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	Value Type	Network Comparison Type	Filtered	Interaction Map	network_comparison	red	green

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Showing element 1 to 50 of 12912 in total

Network Comparison Type  : Divided
Filtered  : 1
Interaction Map  : High confidence

Rank	description	Value Type	network_comparison	red	green
1	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Ranked	2.4	10	24
	rad50-interacting protein 1. [refseq;acc:nm_021930]	Measured	5.31521	450.5	2394.5
		Squared	28.2513	48.0356	1357.07
		Rooted	2.30547	21.225	48.9336
2	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]	Ranked	1.86667	15	28
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Measured	5.31521	450.5	2394.5
		Squared	28.2513	48.0356	1357.07
		Rooted	2.30547	21.225	48.9336
3	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	Ranked	1.86667	15	28
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Measured	3.71868	2597.5	698.5
		Squared	13.8285	1596.92	115.48
		Rooted	1.92839	50.9657	26.4292
4	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Ranked	1.86667	15	28
	hbs1-like. [refseq;acc:nm_006620]	Measured	3.71868	2597.5	698.5
		Squared	13.8285	1596.92	115.48
		Rooted	1.92839	50.9657	26.4292
5	cytohesin 4. [swissprot;acc:q9uia0]	Ranked	1.86667	15	28
	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	Measured	3.39764	1153.5	339.5
		Squared	11.544	314.926	27.2805
		Rooted	1.84327	33.9632	18.4255
6	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	Ranked	1.86667	15	28
	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	Measured	3.39764	1153.5	339.5
		Squared	11.544	314.926	27.2805
		Rooted	1.84327	33.9632	18.4255
7	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Ranked	1.49767	215	322
	sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906]	Measured	3.39764	1153.5	339.5
		Squared	11.544	314.926	27.2805
		Rooted	1.84327	33.9632	18.4255
8	db83 protein. [swissprot;acc:p57088]	Measured	3.39764	1153.5	339.5
		Squared	11.544	314.926	27.2805
		Rooted	1.84327	33.9632	18.4255
	hbs1-like. [refseq;acc:nm_006620]	Ranked	1.49767	215	322
9	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Measured	3.21581	398.5	1281.5
		Squared	10.3414	37.5863	388.696
		Rooted	1.79326	19.9625	35.798
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Ranked	1.45755	212	309
10	protein x 0004. [refseq;acc:nm_016301]
	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Measured	3.21581	398.5	1281.5
		Squared	10.3414	37.5863	388.696
		Rooted	1.79326	19.9625	35.798
11	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	Measured	3.21581	398.5	1281.5
		Squared	10.3414	37.5863	388.696
		Rooted	1.79326	19.9625	35.798
	rad50-interacting protein 1. [refseq;acc:nm_021930]	Ranked	1.45259	337	232
12	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	Measured	3.21581	398.5	1281.5
		Squared	10.3414	37.5863	388.696
		Rooted	1.79326	19.9625	35.798
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Ranked	1.45259	337	232
13	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	Measured	3.21581	398.5	1281.5
		Squared	10.3414	37.5863	388.696

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.