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	red	Value Type	Network Comparison Type	Interaction Map	network_comparison	Filtered	green

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Showing element 51 to 100 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

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

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.