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

Results: HTML CSV LaTeX

Showing element 3180 to 3228 of 3228 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
red  : 0.00001
green  : 0.00001
network_comparison  : 1

Rank	description
3180	3-hydroxyacyl-coa dehydrogenase type ii (ec 1.1.1.35) (type ii hadh) (endoplasmic reticulum-associated amyloid beta-peptide binding protein) (short-chain type dehydrogenase/reductase xh98g2). [swissprot;acc:q99714]
3181	fatty aldehyde dehydrogenase (ec 1.2.1.3) (aldehyde dehydrogenase, microsomal) (aldh class 3). [swissprot;acc:p51648]
3182	transcription factor e2-alpha (immunoglobulin enhancer binding factor e12/e47) (transcription factor-3) (tcf-3) (immunoglobulin transcription factor-1) (transcription factor itf-1) (kappa-e2-binding factor). [swissprot;acc:p15923]
3183	core-binding factor, beta subunit (cbf-beta) (polyomavirus enhancer binding protein 2 beta subunit) (pebp2-beta) (pea2-beta) (sl3-3 enhancer factor 1 beta subunit) (sl3/akv core-binding factor beta subunit). [swissprot;acc:q13951]
3184	nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497]
3185	ferrochelatase, mitochondrial precursor (ec 4.99.1.1) (protoheme ferro-lyase) (heme synthetase). [swissprot;acc:p22830]
3186	protein kinase c, theta type (ec 2.7.1.-) (npkc-theta). [swissprot;acc:q04759]
3187	doublesex and mab-3 related transcription factor 3; testis-specific protein; dmrt-like family a3. [refseq;acc:nm_021240]
3188	connective tissue growth factor-like protein precursor (ctgf-l) (wnt1 inducible signaling pathway protein 2) (wisp-2) (connective tissue growth factor-related protein 58). [swissprot;acc:o76076]
3189	ring finger protein 4. [swissprot;acc:p78317]
3190	myotubularin-related protein 1 (ec 3.1.3.-). [swissprot;acc:q13613]
3191	amyloid beta precursor protein-binding protein 2; amyloid beta precursor protein (cytoplasmic tail)-binding protein 2; protein interacting with app tail 1. [refseq;acc:nm_006380]
3192	ubiquitin carboxyl-terminal hydrolase 13 (ec 3.1.2.15) (ubiquitin thiolesterase 13) (ubiquitin-specific processing protease 13) (deubiquitinating enzyme 13) (isopeptidase t-3) (isot-3). [swissprot;acc:q92995]
3193	rab gdp dissociation inhibitor beta (rab gdi beta) (gdi-2). [swissprot;acc:p50395]
3194	muts protein homolog 4. [swissprot;acc:o15457]
3195	integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [swissprot;acc:p05106]
3196	homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein (methyl methanesulfonate (mmf)-inducible fragment protein 1). [swissprot;acc:q15011]
3197	cisplatin resistance related protein crr9p. [refseq;acc:nm_030782]
3198	rp42 homolog; squamous cell carcinoma-related oncogene. [refseq;acc:nm_020640]
3199	complement component c6 precursor. [swissprot;acc:p13671]
3200	endosome-associated fyve-domain protein. [refseq;acc:nm_014733]
3201	recessive polycystic kidney disease protein tg737 homolog. [swissprot;acc:q13099]
3202	ran binding protein 3 isoform ranbp3-d; ran-binding protein-3. [refseq;acc:nm_007322]
3203	high mobility group protein 4 (hmg-4) (high mobility group protein 2a) (hmg-2a). [swissprot;acc:o15347]
3204	vaccinia related kinase 2; vaccinia-related kinase-2. [refseq;acc:nm_006296]
3205	rb1-inducible coiled coil protein 1. [refseq;acc:nm_014781]
3206	protein c20orf43 (hspc164/hspc169) (ad-007) (cda05). [swissprot;acc:q9by42]
3207	complement component c8 beta chain precursor. [swissprot;acc:p07358]
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]

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.