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

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Showing element 51 to 100 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison
7	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Squared	Subtracted	310840	442993	132153
	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
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Ranked		288.754	212.554	76.2
	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
8	db83 protein. [swissprot;acc:p57088]	Measured		1153.5	339.5	3.39764
		Squared		314.926	27.2805	11.544
		Rooted		33.9632	18.4255	1.84327
	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Squared	Subtracted	250303	354894	104591
	hbs1-like. [refseq;acc:nm_006620]	Ranked	Divided	215	322	1.49767
	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]		Subtracted	288	362	74
	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	Measured		21185	28492	7307
	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	Rooted		145.551	168.796	23.245
9	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	Ranked		288	362	74
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Rooted		145.551	168.796	23.245
	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	Measured		21185	28492	7307
	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	Squared		256169	162517	93652
	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
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Ranked		212	309	1.45755
10	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Squared	Subtracted	219048	129762	89286
	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	Measured		21185	28492	7307
	protein x 0004. [refseq;acc:nm_016301]	Ranked	Divided	212	309	1.45755
	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]		Subtracted	288	362	74
	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Measured	Divided	398.5	1281.5	3.21581
		Squared		37.5863	388.696	10.3414
		Rooted		19.9625	35.798	1.79326
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]		Subtracted	51.6817	29.5127	22.169
11	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	Measured	Divided	398.5	1281.5	3.21581
		Squared		37.5863	388.696	10.3414
		Rooted		19.9625	35.798	1.79326
	db83 protein. [swissprot;acc:p57088]	Ranked	Subtracted	288	362	74
	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	Squared		219048	129762	89286
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Measured		21185	28492	7307
	protein x 0004. [refseq;acc:nm_016301]	Rooted		51.6817	29.5127	22.169
	rad50-interacting protein 1. [refseq;acc:nm_021930]	Ranked	Divided	337	232	1.45259
12	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	Rooted	Subtracted	80.4705	101.526	21.0555
	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	Measured	Divided	398.5	1281.5	3.21581
		Squared		37.5863	388.696	10.3414
		Rooted		19.9625	35.798	1.79326
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	Ranked	Subtracted	266.856	336.233	69.377
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Squared		219048	129762	89286
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Measured		34190.9	40795.8	6604.9
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Ranked	Divided	337	232	1.45259
13	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	Rooted	Subtracted	80.4705	101.526	21.0555
	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	Measured	Divided	398.5	1281.5	3.21581
		Squared		37.5863	388.696	10.3414
		Rooted		19.9625	35.798	1.79326

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.