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	network_comparison	green

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

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.