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

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Showing element 1 to 50 of 38536 in total

Network Comparison Type  : Divided

Rank	Interaction Map	green	Value Type	description	Filtered	network_comparison	red
1	High confidence	0.00001	Measured	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0	36400000	364
			Rooted			1907880	19.0788
		7.16592	Squared	cab2. [refseq;acc:nm_033419]		716592	0.00001
		24	Ranked	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	1	2.4	10
		48.9336	Rooted	rad50-interacting protein 1. [refseq;acc:nm_021930]		2.30547	21.225
		1357.07	Squared			28.2513	48.0356
		2394.5	Measured			5.31521	450.5
		15915	Ranked	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	0	3.70633	4294
	Low confidence	0.00001	Measured	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]		36400000	364
			Rooted			1907880	19.0788
		1.87479	Squared	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		187479	0.00001
		23.3131	Rooted	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	1	2.10117	48.9847
		32	Ranked	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]		2	16
		69.9153	Squared	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]		19.4914	1362.75
		543.5	Measured			4.4149	2399.5
		14977	Ranked	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	0	2.55362	5865
2	High confidence	0.00001	Squared	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]		561325	5.61325
			Rooted			1240970	12.4097
		28	Ranked	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	1.86667	15
		48.9336	Rooted	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]		2.30547	21.225
		174	Measured	cab2. [refseq;acc:nm_033419]	0	17400000	0.00001
		1357.07	Squared	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	1	28.2513	48.0356
		2394.5	Measured			5.31521	450.5
		14977	Ranked	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	0	2.55362	5865
	Low confidence	1.87479	Squared	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]		187479	0.00001
		9.43398	Rooted	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		943398
		23.3131		cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	1	2.10117	48.9847
		69.9153	Squared			19.4914	1362.75
		89	Measured	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0	8900000	0.00001
		330	Ranked	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	1	1.47982	223
		543.5	Measured	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]		4.4149	2399.5
		21883	Ranked	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0	2.45711	8906
3	High confidence	0.00001	Squared	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]		561325	5.61325
			Rooted			1240970	12.4097
		26.4292		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	1	1.92839	50.9657
		28	Ranked	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]		1.86667	15
		109	Measured	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	0	10900000	0.00001
		115.48	Squared	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	1	13.8285	1596.92
		698.5	Measured			3.71868	2597.5
		11083.9	Ranked	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	0	2.47638	4475.84
	Low confidence	1.87479	Squared	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]		187479	0.00001
		9.43398	Rooted	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]		943398
		23.3131		cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	1	2.10117	48.9847
		69.9153	Squared			19.4914	1362.75
		89	Measured	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	0	8900000	0.00001
		330	Ranked	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	1	1.47982	223
		543.5	Measured	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]		4.4149	2399.5
		20617	Ranked	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	0	2.14604	9607
4	High confidence	2.81207	Squared	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]		281207	0.00001
		10.4403	Rooted			1044030

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.