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

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Showing element 23 to 72 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	Hugo	description	Value Type	Network Comparison Type	red	green	network_comparison
3	PSCD2	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Measured	Subtracted	41482.5	33356.5	8126
	RINT1	rad50-interacting protein 1. [refseq;acc:nm_021930]	Ranked		337	232	105
4	HBS1L	hbs1-like. [refseq;acc:nm_006620]	Measured	Divided	2597.5	698.5	3.71868
			Squared		1596.92	115.48	13.8285
			Rooted		50.9657	26.4292	1.92839
				Subtracted			24.5365
	PSCD2	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Ranked	Divided	15	28	1.86667
			Squared	Subtracted	407289	263351	143938
	PSCD4	cytohesin 4. [swissprot;acc:q9uia0]	Measured		41482.5	33356.5	8126
	RHOBTB2	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Ranked		337	232	105
5	JPH3	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	Measured	Divided	1153.5	339.5	3.39764
			Squared		314.926	27.2805	11.544
			Rooted		33.9632	18.4255	1.84327
	MRPS17	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]		Subtracted	145.551	168.796	23.245
	PSCD3	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	Measured		41482.5	33356.5	8126
	PSCD4	cytohesin 4. [swissprot;acc:q9uia0]	Ranked	Divided	15	28	1.86667
			Squared	Subtracted	407289	263351	143938
	XAB1	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Ranked		212	309	97
6	ATPBD1C	protein x 0004. [refseq;acc:nm_016301]
	JPH2	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	Measured	Divided	1153.5	339.5	3.39764
			Squared		314.926	27.2805	11.544
			Rooted		33.9632	18.4255	1.84327
	PANK1	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]		Subtracted	145.551	168.796	23.245
	PSCD3	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	Ranked	Divided	15	28	1.86667
			Squared	Subtracted	407289	263351	143938
	UBAC1	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Measured		44490.5	36927.5	7563
7	no value	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Squared		310840	442993	132153
	HLX	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Ranked	Divided	215	322	1.49767
	MRPS17	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Measured	Subtracted	21185	28492	7307
	PANK2	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	Rooted		145.551	168.796	23.245
	SMPD2	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]	Measured	Divided	1153.5	339.5	3.39764
			Squared		314.926	27.2805	11.544
			Rooted		33.9632	18.4255	1.84327
	UFC1	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Ranked	Subtracted	288.754	212.554	76.2
8	DNASE2B	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Squared		250303	354894	104591
	HBS1L	hbs1-like. [refseq;acc:nm_006620]	Ranked	Divided	215	322	1.49767
	JPH3	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]		Subtracted	288	362	74
	PANK1	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	Measured		21185	28492	7307
	PANK3	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	Rooted		145.551	168.796	23.245
	TMEM33	db83 protein. [swissprot;acc:p57088]	Measured	Divided	1153.5	339.5	3.39764
			Squared		314.926	27.2805	11.544
			Rooted		33.9632	18.4255	1.84327
9	JPH2	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	Ranked	Subtracted	288	362	74
	PANK2	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	Measured		21185	28492	7307
	PPP1R7	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	Squared		256169	162517	93652
	SLC25A43	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Rooted		145.551	168.796	23.245
	TOB2	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Measured	Divided	398.5	1281.5	3.21581
			Squared		37.5863	388.696	10.3414
			Rooted		19.9625	35.798	1.79326
	XAB1	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Ranked		212	309	1.45755

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.