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

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Showing element 458 to 507 of 3228 in total

Network Comparison Type  : Divided
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1

red	Rank	green	description	network_comparison
0.00001	3213	0.00001	malate dehydrogenase, cytoplasmic (ec 1.1.1.37). [swissprot;acc:p40925]	1
	3214		bs4 protein (ny-ren-18 antigen). [swissprot;acc:q9y5a7]
	3215		membrane-bound transcription factor site 2 protease (ec 3.4.24.-) (site-2 protease) (sterol-regulatory element-binding proteins intramembrane protease). [swissprot;acc:o43462]
	3216		dna excision repair protein ercc-1. [swissprot;acc:p07992]
	3217		sex comb on midleg homolog 1. [refseq;acc:nm_012236]
	3218		williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71]
	3219		protein c6orf55 (dopamine responsive protein drg-1) (my012 protein) (hspc228). [swissprot;acc:q9np79]
	3220		transcription factor ap-2 beta (ap2-beta) (activating enhancer-binding protein 2 beta). [swissprot;acc:q92481]
	3221		platelet-activating factor acetylhydrolase ib alpha subunit (ec 3.1.1.47) (paf acetylhydrolase 45 kda subunit) (paf-ah 45 kda subunit) (paf-ah alpha) (pafah alpha) (lissencephaly-1 protein) (lis- 1). [swissprot;acc:p43034]
	3222		aldehyde dehydrogenase 7 (ec 1.2.1.5). [swissprot;acc:p43353]
	3223		ras-related protein ral-a. [swissprot;acc:p11233]
	3224		integrin alpha-3 precursor (galactoprotein b3) (gapb3) (vla-3 alpha chain) (cd49c). [swissprot;acc:p26006]
	3225		heat-shock 20 kda like-protein p20. [swissprot;acc:o14558]
	3226		ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1]
	3227		69 kda islet cell autoantigen (ica69) (islet cell autoantigen 1) (islet cell autoantigen p69) (icap69). [swissprot;acc:q05084]
	3228		ezrin-binding partner pace-1 isoform 1. [refseq;acc:nm_020423]
398.5	9	1281.5	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	3.21581
	10		tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]
	11		dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]
	12		cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]
	13		cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]
	14		ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]
450.5	1	2394.5	rad50-interacting protein 1. [refseq;acc:nm_021930]	5.31521
	2		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]
460	17	1365	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	2.96739
677.5	18	1865.5	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	2.75351
	19		microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]
	20		protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]
	21		ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]
	22		protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]
699.76	23	1894.39	gbp protein isoform a. [refseq;acc:nm_017870]	2.7072
779.167	46	1390.33	neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	1.78438
	47		chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]
	48		doc-1 related protein (doc-1r). [swissprot;acc:o75956]
	49		neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8]
	50		neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562]
	51		neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]
	52		chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]
	53		cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519]
950.561	24	2108.52	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	2.21818
1153.5	5	339.5	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	3.39764
	6		junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]
	7		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]
	8		db83 protein. [swissprot;acc:p57088]
1618.84	54	2651.88	deltex 2. [refseq;acc:nm_020892]	1.63814
1629.21	55	2662.12	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	1.63399
1631.67	56	2664.55	t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492]	1.63302
	57		kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]
	58		kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559]
	59		kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]

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.