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

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Showing element 1 to 50 of 12912 in total

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

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

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.