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

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Showing element 1 to 50 of 29840 in total

Interaction Map  : High confidence

Rank	Value Type	description	green	Network Comparison Type	Filtered	red	network_comparison
1	Measured	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	6410	Subtracted	0	85	6325
		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]	33356.5		1	41482.5	8126
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0.00001	Divided	0	364	36400000
		rad50-interacting protein 1. [refseq;acc:nm_021930]	2394.5		1	450.5	5.31521
	Ranked	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	15915		0	4294	3.70633
		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	322	Subtracted	1	215	107
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	21883		0	8906	12977
		putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	24	Divided	1	10	2.4
	Squared	cab2. [refseq;acc:nm_033419]	7.16592		0	0.00001	716592
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	160184	Subtracted		232467	72283
		putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	322755		1	468498	145743
		rad50-interacting protein 1. [refseq;acc:nm_021930]	1357.07	Divided		48.0356	28.2513
	Rooted	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	60.0707	Subtracted	0	9.20014	50.8706
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0.00001	Divided		19.0788	1907880
		rad50-interacting protein 1. [refseq;acc:nm_021930]	48.9336		1	21.225	2.30547
				Subtracted			27.7086
2	Measured	cab2. [refseq;acc:nm_033419]	174	Divided	0	0.00001	17400000
		cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	33356.5	Subtracted	1	41482.5	8126
		lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	6410		0	85	6325
		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	2394.5	Divided	1	450.5	5.31521
	Ranked	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	15915	Subtracted	0	4294	11621
		hbs1-like. [refseq;acc:nm_006620]	322		1	215	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]	28	Divided		15	1.86667
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	14977		0	5865	2.55362
	Squared	histone h4. [swissprot;acc:p02304]	345123	Subtracted		273623	71500
		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]	263351		1	407289	143938
		nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	0.00001	Divided	0	5.61325	561325
		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	1357.07		1	48.0356	28.2513
	Rooted	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	60.0707	Subtracted	0	9.20014	50.8706
		nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	0.00001	Divided		12.4097	1240970
		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	48.9336		1	21.225	2.30547
				Subtracted			27.7086
3	Measured	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	33356.5			41482.5	8126
		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	698.5	Divided		2597.5	3.71868
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	19621.3	Subtracted	0	23818.1	4196.8
		pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	109	Divided		0.00001	10900000
	Ranked	cab2. [refseq;acc:nm_033419]	10950	Subtracted		21866	10916
		cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	28	Divided	1	15	1.86667
		nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	11083.9		0	4475.84	2.47638
		rad50-interacting protein 1. [refseq;acc:nm_021930]	232	Subtracted	1	337	105
	Squared	apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	170628		0	135280	35348
		cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	263351		1	407289	143938
		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	115.48	Divided		1596.92	13.8285
		transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	0.00001		0	5.61325	561325
	Rooted	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	6.85565	Subtracted		36.9188	30.0631
		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	26.4292	Divided	1	50.9657	1.92839
				Subtracted			24.5365
		transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	0.00001	Divided	0	12.4097	1240970
4	Measured	cytohesin 4. [swissprot;acc:q9uia0]	33356.5	Subtracted	1	41482.5	8126
		hbs1-like. [refseq;acc:nm_006620]	698.5	Divided		2597.5	3.71868

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.