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