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

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Showing element 1 to 50 of 14920 in total

Interaction Map  : High confidence
Network Comparison Type  : Divided

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

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.