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

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Showing element 62 to 111 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	Network Comparison Type	Hugo	Value Type	description	red	network_comparison	green
8	Subtracted	JPH3	Ranked	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	288	74	362
		PANK1	Measured	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	21185	7307	28492
		PANK3	Rooted	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	145.551	23.245	168.796
9	Divided	TOB2	Measured	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	398.5	3.21581	1281.5
			Squared		37.5863	10.3414	388.696
			Rooted		19.9625	1.79326	35.798
		XAB1	Ranked	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	212	1.45755	309
	Subtracted	JPH2		junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	288	74	362
		PANK2	Measured	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	21185	7307	28492
		PPP1R7	Squared	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	256169	93652	162517
		SLC25A43	Rooted	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	145.551	23.245	168.796
10	Divided	ATPBD1C	Ranked	protein x 0004. [refseq;acc:nm_016301]	212	1.45755	309
		TOB1	Measured	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	398.5	3.21581	1281.5
			Squared		37.5863	10.3414	388.696
			Rooted		19.9625	1.79326	35.798
	Subtracted	MAGED4	Squared	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	219048	89286	129762
		PANK3	Measured	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	21185	7307	28492
		SMPD2	Ranked	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	74	362
		XAB1	Rooted	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	51.6817	22.169	29.5127
11	Divided	DAB2IP	Measured	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	398.5	3.21581	1281.5
			Squared		37.5863	10.3414	388.696
			Rooted		19.9625	1.79326	35.798
		RINT1	Ranked	rad50-interacting protein 1. [refseq;acc:nm_021930]	337	1.45259	232
	Subtracted	ATPBD1C	Rooted	protein x 0004. [refseq;acc:nm_016301]	51.6817	22.169	29.5127
		MAGEE2	Squared	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	219048	89286	129762
		SLC25A43	Measured	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	21185	7307	28492
		TMEM33	Ranked	db83 protein. [swissprot;acc:p57088]	288	74	362
12	Divided	CPEB4	Measured	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	398.5	3.21581	1281.5
			Squared		37.5863	10.3414	388.696
			Rooted		19.9625	1.79326	35.798
		RHOBTB2	Ranked	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	337	1.45259	232
	Subtracted	no value	Measured	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	34190.9	6604.9	40795.8
			Ranked	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	266.856	69.377	336.233
			Squared	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	219048	89286	129762
		ARRB2	Rooted	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	80.4705	21.0555	101.526
13	Divided	CPEB3	Measured	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	398.5	3.21581	1281.5
			Squared		37.5863	10.3414	388.696
			Rooted		19.9625	1.79326	35.798
		UFC1	Ranked	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	288.754	1.3585	212.554
	Subtracted	ARRB1	Rooted	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	80.4705	21.0555	101.526
		GNG12	Ranked	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6]	266.856	69.377	336.233
		MAGEA11	Squared	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	219048	89286	129762
		MYO5B	Measured	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	21591.5	6313	27904.5
14	Divided	ATG4A	Ranked	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	56.6768	1.32952	75.3531
		RASAL2	Measured	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	398.5	3.21581	1281.5
			Squared		37.5863	10.3414	388.696
			Rooted		19.9625	1.79326	35.798
	Subtracted	GNG4	Ranked	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	266.863	69.328	336.191
		MAGEA2B	Squared	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	219048	89286	129762
		MYO5C	Measured	myosin vc (myosin 5c). [swissprot;acc:q9nqx4]	21591.5	6313	27904.5

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
- 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.