Rett syndrome causing genes (Homo sapiens)

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Protein - protein interaction between genes that are associated with Rett syndrome like phenotype according to the paper Ehrhart et al. 2018 "current developments in the genetics of Rett and Rett-like syndrome" Curr. Psy.

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  1. Kearney JA, Yang Y, Beyer B, Bergren SK, Claes L, Dejonghe P, Frankel WN; ''Severe epilepsy resulting from genetic interaction between Scn2a and Kcnq2.''; Hum Mol Genet, 2006 PubMed Europe PMC
  2. Banting GS, Barak O, Ames TM, Burnham AC, Kardel MD, Cooch NS, Davidson CE, Godbout R, McDermid HE, Shiekhattar R; ''CECR2, a protein involved in neurulation, forms a novel chromatin remodeling complex with SNF2L.''; Hum Mol Genet, 2005 PubMed Europe PMC
  3. Kuroda Y, Oma Y, Nishimori K, Ohta T, Harata M; ''Brain-specific expression of the nuclear actin-related protein ArpNalpha and its involvement in mammalian SWI/SNF chromatin remodeling complex.''; Biochem Biophys Res Commun, 2002 PubMed Europe PMC
  4. Grainger RJ, Barrass JD, Jacquier A, Rain JC, Beggs JD; ''Physical and genetic interactions of yeast Cwc21p, an ortholog of human SRm300/SRRM2, suggest a role at the catalytic center of the spliceosome.''; RNA, 2009 PubMed Europe PMC
  5. Gyorgy AB, Szemes M, de Juan Romero C, Tarabykin V, Agoston DV; ''SATB2 interacts with chromatin-remodeling molecules in differentiating cortical neurons.''; Eur J Neurosci, 2008 PubMed Europe PMC
  6. Kyle SM, Saha PK, Brown HM, Chan LC, Justice MJ; ''MeCP2 co-ordinates liver lipid metabolism with the NCoR1/HDAC3 corepressor complex.''; Hum Mol Genet, 2016 PubMed Europe PMC
  7. Li J, Wilkinson B, Clementel VA, Hou J, O'Dell TJ, Coba MP; ''Long-term potentiation modulates synaptic phosphorylation networks and reshapes the structure of the postsynaptic interactome.''; Sci Signal, 2016 PubMed Europe PMC
  8. Havugimana PC, Hart GT, Nepusz T, Yang H, Turinsky AL, Li Z, Wang PI, Boutz DR, Fong V, Phanse S, Babu M, Craig SA, Hu P, Wan C, Vlasblom J, Dar VU, Bezginov A, Clark GW, Wu GC, Wodak SJ, Tillier ER, Paccanaro A, Marcotte EM, Emili A; ''A census of human soluble protein complexes.''; Cell, 2012 PubMed Europe PMC
  9. Potts RC, Zhang P, Wurster AL, Precht P, Mughal MR, Wood WH 3rd, Zhang Y, Becker KG, Mattson MP, Pazin MJ; ''CHD5, a brain-specific paralog of Mi2 chromatin remodeling enzymes, regulates expression of neuronal genes.''; PLoS One, 2011 PubMed Europe PMC
  10. Jacob FD, Ramaswamy V, Andersen J, Bolduc FV; ''Atypical Rett syndrome with selective FOXG1 deletion detected by comparative genomic hybridization: case report and review of literature.''; Eur J Hum Genet, 2009 PubMed Europe PMC
  11. Nan X, Ng HH, Johnson CA, Laherty CD, Turner BM, Eisenman RN, Bird A; ''Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex.''; Nature, 1998 PubMed Europe PMC
  12. Oliva M, Berkovic SF, Petrou S; ''Sodium channels and the neurobiology of epilepsy.''; Epilepsia, 2012 PubMed Europe PMC
  13. Kaltenbach LS, Romero E, Becklin RR, Chettier R, Bell R, Phansalkar A, Strand A, Torcassi C, Savage J, Hurlburt A, Cha GH, Ukani L, Chepanoske CL, Zhen Y, Sahasrabudhe S, Olson J, Kurschner C, Ellerby LM, Peltier JM, Botas J, Hughes RE; ''Huntingtin interacting proteins are genetic modifiers of neurodegeneration.''; PLoS Genet, 2007 PubMed Europe PMC
  14. Srivastava S, Engels H, Schanze I, Cremer K, Wieland T, Menzel M, Schubach M, Biskup S, Kreiß M, Endele S, Strom TM, Wieczorek D, Zenker M, Gupta S, Cohen J, Zink AM, Naidu S; ''Loss-of-function variants in HIVEP2 are a cause of intellectual disability.''; Eur J Hum Genet, 2016 PubMed Europe PMC
  15. Forrest MP, Waite AJ, Martin-Rendon E, Blake DJ; ''Knockdown of human TCF4 affects multiple signaling pathways involved in cell survival, epithelial to mesenchymal transition and neuronal differentiation.''; PLoS One, 2013 PubMed Europe PMC
  16. Waga C, Asano H, Sanagi T, Suzuki E, Nakamura Y, Tsuchiya A, Itoh M, Goto Y, Kohsaka S, Uchino S; ''Identification of two novel Shank3 transcripts in the developing mouse neocortex.''; J Neurochem, 2014 PubMed Europe PMC
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  18. Kutney SN, Hong R, Macfarlan T, Chakravarti D; ''A signaling role of histone-binding proteins and INHAT subunits pp32 and Set/TAF-Ibeta in integrating chromatin hypoacetylation and transcriptional repression.''; J Biol Chem, 2004 PubMed Europe PMC
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  20. Yao J, Lai E, Stifani S; ''The winged-helix protein brain factor 1 interacts with groucho and hes proteins to repress transcription.''; Mol Cell Biol, 2001 PubMed Europe PMC
  21. Myagmar BE, Umikawa M, Asato T, Taira K, Oshiro M, Hino A, Takei K, Uezato H, Kariya K; ''PARG1, a protein-tyrosine phosphatase-associated RhoGAP, as a putative Rap2 effector.''; Biochem Biophys Res Commun, 2005 PubMed Europe PMC
  22. McMahon SB, Wood MA, Cole MD; ''The essential cofactor TRRAP recruits the histone acetyltransferase hGCN5 to c-Myc.''; Mol Cell Biol, 2000 PubMed Europe PMC
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  28. Mari F, Azimonti S, Bertani I, Bolognese F, Colombo E, Caselli R, Scala E, Longo I, Grosso S, Pescucci C, Ariani F, Hayek G, Balestri P, Bergo A, Badaracco G, Zappella M, Broccoli V, Renieri A, Kilstrup-Nielsen C, Landsberger N; ''CDKL5 belongs to the same molecular pathway of MeCP2 and it is responsible for the early-onset seizure variant of Rett syndrome.''; Hum Mol Genet, 2005 PubMed Europe PMC


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104287view12:47, 15 May 2019FehrhartOntology Term : 'neuron' added !
101964view11:00, 21 November 2018DeSlAdded ID for last wrong interaction drawing as a comment (for easy fixing later on).
101963view10:53, 21 November 2018DeSlFixed one before last wrong interaction link (keeping one for new Jenkins Test).
101962view10:51, 21 November 2018DeSlChanged more names of PWs on interactions to corresponding ID; added name to comments.
101958view10:42, 21 November 2018DeSlAdded name of "Viral carcinogenesis" to interaction as comment.
101957view10:30, 21 November 2018DeSlChanged Viral carcinogenesis pathway to ID from KEGG.
98050view05:39, 13 July 2018Fehrhartfixed unconnected line
98028view10:03, 4 July 2018FehrhartModified description
98026view09:33, 4 July 2018DeSlChanged Ref. layout
98024view09:25, 4 July 2018DeSlChanged Ref. layout
98023view09:23, 4 July 2018DeSlChanged Ref. layout
98022view09:22, 4 July 2018FehrhartModified description
98021view09:22, 4 July 2018FehrhartModified description
98020view09:21, 4 July 2018FehrhartModified description
98019view09:06, 4 July 2018DeSlChanges layout (again).
98018view09:05, 4 July 2018DeSlMore layout changes, every single line should be visible now in terms of connectivity
98017view09:02, 4 July 2018DeSlChanged layout some more
98016view09:00, 4 July 2018DeSlChanged layout, how lines are connected etc.
98015view08:52, 4 July 2018DeSlFound Gene ID in left bottom corner, which screwed up visualisation
98009view08:13, 3 July 2018FehrhartModified description
98008view08:11, 3 July 2018Fehrhartaesthetics
97973view09:16, 28 June 2018Fehrhartsome aesthetic details
97972view09:12, 28 June 2018FehrhartModified title
97971view07:25, 28 June 2018FehrhartOntology Term : 'disease pathway' added !
97970view07:24, 28 June 2018FehrhartOntology Term : 'Rett syndrome' added !
97969view07:24, 28 June 2018FehrhartModified title
97892view11:05, 20 June 2018MaxvansonErased some unnecessary genes that were not present in the pathway
97891view10:12, 20 June 2018MaxvansonNew pathway

External references


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NameTypeDatabase referenceComment
ACTL6BGeneProductENSG00000077080 (Ensembl)
BRAFGeneProductENSG00000157764 (Ensembl)
CDKL5 GeneProductENSG00000008086 (Ensembl)
CECR2GeneProductENSG00000099954 (Ensembl)
CHD4GeneProductENSG00000111642 (Ensembl)
CRKGeneProductENSG00000167193 (Ensembl)
EIF2B2GeneProductENSG00000119718 (Ensembl)
FOXG1 GeneProductENSG00000176165 (Ensembl)
GABBR2GeneProductENSG00000136928 (Ensembl)
GABRA3GeneProductENSG00000011677 (Ensembl)
GABRDGeneProductENSG00000187730 (Ensembl)
GNAO1GeneProductENSG00000087258 (Ensembl)
GPS2GeneProductENSG00000132522 (Ensembl)
GRIN2AGeneProductENSG00000183454 (Ensembl)
GRIN2BGeneProductENSG00000273079 (Ensembl)
HAP1GeneProductENSG00000173805 (Ensembl)
HDAC1GeneProductENSG00000116478 (Ensembl)
HDAC5GeneProductENSG00000108840 (Ensembl)
HDAC8GeneProductENSG00000147099 (Ensembl)
HIVEP2GeneProductENSG00000010818 (Ensembl) Type your comment here
HTTGeneProductENSG00000197386 (Ensembl)
IMPDH2GeneProductENSG00000178035 (Ensembl)
JARID1B GeneProductENSG00000117139 (Ensembl)
KCNJ10GeneProductENSG00000177807 (Ensembl)
KCNQ2GeneProductENSG00000281151 (Ensembl)
MECP2 GeneProductENSG00000169057 (Ensembl)
MEF2CGeneProductENSG00000081189 (Ensembl)
NCOR1GeneProductENSG00000141027 (Ensembl)
NCOR2GeneProductENSG00000196498 (Ensembl)
RHOBTB2GeneProductENSG00000008853 (Ensembl)
SATB2GeneProductENSG00000119042 (Ensembl)
SCN1AGeneProductENSG00000144285 (Ensembl)
SCN2AGeneProductENSG00000136531 (Ensembl)
SCN8AGeneProductENSG00000196876 (Ensembl)
SHANK3GeneProductENSG00000251322 (Ensembl)
SMARCA1GeneProductENSG00000102038 (Ensembl)
SMARCA2 GeneProductENSG00000080503 (Ensembl)
SMARCA4 GeneProductENSG00000127616 (Ensembl)
SMC1AGeneProductENSG00000072501 (Ensembl)
SRRM3GeneProductENSG00000177679 (Ensembl)
STXBP1GeneProductENSG00000136854 (Ensembl)
SYNE2GeneProductENSG00000054654 (Ensembl)
SYNGAP1GeneProductENSG00000197283 (Ensembl)
TAF1BGeneProductENSG00000115750 (Ensembl)
TBL1XGeneProductENSG00000101849 (Ensembl)
TBL1XR1GeneProductENSG00000177565 (Ensembl)
TCF4GeneProductENSG00000196628 (Ensembl)
TRRAPGeneProductENSG00000196367 (Ensembl)
XAB2GeneProductENSG00000076924 (Ensembl)

Annotated Interactions

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SourceTargetTypeDatabase referenceComment
CRKBRAFmim-gapNeurotrophin signaling pathway (KEGG Pathway) map04722 is ID corresponding to name of PW.
GABRDGABRA3mim-bindingmap05033 (KEGG Pathway) Nicotine addiction
GNAO1GABBR2mim-stimulationmap04727 (KEGG Pathway) GABAergic Synapse
GNAO1mim-inhibitionmap04728 (KEGG Pathway) Dopaminergic Synapse
GRIN2BGRIN2Amim-bindingmap05034 (KEGG Pathway) Alcoholism
HAP1GABRA3mim-bindingmap04727 (KEGG Pathway) GABAergic synapse
HAP1GABRDmim-bindingmap04727 (KEGG Pathway) GABAergic synapse
HDAC5mim-stimulationmap05203 (KEGG Pathway) Viral carcinogenesis
HDAC8HDAC5mim-bindingmap05034 (KEGG Pathway) Alcoholism
HTTGRIN2Bmim-cleavagemap05016 (KEGG Pathway) Huntington Disease
KCNJ10GABBR2mim-stimulationR-HSA-1013011 (Reactome) GABA B receptor G-protein beta-gamma and Kir3 channel complex
SYNE2SMC1Amim-gapR-HSA-1221632 (Reactome) Meiotic synapsis pathway
TAF1BCHD4mim-stimulationR-HSA-427359 (Reactome) SIRT1 negatively regulates rRNA expression
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