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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 29840 in total

Interaction Map  : High confidence

Rank	Value Type	green	Network Comparison Type	network_comparison	description	red	Filtered
1	Measured	0.00001	Divided	36400000	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	364	0
		2394.5		5.31521	rad50-interacting protein 1. [refseq;acc:nm_021930]	450.5	1
		6410	Subtracted	6325	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	85	0
		33356.5		8126	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]	41482.5	1
	Ranked	24	Divided	2.4	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	10
		322	Subtracted	107	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	215
		15915	Divided	3.70633	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	4294	0
		21883	Subtracted	12977	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	8906
	Squared	7.16592	Divided	716592	cab2. [refseq;acc:nm_033419]	0.00001
		1357.07		28.2513	rad50-interacting protein 1. [refseq;acc:nm_021930]	48.0356	1
		160184	Subtracted	72283	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	232467	0
		322755		145743	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	468498	1
	Rooted	0.00001	Divided	1907880	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	19.0788	0
		48.9336		2.30547	rad50-interacting protein 1. [refseq;acc:nm_021930]	21.225	1
			Subtracted	27.7086
		60.0707		50.8706	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	9.20014	0
2	Measured	174	Divided	17400000	cab2. [refseq;acc:nm_033419]	0.00001
		2394.5		5.31521	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	450.5	1
		6410	Subtracted	6325	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	85	0
		33356.5		8126	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	41482.5	1
	Ranked	28	Divided	1.86667	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]	15
		322	Subtracted	107	hbs1-like. [refseq;acc:nm_006620]	215
		14977	Divided	2.55362	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	5865	0
		15915	Subtracted	11621	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	4294
	Squared	0.00001	Divided	561325	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	5.61325
		1357.07		28.2513	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	48.0356	1
		263351	Subtracted	143938	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]	407289
		345123		71500	histone h4. [swissprot;acc:p02304]	273623	0
	Rooted	0.00001	Divided	1240970	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	12.4097
		48.9336		2.30547	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	21.225	1
			Subtracted	27.7086
		60.0707		50.8706	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	9.20014	0
3	Measured	109	Divided	10900000	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	0.00001
		698.5		3.71868	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	2597.5	1
		19621.3	Subtracted	4196.8	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	23818.1	0
		33356.5		8126	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	41482.5	1
	Ranked	28	Divided	1.86667	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	15
		232	Subtracted	105	rad50-interacting protein 1. [refseq;acc:nm_021930]	337
		10950		10916	cab2. [refseq;acc:nm_033419]	21866	0
		11083.9	Divided	2.47638	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	4475.84
	Squared	0.00001		561325	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	5.61325
		115.48		13.8285	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	1596.92	1
		170628	Subtracted	35348	apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	135280	0
		263351		143938	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	407289	1
	Rooted	0.00001	Divided	1240970	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	12.4097	0
		6.85565	Subtracted	30.0631	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	36.9188
		26.4292	Divided	1.92839	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	50.9657	1
			Subtracted	24.5365
4	Measured	89	Divided	8900000	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0.00001	0
		698.5		3.71868	hbs1-like. [refseq;acc:nm_006620]	2597.5	1

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.