseq;acc:nm_006768]
	Ranked
	Squared
	Rooted

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.