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

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Showing element 1 to 50 of 38536 in total

Network Comparison Type  : Divided

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

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.