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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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