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

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Showing element 1 to 50 of 25824 in total

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

Rank	Value Type	description	green	red	network_comparison
1	Measured	rad50-interacting protein 1. [refseq;acc:nm_021930]	2394.5	450.5	5.31521
	Ranked	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	24	10	2.4
	Squared	rad50-interacting protein 1. [refseq;acc:nm_021930]	1357.07	48.0356	28.2513
	Rooted		48.9336	21.225	2.30547
2	Measured	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	2394.5	450.5	5.31521
	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]	28	15	1.86667
	Squared	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	1357.07	48.0356	28.2513
	Rooted		48.9336	21.225	2.30547
3	Measured	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	698.5	2597.5	3.71868
	Ranked	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	28	15	1.86667
	Squared	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	115.48	1596.92	13.8285
	Rooted		26.4292	50.9657	1.92839
4	Measured	hbs1-like. [refseq;acc:nm_006620]	698.5	2597.5	3.71868
	Ranked	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	28	15	1.86667
	Squared	hbs1-like. [refseq;acc:nm_006620]	115.48	1596.92	13.8285
	Rooted		26.4292	50.9657	1.92839
5	Measured	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	339.5	1153.5	3.39764
	Ranked	cytohesin 4. [swissprot;acc:q9uia0]	28	15	1.86667
	Squared	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	27.2805	314.926	11.544
	Rooted		18.4255	33.9632	1.84327
6	Measured	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	339.5	1153.5	3.39764
	Ranked	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	28	15	1.86667
	Squared	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	27.2805	314.926	11.544
	Rooted		18.4255	33.9632	1.84327
7	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]	339.5	1153.5	3.39764
	Ranked	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	322	215	1.49767
	Squared	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]	27.2805	314.926	11.544
	Rooted		18.4255	33.9632	1.84327
8	Measured	db83 protein. [swissprot;acc:p57088]	339.5	1153.5	3.39764
	Ranked	hbs1-like. [refseq;acc:nm_006620]	322	215	1.49767
	Squared	db83 protein. [swissprot;acc:p57088]	27.2805	314.926	11.544
	Rooted		18.4255	33.9632	1.84327
9	Measured	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	1281.5	398.5	3.21581
	Ranked	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	309	212	1.45755
	Squared	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	388.696	37.5863	10.3414
	Rooted		35.798	19.9625	1.79326
10	Measured	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	1281.5	398.5	3.21581
	Ranked	protein x 0004. [refseq;acc:nm_016301]	309	212	1.45755
	Squared	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	388.696	37.5863	10.3414
	Rooted		35.798	19.9625	1.79326
11	Measured	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	1281.5	398.5	3.21581
	Ranked	rad50-interacting protein 1. [refseq;acc:nm_021930]	232	337	1.45259
	Squared	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	388.696	37.5863	10.3414
	Rooted		35.798	19.9625	1.79326
12	Measured	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	1281.5	398.5	3.21581
	Ranked	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	232	337	1.45259
	Squared	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	388.696	37.5863	10.3414
	Rooted		35.798	19.9625	1.79326
13	Measured	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	1281.5	398.5	3.21581
	Ranked	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	212.554	288.754	1.3585

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.