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	description	Value Type	Network Comparison Type	Interaction Map	Filtered	green	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	Hugo	description	Value Type	green	red	network_comparison
1	RINT1	rad50-interacting protein 1. [refseq;acc:nm_021930]	Measured	2394.5	450.5	5.31521
			Squared	1357.07	48.0356	28.2513
			Rooted	48.9336	21.225	2.30547
	UBAC1	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Ranked	24	10	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]		28	15	1.86667
	RHOBTB2	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Measured	2394.5	450.5	5.31521
			Squared	1357.07	48.0356	28.2513
			Rooted	48.9336	21.225	2.30547
3	HLX	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Measured	698.5	2597.5	3.71868
			Squared	115.48	1596.92	13.8285
			Rooted	26.4292	50.9657	1.92839
	PSCD1	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	Ranked	28	15	1.86667
4	HBS1L	hbs1-like. [refseq;acc:nm_006620]	Measured	698.5	2597.5	3.71868
			Squared	115.48	1596.92	13.8285
			Rooted	26.4292	50.9657	1.92839
	PSCD2	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Ranked	28	15	1.86667
5	JPH3	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	Measured	339.5	1153.5	3.39764
			Squared	27.2805	314.926	11.544
			Rooted	18.4255	33.9632	1.84327
	PSCD4	cytohesin 4. [swissprot;acc:q9uia0]	Ranked	28	15	1.86667
6	JPH2	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	Measured	339.5	1153.5	3.39764
			Squared	27.2805	314.926	11.544
			Rooted	18.4255	33.9632	1.84327
	PSCD3	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	Ranked	28	15	1.86667
7	HLX	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]		322	215	1.49767
	SMPD2	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	339.5	1153.5	3.39764
			Squared	27.2805	314.926	11.544
			Rooted	18.4255	33.9632	1.84327
8	HBS1L	hbs1-like. [refseq;acc:nm_006620]	Ranked	322	215	1.49767
	TMEM33	db83 protein. [swissprot;acc:p57088]	Measured	339.5	1153.5	3.39764
			Squared	27.2805	314.926	11.544
			Rooted	18.4255	33.9632	1.84327
9	TOB2	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Measured	1281.5	398.5	3.21581
			Squared	388.696	37.5863	10.3414
			Rooted	35.798	19.9625	1.79326
	XAB1	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Ranked	309	212	1.45755
10	ATPBD1C	protein x 0004. [refseq;acc:nm_016301]
	TOB1	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Measured	1281.5	398.5	3.21581
			Squared	388.696	37.5863	10.3414
			Rooted	35.798	19.9625	1.79326
11	DAB2IP	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	Measured	1281.5	398.5	3.21581
			Squared	388.696	37.5863	10.3414
			Rooted	35.798	19.9625	1.79326
	RINT1	rad50-interacting protein 1. [refseq;acc:nm_021930]	Ranked	232	337	1.45259
12	CPEB4	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	Measured	1281.5	398.5	3.21581
			Squared	388.696	37.5863	10.3414
			Rooted	35.798	19.9625	1.79326
	RHOBTB2	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Ranked	232	337	1.45259
13	CPEB3	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	Measured	1281.5	398.5	3.21581
			Squared	388.696	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
- 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.