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

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Showing element 51 to 100 of 29840 in total

Interaction Map  : High confidence

Rank	Value Type	Network Comparison Type	description	green	network_comparison	Filtered	red
4	Measured	Subtracted	cytohesin 4. [swissprot;acc:q9uia0]	33356.5	8126	1	41482.5
			small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	21730	3026	0	18704
	Ranked	Divided	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	28	1.86667	1	15
			mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	21883	2.45711	0	8906
		Subtracted	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	21888	10363		11525
			rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	232	105	1	337
	Squared	Divided	hbs1-like. [refseq;acc:nm_006620]	115.48	13.8285		1596.92
			pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	2.81207	281207	0	0.00001
		Subtracted	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	263351	143938	1	407289
			similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	105900	30453.3	0	75446.7
	Rooted	Divided	hbs1-like. [refseq;acc:nm_006620]	26.4292	1.92839	1	50.9657
			pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	10.4403	1044030	0	0.00001
		Subtracted	hbs1-like. [refseq;acc:nm_006620]	26.4292	24.5365	1	50.9657
			mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	7.61577	21.6929	0	29.3087
5	Measured	Divided	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	89	8900000		0.00001
			junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	339.5	3.39764	1	1153.5
		Subtracted	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	33356.5	8126		41482.5
			histone h4. [swissprot;acc:p02304]	24446.3	2673.2	0	21773.1
	Ranked	Divided	cytohesin 4. [swissprot;acc:q9uia0]	28	1.86667	1	15
			ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	11965.7	2.17144	0	5510.5
		Subtracted	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	21888	10363		11525
			xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	309	97	1	212
	Squared	Divided	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	1.87479	187479	0	0.00001
			junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	27.2805	11.544	1	314.926
		Subtracted	cytohesin 4. [swissprot;acc:q9uia0]	263351	143938		407289
			zinc finger protein 277. [swissprot;acc:q9nrm2]	105900	30453.3	0	75446.7
	Rooted	Divided	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	9.43398	943398		0.00001
			junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	18.4255	1.84327	1	33.9632
		Subtracted	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	168.796	23.245		145.551
			mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0	19.0788	0	19.0788
6	Measured	Divided	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	89	8900000		0.00001
			junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	339.5	3.39764	1	1153.5
		Subtracted	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	36927.5	7563		44490.5
			similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	15605.1	2430.4	0	13174.7
	Ranked	Divided	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	28	1.86667	1	15
			ubiquitin protein ligase. [refseq;acc:nm_130466]	15339.2	2.03897	0	7523
		Subtracted	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	14977	9112		5865
			protein x 0004. [refseq;acc:nm_016301]	309	97	1	212
	Squared	Divided	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	1.87479	187479	0	0.00001
			junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	27.2805	11.544	1	314.926
		Subtracted	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]	102814	29733.2	0	73080.8
			cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	263351	143938	1	407289
	Rooted	Divided	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	9.43398	943398	0	0.00001
			junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	18.4255	1.84327	1	33.9632
		Subtracted	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	168.796	23.245		145.551
			potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	27.8029	15.6374	0	12.1655
7	Measured	Divided	sedlin. [swissprot;acc:o14582]	43	4300000		0.00001
			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]	339.5	3.39764	1	1153.5
		Subtracted	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	28492	7307		21185
			zinc finger protein 277. [swissprot;acc:q9nrm2]	15605.1	2430.4	0	13174.7

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.