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

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Showing element 1 to 50 of 38536 in total

Network Comparison Type  : Divided

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

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.