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

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Showing element 551 to 600 of 77072 in total

green  : 0
Filtered  : 1
Value Type  : Measured
red  : 0
Network Comparison Type  : Subtracted
network_comparison  : 0

Interaction Map	Rank	description
High confidence	3208	runt-related transcription factor 3 (core-binding factor, alpha 3 subunit) (cbf-alpha 3) (acute myeloid leukemia 2 protein) (oncogene aml-2) (polyomavirus enhancer binding protein 2 alpha c subunit) (pebp2-alpha c) (pea2-alpha c) (sl3-3 enhancer factor 1 alpha c subunit) (sl3/akv core-binding factor alpha c subunit). [swissprot;acc:q13761]
	3209	cdk-activating kinase assembly factor mat1 (ring finger protein mat1) (menage a trois) (cdk7/cyclin h assembly factor) (p36) (p35) (cyclin g1 interacting protein). [swissprot;acc:p51948]
	3210	trabid protein. [swissprot;acc:q9ugi0]
	3211	cytochrome p450 24a1, mitochondrial precursor (ec 1.14.-.-) (p450- cc24) (vitamin d(3) 24-hydroxylase) (1,25-dihydroxyvitamin d(3) 24- hydroxylase) (24-ohase). [swissprot;acc:q07973]
	3212	rala binding protein 1; rala-binding protein. [refseq;acc:nm_006788]
	3213	malate dehydrogenase, cytoplasmic (ec 1.1.1.37). [swissprot;acc:p40925]
	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]
Low confidence	5020	jerky protein homolog like (hhmjg). [swissprot;acc:q9y4a0]
	5021	gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]
	5022	histone deacetylase 3 (hd3) (rpd3-2). [swissprot;acc:o15379]
	5023	tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702]
	5024	spinster-like protein. [sptrembl;acc:q9h2v7]
	5025	thymidine kinase 2, mitochondrial precursor (ec 2.7.1.21) (mt-tk). [swissprot;acc:o00142]
	5026	tigger transposable element derived 6. [refseq;acc:nm_030953]
	5027	runt-related transcription factor 1 (core-binding factor, alpha 2 subunit) (cbf-alpha 2) (acute myeloid leukemia 1 protein) (oncogene aml-1) (polyomavirus enhancer binding protein 2 alpha b subunit) (pebp2-alpha b) (pea2-alpha b) (sl3-3 enhancer factor 1 alpha b subunit) (sl3/akv core-binding factor alpha b subunit). [swissprot;acc:q01196]
	5028	collectin sub-family member 12 isoform i; scavenger receptor with c-type lectin; collectin placenta 1; scavenger receptor class a, member 4. [refseq;acc:nm_130386]
	5029	likely ortholog of mouse c-type (calcium dependent, carbohydrate recognition domain) lectin, superfamily member 13; c-type lectin 13; likely ortholog of rat kupffer cell c-type lectin receptor. [refseq;acc:nm_173535]
	5030	gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]
	5031	cobw-like protein. [refseq;acc:nm_018491]
	5032	tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208]
	5033	signal recognition particle 14 kda protein (srp14) (18 kda alu rna binding protein). [swissprot;acc:p37108]
	5034	rap1 gtpase-gdp dissociation stimulator 1 (smg p21 stimulatory gdp/gtp exchange protein) (smg gds protein) (exchange factor smggds). [swissprot;acc:p52306]
	5035	solute carrier family 21 member 15 (organic anion transporter polypeptide-related protein 4) (oatp-rp4) (oatprp4). [swissprot;acc:q9h2y9]
	5036	lipin 1. [swissprot;acc:q14693]
	5037	lipin 3 (lipin 3-like) (fragments). [swissprot;acc:q9bqk8]
	5038	myeloblast kiaa0230 (fragment). [sptrembl;acc:q92626]
	5039	testis specific leucine rich repeat protein. [refseq;acc:nm_012472]
	5040	major centromere autoantigen b (centromere protein b) (cenp-b). [swissprot;acc:p07199]
	5041	leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735]
	5042	n-acetylglucosamine kinase (ec 2.7.1.59) (glcnac kinase). [swissprot;acc:q9uj70]
	5043	transthyretin precursor (prealbumin) (tbpa) (ttr) (attr). [swissprot;acc:p02766]
	5044	late endosomal/lysosomal mp1 interacting protein (p14) (hspc003). [swissprot;acc:q9y2q5]
	5045	langerhans cell specific c-type lectin. [refseq;acc:nm_015717]
	5046	putative tumor suppressor 101f6. [refseq;acc:nm_007022]
	5047	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
	5048	double-stranded rna-binding zinc finger protein jaz. [refseq;acc:nm_012279]

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.