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	Hugo	Value Type	description	Network Comparison Type	Interaction Map	Filtered	red	green	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	Hugo	Value Type	description	red	green	network_comparison
1	RINT1	Measured	rad50-interacting protein 1. [refseq;acc:nm_021930]	450.5	2394.5	5.31521
		Squared		48.0356	1357.07	28.2513
		Rooted		21.225	48.9336	2.30547
	UBAC1	Ranked	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	10	24	2.4
2	no value		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	28	1.86667
	RHOBTB2	Measured	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	450.5	2394.5	5.31521
		Squared		48.0356	1357.07	28.2513
		Rooted		21.225	48.9336	2.30547
3	HLX	Measured	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	2597.5	698.5	3.71868
		Squared		1596.92	115.48	13.8285
		Rooted		50.9657	26.4292	1.92839
	PSCD1	Ranked	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	15	28	1.86667
4	HBS1L	Measured	hbs1-like. [refseq;acc:nm_006620]	2597.5	698.5	3.71868
		Squared		1596.92	115.48	13.8285
		Rooted		50.9657	26.4292	1.92839
	PSCD2	Ranked	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	15	28	1.86667
5	JPH3	Measured	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	1153.5	339.5	3.39764
		Squared		314.926	27.2805	11.544
		Rooted		33.9632	18.4255	1.84327
	PSCD4	Ranked	cytohesin 4. [swissprot;acc:q9uia0]	15	28	1.86667
6	JPH2	Measured	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	1153.5	339.5	3.39764
		Squared		314.926	27.2805	11.544
		Rooted		33.9632	18.4255	1.84327
	PSCD3	Ranked	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	15	28	1.86667
7	HLX		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	215	322	1.49767
	SMPD2	Measured	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]	1153.5	339.5	3.39764
		Squared		314.926	27.2805	11.544
		Rooted		33.9632	18.4255	1.84327
8	HBS1L	Ranked	hbs1-like. [refseq;acc:nm_006620]	215	322	1.49767
	TMEM33	Measured	db83 protein. [swissprot;acc:p57088]	1153.5	339.5	3.39764
		Squared		314.926	27.2805	11.544
		Rooted		33.9632	18.4255	1.84327
9	TOB2	Measured	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	398.5	1281.5	3.21581
		Squared		37.5863	388.696	10.3414
		Rooted		19.9625	35.798	1.79326
	XAB1	Ranked	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	212	309	1.45755
10	ATPBD1C		protein x 0004. [refseq;acc:nm_016301]
	TOB1	Measured	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	398.5	1281.5	3.21581
		Squared		37.5863	388.696	10.3414
		Rooted		19.9625	35.798	1.79326
11	DAB2IP	Measured	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	398.5	1281.5	3.21581
		Squared		37.5863	388.696	10.3414
		Rooted		19.9625	35.798	1.79326
	RINT1	Ranked	rad50-interacting protein 1. [refseq;acc:nm_021930]	337	232	1.45259
12	CPEB4	Measured	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	398.5	1281.5	3.21581
		Squared		37.5863	388.696	10.3414
		Rooted		19.9625	35.798	1.79326
	RHOBTB2	Ranked	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	337	232	1.45259
13	CPEB3	Measured	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	398.5	1281.5	3.21581
		Squared		37.5863	388.696	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
- Hugo is the HGNC identifier if it exists
- 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.