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	network_comparison	Interaction Map	Filtered	Value Type	green	Network Comparison Type	red

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Showing element 1 to 50 of 38536 in total

Network Comparison Type  : Divided

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