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

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Showing element 1 to 50 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	Network Comparison Type	Hugo	Value Type	description	red	network_comparison	green
1	Divided	RINT1	Measured	rad50-interacting protein 1. [refseq;acc:nm_021930]	450.5	5.31521	2394.5
			Squared		48.0356	28.2513	1357.07
			Rooted		21.225	2.30547	48.9336
		UBAC1	Ranked	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	10	2.4	24
	Subtracted	no value	Measured	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]	41482.5	8126	33356.5
		HLX	Ranked	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	215	107	322
		RINT1	Rooted	rad50-interacting protein 1. [refseq;acc:nm_021930]	21.225	27.7086	48.9336
		UBAC1	Squared	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	468498	145743	322755
2	Divided	no value	Ranked	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]	15	1.86667	28
		RHOBTB2	Measured	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	450.5	5.31521	2394.5
			Squared		48.0356	28.2513	1357.07
			Rooted		21.225	2.30547	48.9336
	Subtracted	no value	Squared	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]	407289	143938	263351
		HBS1L	Ranked	hbs1-like. [refseq;acc:nm_006620]	215	107	322
		PSCD1	Measured	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	41482.5	8126	33356.5
		RHOBTB2	Rooted	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	21.225	27.7086	48.9336
3	Divided	HLX	Measured	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	2597.5	3.71868	698.5
			Squared		1596.92	13.8285	115.48
			Rooted		50.9657	1.92839	26.4292
		PSCD1	Ranked	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	15	1.86667	28
	Subtracted	HLX	Rooted	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	50.9657	24.5365	26.4292
		PSCD1	Squared	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	407289	143938	263351
		PSCD2	Measured	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	41482.5	8126	33356.5
		RINT1	Ranked	rad50-interacting protein 1. [refseq;acc:nm_021930]	337	105	232
4	Divided	HBS1L	Measured	hbs1-like. [refseq;acc:nm_006620]	2597.5	3.71868	698.5
			Squared		1596.92	13.8285	115.48
			Rooted		50.9657	1.92839	26.4292
		PSCD2	Ranked	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	15	1.86667	28
	Subtracted	HBS1L	Rooted	hbs1-like. [refseq;acc:nm_006620]	50.9657	24.5365	26.4292
		PSCD2	Squared	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	407289	143938	263351
		PSCD4	Measured	cytohesin 4. [swissprot;acc:q9uia0]	41482.5	8126	33356.5
		RHOBTB2	Ranked	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	337	105	232
5	Divided	JPH3	Measured	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	1153.5	3.39764	339.5
			Squared		314.926	11.544	27.2805
			Rooted		33.9632	1.84327	18.4255
		PSCD4	Ranked	cytohesin 4. [swissprot;acc:q9uia0]	15	1.86667	28
	Subtracted	MRPS17	Rooted	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	145.551	23.245	168.796
		PSCD3	Measured	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	41482.5	8126	33356.5
		PSCD4	Squared	cytohesin 4. [swissprot;acc:q9uia0]	407289	143938	263351
		XAB1	Ranked	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	212	97	309
6	Divided	JPH2	Measured	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	1153.5	3.39764	339.5
			Squared		314.926	11.544	27.2805
			Rooted		33.9632	1.84327	18.4255
		PSCD3	Ranked	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	15	1.86667	28
	Subtracted	ATPBD1C		protein x 0004. [refseq;acc:nm_016301]	212	97	309
		PANK1	Rooted	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	145.551	23.245	168.796
		PSCD3	Squared	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	407289	143938	263351
		UBAC1	Measured	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	44490.5	7563	36927.5
7	Divided	HLX	Ranked	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	215	1.49767	322
		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	3.39764	339.5

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.