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	Value Type	green	description	Network Comparison Type	Interaction Map	network_comparison	red

Results: HTML CSV LaTeX

Showing element 1 to 50 of 12912 in total

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

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