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

Results: HTML CSV LaTeX

Showing element 51 to 100 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

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