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

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Showing element 1 to 50 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	network_comparison	green
1	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Ranked	Divided	0	4294	3.70633	15915
	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Measured	Subtracted		85	6325	6410
		Rooted			9.20014	50.8706	60.0707
	cab2. [refseq;acc:nm_033419]	Squared	Divided		0.00001	716592	7.16592
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Ranked	Subtracted	1	215	107	322
	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]	Measured			41482.5	8126	33356.5
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]		Divided	0	364	36400000	0.00001
		Ranked	Subtracted		8906	12977	21883
		Rooted	Divided		19.0788	1907880	0.00001
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Squared	Subtracted		232467	72283	160184
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Ranked	Divided	1	10	2.4	24
		Squared	Subtracted		468498	145743	322755
	rad50-interacting protein 1. [refseq;acc:nm_021930]	Measured	Divided		450.5	5.31521	2394.5
		Squared			48.0356	28.2513	1357.07
		Rooted			21.225	2.30547	48.9336
			Subtracted			27.7086
2	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Ranked		0	4294	11621	15915
	cab2. [refseq;acc:nm_033419]	Measured	Divided		0.00001	17400000	174
	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]		Subtracted	1	41482.5	8126	33356.5
	hbs1-like. [refseq;acc:nm_006620]	Ranked			215	107	322
	histone h4. [swissprot;acc:p02304]	Squared		0	273623	71500	345123
	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Measured			85	6325	6410
		Rooted			9.20014	50.8706	60.0707
	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]	Ranked	Divided	1	15	1.86667	28
		Squared	Subtracted		407289	143938	263351
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Ranked	Divided	0	5865	2.55362	14977
	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Squared			5.61325	561325	0.00001
		Rooted			12.4097	1240970
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Measured		1	450.5	5.31521	2394.5
		Squared			48.0356	28.2513	1357.07
		Rooted			21.225	2.30547	48.9336
			Subtracted			27.7086
3	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]			0	36.9188	30.0631	6.85565
	apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	Squared			135280	35348	170628
	cab2. [refseq;acc:nm_033419]	Ranked			21866	10916	10950
	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]		Divided	1	15	1.86667	28
		Squared	Subtracted		407289	143938	263351
	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Measured			41482.5	8126	33356.5
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]		Divided		2597.5	3.71868	698.5
		Squared			1596.92	13.8285	115.48
		Rooted			50.9657	1.92839	26.4292
			Subtracted			24.5365
	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	Ranked	Divided	0	4475.84	2.47638	11083.9
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Measured	Subtracted		23818.1	4196.8	19621.3
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]		Divided		0.00001	10900000	109
	rad50-interacting protein 1. [refseq;acc:nm_021930]	Ranked	Subtracted	1	337	105	232
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Squared	Divided	0	5.61325	561325	0.00001
		Rooted			12.4097	1240970
4	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Ranked		1	15	1.86667	28
		Squared	Subtracted		407289	143938	263351

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.