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

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Showing element 1 to 50 of 14920 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence

Rank	description	Value Type	red	green	network_comparison	Filtered
1	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Ranked	4294	15915	3.70633	0
	cab2. [refseq;acc:nm_033419]	Squared	0.00001	7.16592	716592
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Measured	364	0.00001	36400000
		Rooted	19.0788		1907880
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Ranked	10	24	2.4	1
	rad50-interacting protein 1. [refseq;acc:nm_021930]	Measured	450.5	2394.5	5.31521
		Squared	48.0356	1357.07	28.2513
		Rooted	21.225	48.9336	2.30547
2	cab2. [refseq;acc:nm_033419]	Measured	0.00001	174	17400000	0
	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]	Ranked	15	28	1.86667	1
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]		5865	14977	2.55362	0
	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Squared	5.61325	0.00001	561325
		Rooted	12.4097		1240970
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Measured	450.5	2394.5	5.31521	1
		Squared	48.0356	1357.07	28.2513
		Rooted	21.225	48.9336	2.30547
3	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	Ranked	15	28	1.86667
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Measured	2597.5	698.5	3.71868
		Squared	1596.92	115.48	13.8285
		Rooted	50.9657	26.4292	1.92839
	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	Ranked	4475.84	11083.9	2.47638	0
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	Measured	0.00001	109	10900000
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Squared	5.61325	0.00001	561325
		Rooted	12.4097		1240970
4	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Ranked	15	28	1.86667	1
	hbs1-like. [refseq;acc:nm_006620]	Measured	2597.5	698.5	3.71868
		Squared	1596.92	115.48	13.8285
		Rooted	50.9657	26.4292	1.92839
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Measured	0.00001	89	8900000	0
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Ranked	8906	21883	2.45711
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	Squared	0.00001	2.81207	281207
		Rooted		10.4403	1044030
5	cytohesin 4. [swissprot;acc:q9uia0]	Ranked	15	28	1.86667	1
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Squared	0.00001	1.87479	187479	0
		Rooted		9.43398	943398
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Measured		89	8900000
	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]		1153.5	339.5	3.39764	1
		Squared	314.926	27.2805	11.544
		Rooted	33.9632	18.4255	1.84327
	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	Ranked	5510.5	11965.7	2.17144	0
6	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]		15	28	1.86667	1
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Measured	0.00001	89	8900000	0
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Squared		1.87479	187479
		Rooted		9.43398	943398
	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	Measured	1153.5	339.5	3.39764	1
		Squared	314.926	27.2805	11.544
		Rooted	33.9632	18.4255	1.84327
	ubiquitin protein ligase. [refseq;acc:nm_130466]	Ranked	7523	15339.2	2.03897	0
7	cab2. [refseq;acc:nm_033419]		21866	10950	1.99689
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]		215	322	1.49767	1

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.