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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 38536 in total

Interaction Map  : High confidence
Network Comparison Type  : Divided

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

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.