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 25 to 74 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	Value Type	description	Network Comparison Type	red	green	network_comparison
4	Measured	cytohesin 4. [swissprot;acc:q9uia0]	Subtracted	41482.5	33356.5	8126
		hbs1-like. [refseq;acc:nm_006620]	Divided	2597.5	698.5	3.71868
	Ranked	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]		15	28	1.86667
		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Subtracted	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
	Rooted			50.9657	26.4292	1.92839
			Subtracted			24.5365
5	Measured	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]		41482.5	33356.5	8126
		junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	Divided	1153.5	339.5	3.39764
	Ranked	cytohesin 4. [swissprot;acc:q9uia0]		15	28	1.86667
		xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Subtracted	212	309	97
	Squared	cytohesin 4. [swissprot;acc:q9uia0]		407289	263351	143938
		junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	Divided	314.926	27.2805	11.544
	Rooted	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Subtracted	145.551	168.796	23.245
		junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	Divided	33.9632	18.4255	1.84327
6	Measured	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]		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
	Ranked	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	Divided	15	28	1.86667
		protein x 0004. [refseq;acc:nm_016301]	Subtracted	212	309	97
	Squared	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]		407289	263351	143938
		junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	Divided	314.926	27.2805	11.544
	Rooted			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
7	Measured	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]		21185	28492	7307
		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]	Divided	1153.5	339.5	3.39764
	Ranked	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]		215	322	1.49767
		protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Subtracted	288.754	212.554	76.2
	Squared	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]		310840	442993	132153
		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]	Divided	314.926	27.2805	11.544
	Rooted	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	Subtracted	145.551	168.796	23.245
		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]	Divided	33.9632	18.4255	1.84327
8	Measured	db83 protein. [swissprot;acc:p57088]		1153.5	339.5	3.39764
		pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	Subtracted	21185	28492	7307
	Ranked	hbs1-like. [refseq;acc:nm_006620]	Divided	215	322	1.49767
		junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	Subtracted	288	362	74
	Squared	db83 protein. [swissprot;acc:p57088]	Divided	314.926	27.2805	11.544
		deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Subtracted	250303	354894	104591
	Rooted	db83 protein. [swissprot;acc:p57088]	Divided	33.9632	18.4255	1.84327
		pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	Subtracted	145.551	168.796	23.245
9	Measured	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]		21185	28492	7307
		tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Divided	398.5	1281.5	3.21581
	Ranked	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	Subtracted	288	362	74
		xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Divided	212	309	1.45755
	Squared	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	Subtracted	256169	162517	93652
		tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Divided	37.5863	388.696	10.3414
	Rooted	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Subtracted	145.551	168.796	23.245
		tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Divided	19.9625	35.798	1.79326
10	Measured	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	Subtracted	21185	28492	7307
		tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Divided	398.5	1281.5	3.21581

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.