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

Results: HTML CSV LaTeX

Showing element 51 to 100 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	Value Type	red	green	description	Network Comparison Type	network_comparison
7	Ranked	215	322	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Divided	1.49767
		288.754	212.554	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Subtracted	76.2
	Squared	314.926	27.2805	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	11.544
		310840	442993	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Subtracted	132153
	Rooted	33.9632	18.4255	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	1.84327
		145.551	168.796	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	Subtracted	23.245
8	Measured	1153.5	339.5	db83 protein. [swissprot;acc:p57088]	Divided	3.39764
		21185	28492	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	Subtracted	7307
	Ranked	215	322	hbs1-like. [refseq;acc:nm_006620]	Divided	1.49767
		288	362	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	Subtracted	74
	Squared	314.926	27.2805	db83 protein. [swissprot;acc:p57088]	Divided	11.544
		250303	354894	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Subtracted	104591
	Rooted	33.9632	18.4255	db83 protein. [swissprot;acc:p57088]	Divided	1.84327
		145.551	168.796	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	Subtracted	23.245
9	Measured	398.5	1281.5	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Divided	3.21581
		21185	28492	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	Subtracted	7307
	Ranked	212	309	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Divided	1.45755
		288	362	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	Subtracted	74
	Squared	37.5863	388.696	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Divided	10.3414
		256169	162517	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	Subtracted	93652
	Rooted	19.9625	35.798	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Divided	1.79326
		145.551	168.796	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Subtracted	23.245
10	Measured	398.5	1281.5	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Divided	3.21581
		21185	28492	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	Subtracted	7307
	Ranked	212	309	protein x 0004. [refseq;acc:nm_016301]	Divided	1.45755
		288	362	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	74
	Squared	37.5863	388.696	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Divided	10.3414
		219048	129762	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Subtracted	89286
	Rooted	19.9625	35.798	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Divided	1.79326
		51.6817	29.5127	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Subtracted	22.169
11	Measured	398.5	1281.5	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	Divided	3.21581
		21185	28492	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Subtracted	7307
	Ranked	288	362	db83 protein. [swissprot;acc:p57088]		74
		337	232	rad50-interacting protein 1. [refseq;acc:nm_021930]	Divided	1.45259
	Squared	37.5863	388.696	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]		10.3414
		219048	129762	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	Subtracted	89286
	Rooted	19.9625	35.798	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	Divided	1.79326
		51.6817	29.5127	protein x 0004. [refseq;acc:nm_016301]	Subtracted	22.169
12	Measured	398.5	1281.5	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	Divided	3.21581
		34190.9	40795.8	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Subtracted	6604.9
	Ranked	266.856	336.233	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]		69.377
		337	232	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Divided	1.45259
	Squared	37.5863	388.696	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]		10.3414
		219048	129762	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Subtracted	89286
	Rooted	19.9625	35.798	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	Divided	1.79326
		80.4705	101.526	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	Subtracted	21.0555
13	Measured	398.5	1281.5	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	Divided	3.21581
		21591.5	27904.5	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	Subtracted	6313
	Ranked	266.856	336.233	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6]		69.377
		288.754	212.554	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Divided	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.