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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 14920 in total

Interaction Map  : High confidence
Network Comparison Type  : Divided

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

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.