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

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Showing element 51 to 100 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	Value Type	green	network_comparison	red
7	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Subtracted	Squared	442993	132153	310840
	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]		Rooted	168.796	23.245	145.551
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]		Ranked	212.554	76.2	288.754
	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	Measured	339.5	3.39764	1153.5
			Squared	27.2805	11.544	314.926
			Rooted	18.4255	1.84327	33.9632
8	db83 protein. [swissprot;acc:p57088]		Measured	339.5	3.39764	1153.5
			Squared	27.2805	11.544	314.926
			Rooted	18.4255	1.84327	33.9632
	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Subtracted	Squared	354894	104591	250303
	hbs1-like. [refseq;acc:nm_006620]	Divided	Ranked	322	1.49767	215
	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	Subtracted		362	74	288
	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]		Measured	28492	7307	21185
	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]		Rooted	168.796	23.245	145.551
9	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]		Ranked	362	74	288
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]		Rooted	168.796	23.245	145.551
	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]		Measured	28492	7307	21185
	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]		Squared	162517	93652	256169
	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Divided	Measured	1281.5	3.21581	398.5
			Squared	388.696	10.3414	37.5863
			Rooted	35.798	1.79326	19.9625
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]		Ranked	309	1.45755	212
10	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Subtracted	Squared	129762	89286	219048
	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]		Measured	28492	7307	21185
	protein x 0004. [refseq;acc:nm_016301]	Divided	Ranked	309	1.45755	212
	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		362	74	288
	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Divided	Measured	1281.5	3.21581	398.5
			Squared	388.696	10.3414	37.5863
			Rooted	35.798	1.79326	19.9625
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Subtracted		29.5127	22.169	51.6817
11	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	Divided	Measured	1281.5	3.21581	398.5
			Squared	388.696	10.3414	37.5863
			Rooted	35.798	1.79326	19.9625
	db83 protein. [swissprot;acc:p57088]	Subtracted	Ranked	362	74	288
	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]		Squared	129762	89286	219048
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]		Measured	28492	7307	21185
	protein x 0004. [refseq;acc:nm_016301]		Rooted	29.5127	22.169	51.6817
	rad50-interacting protein 1. [refseq;acc:nm_021930]	Divided	Ranked	232	1.45259	337
12	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	Subtracted	Rooted	101.526	21.0555	80.4705
	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	Divided	Measured	1281.5	3.21581	398.5
			Squared	388.696	10.3414	37.5863
			Rooted	35.798	1.79326	19.9625
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	Subtracted	Ranked	336.233	69.377	266.856
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]		Squared	129762	89286	219048
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]		Measured	40795.8	6604.9	34190.9
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Divided	Ranked	232	1.45259	337
13	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	Subtracted	Rooted	101.526	21.0555	80.4705
	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	Divided	Measured	1281.5	3.21581	398.5
			Squared	388.696	10.3414	37.5863
			Rooted	35.798	1.79326	19.9625

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.