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

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Showing element 1 to 50 of 12912 in total

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

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

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.