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 51 to 100 of 29840 in total

Interaction Map  : High confidence

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

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.