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

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Showing element 18 to 67 of 12912 in total

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

Rank	Hugo	Value Type	description	red	green	network_comparison
5	JPH3	Squared	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	314.926	27.2805	11.544
		Rooted		33.9632	18.4255	1.84327
	PSCD4	Ranked	cytohesin 4. [swissprot;acc:q9uia0]	15	28	1.86667
6	JPH2	Measured	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	1153.5	339.5	3.39764
		Squared		314.926	27.2805	11.544
		Rooted		33.9632	18.4255	1.84327
	PSCD3	Ranked	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	15	28	1.86667
7	HLX		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	215	322	1.49767
	SMPD2	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]	1153.5	339.5	3.39764
		Squared		314.926	27.2805	11.544
		Rooted		33.9632	18.4255	1.84327
8	HBS1L	Ranked	hbs1-like. [refseq;acc:nm_006620]	215	322	1.49767
	TMEM33	Measured	db83 protein. [swissprot;acc:p57088]	1153.5	339.5	3.39764
		Squared		314.926	27.2805	11.544
		Rooted		33.9632	18.4255	1.84327
9	TOB2	Measured	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	398.5	1281.5	3.21581
		Squared		37.5863	388.696	10.3414
		Rooted		19.9625	35.798	1.79326
	XAB1	Ranked	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	212	309	1.45755
10	ATPBD1C		protein x 0004. [refseq;acc:nm_016301]
	TOB1	Measured	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	398.5	1281.5	3.21581
		Squared		37.5863	388.696	10.3414
		Rooted		19.9625	35.798	1.79326
11	DAB2IP	Measured	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	398.5	1281.5	3.21581
		Squared		37.5863	388.696	10.3414
		Rooted		19.9625	35.798	1.79326
	RINT1	Ranked	rad50-interacting protein 1. [refseq;acc:nm_021930]	337	232	1.45259
12	CPEB4	Measured	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	398.5	1281.5	3.21581
		Squared		37.5863	388.696	10.3414
		Rooted		19.9625	35.798	1.79326
	RHOBTB2	Ranked	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	337	232	1.45259
13	CPEB3	Measured	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	398.5	1281.5	3.21581
		Squared		37.5863	388.696	10.3414
		Rooted		19.9625	35.798	1.79326
	UFC1	Ranked	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	288.754	212.554	1.3585
14	ATG4A		cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	56.6768	75.3531	1.32952
	RASAL2	Measured	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	398.5	1281.5	3.21581
		Squared		37.5863	388.696	10.3414
		Rooted		19.9625	35.798	1.79326
15	MAP1LC3B	Ranked	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	56.7244	75.3948	1.32914
	TMEM132A	Rooted	gbp protein isoform a. [refseq;acc:nm_017870]	23.9771	42.4773	1.77158
	XAB1	Measured	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	2671	871	3.06659
		Squared		1688.58	179.56	9.40399
16	ATPBD1C	Measured	protein x 0004. [refseq;acc:nm_016301]	2671	871	3.06659
		Squared		1688.58	179.56	9.40399
	MAP1LC3A	Ranked	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	56.7252	75.3954	1.32913
	XAB1	Rooted	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	51.6817	29.5127	1.75117
17	ATG4B	Ranked	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	56.7841	75.447	1.32866
	ATPBD1C	Rooted	protein x 0004. [refseq;acc:nm_016301]	51.6817	29.5127	1.75117
	DGCR14	Measured	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	460	1365	2.96739

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.