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	Interaction Map	Value Type	Network Comparison Type	Filtered	red	green	network_comparison

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

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.