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

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Showing element 1 to 50 of 38536 in total

Network Comparison Type  : Divided

Rank	Interaction Map	description	Filtered	green	Value Type	network_comparison	red
1	High confidence	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	0	15915	Ranked	3.70633	4294
		cab2. [refseq;acc:nm_033419]		7.16592	Squared	716592	0.00001
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]		0.00001	Measured	36400000	364
					Rooted	1907880	19.0788
		putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	1	24	Ranked	2.4	10
		rad50-interacting protein 1. [refseq;acc:nm_021930]		48.9336	Rooted	2.30547	21.225
				1357.07	Squared	28.2513	48.0356
				2394.5	Measured	5.31521	450.5
	Low confidence	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]		32	Ranked	2	16
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0	1.87479	Squared	187479	0.00001
		lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	1	23.3131	Rooted	2.10117	48.9847
				69.9153	Squared	19.4914	1362.75
				543.5	Measured	4.4149	2399.5
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0	0.00001		36400000	364
					Rooted	1907880	19.0788
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]		14977	Ranked	2.55362	5865
2	High confidence	cab2. [refseq;acc:nm_033419]		174	Measured	17400000	0.00001
		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	28	Ranked	1.86667	15
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	0	14977		2.55362	5865
		nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]		0.00001	Squared	561325	5.61325
					Rooted	1240970	12.4097
		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	1	48.9336		2.30547	21.225
				1357.07	Squared	28.2513	48.0356
				2394.5	Measured	5.31521	450.5
	Low confidence	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]		23.3131	Rooted	2.10117	48.9847
				69.9153	Squared	19.4914	1362.75
				543.5	Measured	4.4149	2399.5
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0	9.43398	Rooted	943398	0.00001
				89	Measured	8900000
		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]		1.87479	Squared	187479
		lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	1	330	Ranked	1.47982	223
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0	21883		2.45711	8906
3	High confidence	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	1	28		1.86667	15
		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]		26.4292	Rooted	1.92839	50.9657
				115.48	Squared	13.8285	1596.92
				698.5	Measured	3.71868	2597.5
		nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	0	11083.9	Ranked	2.47638	4475.84
		pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]		109	Measured	10900000	0.00001
		transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]		0.00001	Squared	561325	5.61325
					Rooted	1240970	12.4097
	Low confidence	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	1	330	Ranked	1.47982	223
		cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]		23.3131	Rooted	2.10117	48.9847
				69.9153	Squared	19.4914	1362.75
				543.5	Measured	4.4149	2399.5
		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	0	1.87479	Squared	187479	0.00001
		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]		9.43398	Rooted	943398
				89	Measured	8900000
		neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]		20617	Ranked	2.14604	9607
4	High confidence	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	1	28		1.86667	15
		hbs1-like. [refseq;acc:nm_006620]		26.4292	Rooted	1.92839	50.9657

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.