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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 1923 in total

Network Comparison Type  : Subtracted
Interaction Map  : High confidence
network_comparison  : 0

Rank	Value Type	red	description	green	Filtered
493	Squared	17901.1	3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]	17901.1	0
494	Measured	0	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
	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]
	Ranked	394	huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]	394
	Squared	0	rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952]	0
	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
2756	Measured		3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]		1
	Ranked
	Squared
	Rooted
2757	Measured		nucleosome assembly protein 1-like 1 (nap-1 related protein). [swissprot;acc:p55209]
	Ranked
	Squared
	Rooted
2758	Measured		nucleosome assembly protein 1-like 2 (brain-specific protein, x- linked). [swissprot;acc:q9ulw6]
	Ranked
	Squared
	Rooted
2759	Measured		retinoic acid receptor rxr-alpha. [swissprot;acc:p19793]
	Ranked
	Squared
	Rooted
2760	Measured		t-cell acute lymphocytic leukemia-2 protein (tal-2 protein). [swissprot;acc:q16559]
	Ranked
	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.