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

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Showing element 51 to 100 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	Network Comparison Type	description	Value Type	green	red	network_comparison
7	Divided	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]	Squared	27.2805	314.926	11.544
			Rooted	18.4255	33.9632	1.84327
	Subtracted	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Measured	28492	21185	7307
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Squared	442993	310840	132153
		pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	Rooted	168.796	145.551	23.245
		protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Ranked	212.554	288.754	76.2
8	Divided	db83 protein. [swissprot;acc:p57088]	Measured	339.5	1153.5	3.39764
			Squared	27.2805	314.926	11.544
			Rooted	18.4255	33.9632	1.84327
		hbs1-like. [refseq;acc:nm_006620]	Ranked	322	215	1.49767
	Subtracted	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Squared	354894	250303	104591
		junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	Ranked	362	288	74
		pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	Measured	28492	21185	7307
		pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	Rooted	168.796	145.551	23.245
9	Divided	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Measured	1281.5	398.5	3.21581
			Squared	388.696	37.5863	10.3414
			Rooted	35.798	19.9625	1.79326
		xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Ranked	309	212	1.45755
	Subtracted	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]		362	288	74
		mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Rooted	168.796	145.551	23.245
		pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	Measured	28492	21185	7307
		protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	Squared	162517	256169	93652
10	Divided	protein x 0004. [refseq;acc:nm_016301]	Ranked	309	212	1.45755
		tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Measured	1281.5	398.5	3.21581
			Squared	388.696	37.5863	10.3414
			Rooted	35.798	19.9625	1.79326
	Subtracted	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Squared	129762	219048	89286
		pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	Measured	28492	21185	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]	Ranked	362	288	74
		xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Rooted	29.5127	51.6817	22.169
11	Divided	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	Measured	1281.5	398.5	3.21581
			Squared	388.696	37.5863	10.3414
			Rooted	35.798	19.9625	1.79326
		rad50-interacting protein 1. [refseq;acc:nm_021930]	Ranked	232	337	1.45259
	Subtracted	db83 protein. [swissprot;acc:p57088]		362	288	74
		hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	Squared	129762	219048	89286
		mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Measured	28492	21185	7307
		protein x 0004. [refseq;acc:nm_016301]	Rooted	29.5127	51.6817	22.169
12	Divided	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	Measured	1281.5	398.5	3.21581
			Squared	388.696	37.5863	10.3414
			Rooted	35.798	19.9625	1.79326
		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Ranked	232	337	1.45259
	Subtracted	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	Rooted	101.526	80.4705	21.0555
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	Ranked	336.233	266.856	69.377
		melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Squared	129762	219048	89286
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Measured	40795.8	34190.9	6604.9
13	Divided	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]		1281.5	398.5	3.21581
			Squared	388.696	37.5863	10.3414
			Rooted	35.798	19.9625	1.79326
		protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Ranked	212.554	288.754	1.3585

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.