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

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Showing element 1 to 50 of 38536 in total

Network Comparison Type  : Divided

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

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.