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

Results: HTML CSV LaTeX

Showing element 51 to 100 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	Network Comparison Type	Value Type	description	green	red	network_comparison
7	Divided	Squared	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	314.926	11.544
		Rooted		18.4255	33.9632	1.84327
	Subtracted	Measured	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	28492	21185	7307
		Ranked	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	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
		Rooted	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	168.796	145.551	23.245
8	Divided	Measured	db83 protein. [swissprot;acc:p57088]	339.5	1153.5	3.39764
		Ranked	hbs1-like. [refseq;acc:nm_006620]	322	215	1.49767
		Squared	db83 protein. [swissprot;acc:p57088]	27.2805	314.926	11.544
		Rooted		18.4255	33.9632	1.84327
	Subtracted	Measured	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	28492	21185	7307
		Ranked	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	362	288	74
		Squared	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	354894	250303	104591
		Rooted	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	168.796	145.551	23.245
9	Divided	Measured	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	1281.5	398.5	3.21581
		Ranked	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	309	212	1.45755
		Squared	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	388.696	37.5863	10.3414
		Rooted		35.798	19.9625	1.79326
	Subtracted	Measured	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	28492	21185	7307
		Ranked	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	362	288	74
		Squared	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	162517	256169	93652
		Rooted	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	168.796	145.551	23.245
10	Divided	Measured	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	1281.5	398.5	3.21581
		Ranked	protein x 0004. [refseq;acc:nm_016301]	309	212	1.45755
		Squared	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	388.696	37.5863	10.3414
		Rooted		35.798	19.9625	1.79326
	Subtracted	Measured	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	28492	21185	7307
		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]	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
		Rooted	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	29.5127	51.6817	22.169
11	Divided	Measured	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	1281.5	398.5	3.21581
		Ranked	rad50-interacting protein 1. [refseq;acc:nm_021930]	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
		Rooted		35.798	19.9625	1.79326
	Subtracted	Measured	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	28492	21185	7307
		Ranked	db83 protein. [swissprot;acc:p57088]	362	288	74
		Squared	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	129762	219048	89286
		Rooted	protein x 0004. [refseq;acc:nm_016301]	29.5127	51.6817	22.169
12	Divided	Measured	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	1281.5	398.5	3.21581
		Ranked	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	232	337	1.45259
		Squared	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	388.696	37.5863	10.3414
		Rooted		35.798	19.9625	1.79326
	Subtracted	Measured	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	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
		Squared	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	129762	219048	89286
		Rooted	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	101.526	80.4705	21.0555
13	Divided	Measured	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	1281.5	398.5	3.21581
		Ranked	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	212.554	288.754	1.3585
		Squared	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	388.696	37.5863	10.3414
		Rooted		35.798	19.9625	1.79326

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.