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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 14920 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence

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

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.