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

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Showing element 1 to 50 of 38536 in total

Network Comparison Type  : Divided

Rank	Value Type	description	Filtered	green	network_comparison	Interaction Map	red
1	Measured	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	1	543.5	4.4149	Low confidence	2399.5
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0	0.00001	36400000	High confidence	364
						Low confidence
		rad50-interacting protein 1. [refseq;acc:nm_021930]	1	2394.5	5.31521	High confidence	450.5
	Ranked	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	0	15915	3.70633		4294
		carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	1	32	2	Low confidence	16
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	0	14977	2.55362		5865
		putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	1	24	2.4	High confidence	10
	Squared	cab2. [refseq;acc:nm_033419]	0	7.16592	716592		0.00001
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		1.87479	187479	Low confidence
		lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	1	69.9153	19.4914		1362.75
		rad50-interacting protein 1. [refseq;acc:nm_021930]		1357.07	28.2513	High confidence	48.0356
	Rooted	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]		23.3131	2.10117	Low confidence	48.9847
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0	0.00001	1907880	High confidence	19.0788
						Low confidence
		rad50-interacting protein 1. [refseq;acc:nm_021930]	1	48.9336	2.30547	High confidence	21.225
2	Measured	cab2. [refseq;acc:nm_033419]	0	174	17400000		0.00001
		cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	1	543.5	4.4149	Low confidence	2399.5
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0	89	8900000		0.00001
		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	1	2394.5	5.31521	High confidence	450.5
	Ranked	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]		330	1.47982	Low confidence	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	1.86667	High confidence	15
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0	21883	2.45711	Low confidence	8906
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]		14977	2.55362	High confidence	5865
	Squared	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	1	69.9153	19.4914	Low confidence	1362.75
		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	0	1.87479	187479		0.00001
		nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]		0.00001	561325	High confidence	5.61325
		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	1	1357.07	28.2513		48.0356
	Rooted	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]		23.3131	2.10117	Low confidence	48.9847
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0	9.43398	943398		0.00001
		nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]		0.00001	1240970	High confidence	12.4097
		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	1	48.9336	2.30547		21.225
3	Measured	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]		543.5	4.4149	Low confidence	2399.5
		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]		698.5	3.71868	High confidence	2597.5
		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	0	89	8900000	Low confidence	0.00001
		pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]		109	10900000	High confidence
	Ranked	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	1	330	1.47982	Low confidence	223
		cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]		28	1.86667	High confidence	15
		neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	0	20617	2.14604	Low confidence	9607
		nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]		11083.9	2.47638	High confidence	4475.84
	Squared	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	1	69.9153	19.4914	Low confidence	1362.75
		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]		115.48	13.8285	High confidence	1596.92
		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	0	1.87479	187479	Low confidence	0.00001
		transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]		0.00001	561325	High confidence	5.61325
	Rooted	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	1	23.3131	2.10117	Low confidence	48.9847
		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]		26.4292	1.92839	High confidence	50.9657
		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	0	9.43398	943398	Low confidence	0.00001
		transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]		0.00001	1240970	High confidence	12.4097
4	Measured	hbs1-like. [refseq;acc:nm_006620]	1	698.5	3.71868		2597.5
		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	0	89	8900000	Low confidence	0.00001

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.