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

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Showing element 1 to 50 of 38536 in total

Network Comparison Type  : Divided

Rank	Filtered	Interaction Map	green	network_comparison	description	Value Type	red
1	0	High confidence	0.00001	1907880	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Rooted	19.0788
				36400000		Measured	364
			7.16592	716592	cab2. [refseq;acc:nm_033419]	Squared	0.00001
			15915	3.70633	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Ranked	4294
		Low confidence	0.00001	1907880	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Rooted	19.0788
				36400000		Measured	364
			1.87479	187479	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Squared	0.00001
			14977	2.55362	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Ranked	5865
	1	High confidence	24	2.4	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]		10
			48.9336	2.30547	rad50-interacting protein 1. [refseq;acc:nm_021930]	Rooted	21.225
			1357.07	28.2513		Squared	48.0356
			2394.5	5.31521		Measured	450.5
		Low confidence	23.3131	2.10117	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Rooted	48.9847
			32	2	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	Ranked	16
			69.9153	19.4914	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Squared	1362.75
			543.5	4.4149		Measured	2399.5
2	0	High confidence	0.00001	561325	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Squared	5.61325
				1240970		Rooted	12.4097
			174	17400000	cab2. [refseq;acc:nm_033419]	Measured	0.00001
			14977	2.55362	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Ranked	5865
		Low confidence	1.87479	187479	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Squared	0.00001
			9.43398	943398	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Rooted
			89	8900000		Measured
			21883	2.45711	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Ranked	8906
	1	High confidence	28	1.86667	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]		15
			48.9336	2.30547	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Rooted	21.225
			1357.07	28.2513		Squared	48.0356
			2394.5	5.31521		Measured	450.5
		Low confidence	23.3131	2.10117	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	Rooted	48.9847
			69.9153	19.4914		Squared	1362.75
			330	1.47982	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Ranked	223
			543.5	4.4149	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	Measured	2399.5
3	0	High confidence	0.00001	561325	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Squared	5.61325
				1240970		Rooted	12.4097
			109	10900000	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	Measured	0.00001
			11083.9	2.47638	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	Ranked	4475.84
		Low confidence	1.87479	187479	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Squared	0.00001
			9.43398	943398	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Rooted
			89	8900000		Measured
			20617	2.14604	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	Ranked	9607
	1	High confidence	26.4292	1.92839	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Rooted	50.9657
			28	1.86667	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	Ranked	15
			115.48	13.8285	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Squared	1596.92
			698.5	3.71868		Measured	2597.5
		Low confidence	23.3131	2.10117	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	Rooted	48.9847
			69.9153	19.4914		Squared	1362.75
			330	1.47982	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	Ranked	223
			543.5	4.4149	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	Measured	2399.5
4	0	High confidence	2.81207	281207	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	Squared	0.00001
			10.4403	1044030		Rooted

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.