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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 14920 in total

Interaction Map  : High confidence
Network Comparison Type  : Divided

Rank	Filtered	Value Type	description	green	network_comparison	red
1	0	Measured	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0.00001	36400000	364
		Ranked	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	15915	3.70633	4294
		Squared	cab2. [refseq;acc:nm_033419]	7.16592	716592	0.00001
		Rooted	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0.00001	1907880	19.0788
	1	Measured	rad50-interacting protein 1. [refseq;acc:nm_021930]	2394.5	5.31521	450.5
		Ranked	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	24	2.4	10
		Squared	rad50-interacting protein 1. [refseq;acc:nm_021930]	1357.07	28.2513	48.0356
		Rooted		48.9336	2.30547	21.225
2	0	Measured	cab2. [refseq;acc:nm_033419]	174	17400000	0.00001
		Ranked	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	14977	2.55362	5865
		Squared	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	0.00001	561325	5.61325
		Rooted			1240970	12.4097
	1	Measured	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	2394.5	5.31521	450.5
		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]	28	1.86667	15
		Squared	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	1357.07	28.2513	48.0356
		Rooted		48.9336	2.30547	21.225
3	0	Measured	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	109	10900000	0.00001
		Ranked	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	11083.9	2.47638	4475.84
		Squared	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	0.00001	561325	5.61325
		Rooted			1240970	12.4097
	1	Measured	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	698.5	3.71868	2597.5
		Ranked	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	28	1.86667	15
		Squared	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	115.48	13.8285	1596.92
		Rooted		26.4292	1.92839	50.9657
4	0	Measured	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	89	8900000	0.00001
		Ranked	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	21883	2.45711	8906
		Squared	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	2.81207	281207	0.00001
		Rooted		10.4403	1044030
	1	Measured	hbs1-like. [refseq;acc:nm_006620]	698.5	3.71868	2597.5
		Ranked	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	28	1.86667	15
		Squared	hbs1-like. [refseq;acc:nm_006620]	115.48	13.8285	1596.92
		Rooted		26.4292	1.92839	50.9657
5	0	Measured	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	89	8900000	0.00001
		Ranked	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	11965.7	2.17144	5510.5
		Squared	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	1.87479	187479	0.00001
		Rooted		9.43398	943398
	1	Measured	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	339.5	3.39764	1153.5
		Ranked	cytohesin 4. [swissprot;acc:q9uia0]	28	1.86667	15
		Squared	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	27.2805	11.544	314.926
		Rooted		18.4255	1.84327	33.9632
6	0	Measured	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	89	8900000	0.00001
		Ranked	ubiquitin protein ligase. [refseq;acc:nm_130466]	15339.2	2.03897	7523
		Squared	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	1.87479	187479	0.00001
		Rooted		9.43398	943398
	1	Measured	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	339.5	3.39764	1153.5
		Ranked	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	28	1.86667	15
		Squared	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	27.2805	11.544	314.926
		Rooted		18.4255	1.84327	33.9632
7	0	Measured	sedlin. [swissprot;acc:o14582]	43	4300000	0.00001
		Ranked	cab2. [refseq;acc:nm_033419]	10950	1.99689	21866

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.