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

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Showing element 12 to 61 of 12912 in total

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

Rank	description	Value Type	red	green	network_comparison
3	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Rooted	50.9657	26.4292	1.92839
4	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Ranked	15	28	1.86667
	hbs1-like. [refseq;acc:nm_006620]	Measured	2597.5	698.5	3.71868
		Squared	1596.92	115.48	13.8285
		Rooted	50.9657	26.4292	1.92839
5	cytohesin 4. [swissprot;acc:q9uia0]	Ranked	15	28	1.86667
	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	Measured	1153.5	339.5	3.39764
		Squared	314.926	27.2805	11.544
		Rooted	33.9632	18.4255	1.84327
6	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	Ranked	15	28	1.86667
	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	Measured	1153.5	339.5	3.39764
		Squared	314.926	27.2805	11.544
		Rooted	33.9632	18.4255	1.84327
7	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Ranked	215	322	1.49767
	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	1153.5	339.5	3.39764
		Squared	314.926	27.2805	11.544
		Rooted	33.9632	18.4255	1.84327
8	db83 protein. [swissprot;acc:p57088]	Measured	1153.5	339.5	3.39764
		Squared	314.926	27.2805	11.544
		Rooted	33.9632	18.4255	1.84327
	hbs1-like. [refseq;acc:nm_006620]	Ranked	215	322	1.49767
9	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Measured	398.5	1281.5	3.21581
		Squared	37.5863	388.696	10.3414
		Rooted	19.9625	35.798	1.79326
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Ranked	212	309	1.45755
10	protein x 0004. [refseq;acc:nm_016301]
	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Measured	398.5	1281.5	3.21581
		Squared	37.5863	388.696	10.3414
		Rooted	19.9625	35.798	1.79326
11	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	Measured	398.5	1281.5	3.21581
		Squared	37.5863	388.696	10.3414
		Rooted	19.9625	35.798	1.79326
	rad50-interacting protein 1. [refseq;acc:nm_021930]	Ranked	337	232	1.45259
12	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	Measured	398.5	1281.5	3.21581
		Squared	37.5863	388.696	10.3414
		Rooted	19.9625	35.798	1.79326
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Ranked	337	232	1.45259
13	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	Measured	398.5	1281.5	3.21581
		Squared	37.5863	388.696	10.3414
		Rooted	19.9625	35.798	1.79326
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Ranked	288.754	212.554	1.3585
14	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]		56.6768	75.3531	1.32952
	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	Measured	398.5	1281.5	3.21581
		Squared	37.5863	388.696	10.3414
		Rooted	19.9625	35.798	1.79326
15	gbp protein isoform a. [refseq;acc:nm_017870]		23.9771	42.4773	1.77158
	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	Ranked	56.7244	75.3948	1.32914
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Measured	2671	871	3.06659
		Squared	1688.58	179.56	9.40399
16	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	Ranked	56.7252	75.3954	1.32913

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.