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

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Showing element 23 to 72 of 12912 in total

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

Rank	Value Type	description	red	green	network_comparison
6	Squared	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	314.926	27.2805	11.544
	Rooted		33.9632	18.4255	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]	1153.5	339.5	3.39764
	Ranked	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	215	322	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]	314.926	27.2805	11.544
	Rooted		33.9632	18.4255	1.84327
8	Measured	db83 protein. [swissprot;acc:p57088]	1153.5	339.5	3.39764
	Ranked	hbs1-like. [refseq;acc:nm_006620]	215	322	1.49767
	Squared	db83 protein. [swissprot;acc:p57088]	314.926	27.2805	11.544
	Rooted		33.9632	18.4255	1.84327
9	Measured	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	398.5	1281.5	3.21581
	Ranked	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	212	309	1.45755
	Squared	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	37.5863	388.696	10.3414
	Rooted		19.9625	35.798	1.79326
10	Measured	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	398.5	1281.5	3.21581
	Ranked	protein x 0004. [refseq;acc:nm_016301]	212	309	1.45755
	Squared	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	37.5863	388.696	10.3414
	Rooted		19.9625	35.798	1.79326
11	Measured	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	398.5	1281.5	3.21581
	Ranked	rad50-interacting protein 1. [refseq;acc:nm_021930]	337	232	1.45259
	Squared	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	37.5863	388.696	10.3414
	Rooted		19.9625	35.798	1.79326
12	Measured	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	398.5	1281.5	3.21581
	Ranked	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	337	232	1.45259
	Squared	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	37.5863	388.696	10.3414
	Rooted		19.9625	35.798	1.79326
13	Measured	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	398.5	1281.5	3.21581
	Ranked	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	288.754	212.554	1.3585
	Squared	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	37.5863	388.696	10.3414
	Rooted		19.9625	35.798	1.79326
14	Measured	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	398.5	1281.5	3.21581
	Ranked	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	56.6768	75.3531	1.32952
	Squared	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	37.5863	388.696	10.3414
	Rooted		19.9625	35.798	1.79326
15	Measured	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	2671	871	3.06659
	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
	Squared	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	1688.58	179.56	9.40399
	Rooted	gbp protein isoform a. [refseq;acc:nm_017870]	23.9771	42.4773	1.77158
16	Measured	protein x 0004. [refseq;acc:nm_016301]	2671	871	3.06659
	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
	Squared	protein x 0004. [refseq;acc:nm_016301]	1688.58	179.56	9.40399
	Rooted	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	51.6817	29.5127	1.75117
17	Measured	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	460	1365	2.96739
	Ranked	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	56.7841	75.447	1.32866
	Squared	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	50.0828	441	8.80542
	Rooted	protein x 0004. [refseq;acc:nm_016301]	51.6817	29.5127	1.75117
18	Measured	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	677.5	1865.5	2.75351
	Ranked	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	185.678	245.247	1.32082
	Squared	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	108.641	823.69	7.58176
	Rooted	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	21.4476	36.9459	1.72261

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.