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	Rank	Gene	Value Type	Hugo	description	Interaction Map	Filtered	red	network_comparison	green

Results: HTML CSV LaTeX

Showing element 432 to 481 of 515 in total

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

Rank	Hugo	description	Interaction Map
3187	DMRT3	doublesex and mab-3 related transcription factor 3; testis-specific protein; dmrt-like family a3. [refseq;acc:nm_021240]	High confidence
3188	WISP2	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	RNF4	ring finger protein 4. [swissprot;acc:p78317]
3190	MTMR1	myotubularin-related protein 1 (ec 3.1.3.-). [swissprot;acc:q13613]
3191	APPBP2	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	USP13	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	GDI2	rab gdp dissociation inhibitor beta (rab gdi beta) (gdi-2). [swissprot;acc:p50395]
3194	MSH4	muts protein homolog 4. [swissprot;acc:o15457]
3195	ITGB3	integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [swissprot;acc:p05106]
3196	HERPUD1	homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein (methyl methanesulfonate (mmf)-inducible fragment protein 1). [swissprot;acc:q15011]
3197	CLPTM1L	cisplatin resistance related protein crr9p. [refseq;acc:nm_030782]
3198	DCUN1D1	rp42 homolog; squamous cell carcinoma-related oncogene. [refseq;acc:nm_020640]
3199	C6	complement component c6 precursor. [swissprot;acc:p13671]
3200	ZFYVE16	endosome-associated fyve-domain protein. [refseq;acc:nm_014733]
3201	IFT88	recessive polycystic kidney disease protein tg737 homolog. [swissprot;acc:q13099]
3202	RANBP3	ran binding protein 3 isoform ranbp3-d; ran-binding protein-3. [refseq;acc:nm_007322]
3203	HMGB3	high mobility group protein 4 (hmg-4) (high mobility group protein 2a) (hmg-2a). [swissprot;acc:o15347]
3204	VRK2	vaccinia related kinase 2; vaccinia-related kinase-2. [refseq;acc:nm_006296]
3205	RB1CC1	rb1-inducible coiled coil protein 1. [refseq;acc:nm_014781]
3206	C20orf43	protein c20orf43 (hspc164/hspc169) (ad-007) (cda05). [swissprot;acc:q9by42]
3207	C8B	complement component c8 beta chain precursor. [swissprot;acc:p07358]
3208	RUNX3	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	MNAT1	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	ZRANB1	trabid protein. [swissprot;acc:q9ugi0]
3211	CYP24A1	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	RALBP1	rala binding protein 1; rala-binding protein. [refseq;acc:nm_006788]
3213	MDH1	malate dehydrogenase, cytoplasmic (ec 1.1.1.37). [swissprot;acc:p40925]
3214	NUB1	bs4 protein (ny-ren-18 antigen). [swissprot;acc:q9y5a7]
3215	MBTPS2	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	ERCC1	dna excision repair protein ercc-1. [swissprot;acc:p07992]
3217	SCMH1	sex comb on midleg homolog 1. [refseq;acc:nm_012236]
3218	MLXIPL	williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71]
3219	VTA1	protein c6orf55 (dopamine responsive protein drg-1) (my012 protein) (hspc228). [swissprot;acc:q9np79]
3220	TFAP2B	transcription factor ap-2 beta (ap2-beta) (activating enhancer-binding protein 2 beta). [swissprot;acc:q92481]
3221	PAFAH1B1	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	ALDH3B1	aldehyde dehydrogenase 7 (ec 1.2.1.5). [swissprot;acc:p43353]
3223	RALA	ras-related protein ral-a. [swissprot;acc:p11233]
3224	ITGA3	integrin alpha-3 precursor (galactoprotein b3) (gapb3) (vla-3 alpha chain) (cd49c). [swissprot;acc:p26006]
3225	HSPB6	heat-shock 20 kda like-protein p20. [swissprot;acc:o14558]
3226	no value	ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1]
3227	ICA1	69 kda islet cell autoantigen (ica69) (islet cell autoantigen 1) (islet cell autoantigen p69) (icap69). [swissprot;acc:q05084]
3228	SCYL3	ezrin-binding partner pace-1 isoform 1. [refseq;acc:nm_020423]
5019	JRKL	jerky protein homolog like (hhmjg). [swissprot;acc:q9y4a0]	Low confidence
5020	no value	gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]
5021	HDAC3	histone deacetylase 3 (hd3) (rpd3-2). [swissprot;acc:o15379]
5022	TIGD1	tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702]
5023	SPNS1	spinster-like protein. [sptrembl;acc:q9h2v7]
5024	TK2	thymidine kinase 2, mitochondrial precursor (ec 2.7.1.21) (mt-tk). [swissprot;acc:o00142]
5025	TIGD6	tigger transposable element derived 6. [refseq;acc:nm_030953]
5026	RUNX1	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]

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
- Hugo is the HGNC identifier if it exists
- 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.