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	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	Value Type	description	Network Comparison Type	Filtered	red	network_comparison	green
1	Measured	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Subtracted	0	85	6325	6410
		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]		1	41482.5	8126	33356.5
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Divided	0	364	36400000	0.00001
		rad50-interacting protein 1. [refseq;acc:nm_021930]		1	450.5	5.31521	2394.5
	Ranked	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]		0	4294	3.70633	15915
		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Subtracted	1	215	107	322
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]		0	8906	12977	21883
		putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Divided	1	10	2.4	24
	Squared	cab2. [refseq;acc:nm_033419]		0	0.00001	716592	7.16592
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Subtracted		232467	72283	160184
		putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]		1	468498	145743	322755
		rad50-interacting protein 1. [refseq;acc:nm_021930]	Divided		48.0356	28.2513	1357.07
	Rooted	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Subtracted	0	9.20014	50.8706	60.0707
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Divided		19.0788	1907880	0.00001
		rad50-interacting protein 1. [refseq;acc:nm_021930]		1	21.225	2.30547	48.9336
			Subtracted			27.7086
2	Measured	cab2. [refseq;acc:nm_033419]	Divided	0	0.00001	17400000	174
		cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	Subtracted	1	41482.5	8126	33356.5
		lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]		0	85	6325	6410
		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Divided	1	450.5	5.31521	2394.5
	Ranked	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Subtracted	0	4294	11621	15915
		hbs1-like. [refseq;acc:nm_006620]		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]	Divided		15	1.86667	28
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]		0	5865	2.55362	14977
	Squared	histone h4. [swissprot;acc:p02304]	Subtracted		273623	71500	345123
		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]		1	407289	143938	263351
		nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Divided	0	5.61325	561325	0.00001
		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]		1	48.0356	28.2513	1357.07
	Rooted	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Subtracted	0	9.20014	50.8706	60.0707
		nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Divided		12.4097	1240970	0.00001
		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]		1	21.225	2.30547	48.9336
			Subtracted			27.7086
3	Measured	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]			41482.5	8126	33356.5
		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Divided		2597.5	3.71868	698.5
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Subtracted	0	23818.1	4196.8	19621.3
		pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	Divided		0.00001	10900000	109
	Ranked	cab2. [refseq;acc:nm_033419]	Subtracted		21866	10916	10950
		cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	Divided	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
		rad50-interacting protein 1. [refseq;acc:nm_021930]	Subtracted	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
		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Divided		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	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Subtracted		36.9188	30.0631	6.85565
		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Divided	1	50.9657	1.92839	26.4292
			Subtracted			24.5365
		transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Divided	0	12.4097	1240970	0.00001
4	Measured	cytohesin 4. [swissprot;acc:q9uia0]	Subtracted	1	41482.5	8126	33356.5
		hbs1-like. [refseq;acc:nm_006620]	Divided		2597.5	3.71868	698.5

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.