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

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Showing element 1 to 16 of 16 in total

Rank  : 3
Interaction Map  : High confidence

Network Comparison Type	Value Type	description	Filtered	red	network_comparison	green
Divided	Measured	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	1	2597.5	3.71868	698.5
		pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	0	0.00001	10900000	109
	Ranked	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	1	15	1.86667	28
		nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	0	4475.84	2.47638	11083.9
	Squared	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	1	1596.92	13.8285	115.48
		transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	0	5.61325	561325	0.00001
	Rooted	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	1	50.9657	1.92839	26.4292
		transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	0	12.4097	1240970	0.00001
Subtracted	Measured	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	1	41482.5	8126	33356.5
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	0	23818.1	4196.8	19621.3
	Ranked	cab2. [refseq;acc:nm_033419]		21866	10916	10950
		rad50-interacting protein 1. [refseq;acc:nm_021930]	1	337	105	232
	Squared	apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	0	135280	35348	170628
		cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	1	407289	143938	263351
	Rooted	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	0	36.9188	30.0631	6.85565
		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	1	50.9657	24.5365	26.4292

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.