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ChiTaRS-3.1—the enhanced chimeric transcripts and RNA-seq database matched with protein–protein interactions

Alessandro Gorohovski, Somnath Tagore, Vikrant Palande, Assaf Malka, Dorith Raviv-Shay, Milana Frenkel-Morgenstern
2016 Nucleic Acids Research  
The enhanced ChiTaRS-3.1 database ( is designed to make widely accessible a wealth of mined data on chimeric RNAs, with easy-to-use analytical tools built-in.  ...  The current improvements in the content and functionality to the ChiTaRS database make it a central resource for the study of chimeric transcripts and fusion proteins.  ...  ACKNOWLEDGEMENTS The authors would like to thank MPLabs LTD for the website design and support, and whose efforts make ChiTaRS-3.1 a reality.  ... 
doi:10.1093/nar/gkw1127 pmid:27899596 pmcid:PMC5210585 fatcat:77dteqiffzapdpiu3xgpa3vbve

ChiTaRS 5.0: the comprehensive database of chimeric transcripts matched with druggable fusions and 3D chromatin maps

2019 Nucleic Acids Research  
ChiTaRS 5.0 ( is the latest and most comprehensive chimeric transcript repository, with 111 582 annotated entries from eight species, including 23 167 known human cancer breakpoints  ...  While these chimeric RNAs produce functional proteins only in certain cases, they play a significant role in disease phenotyping and progression.  ...  ACKNOWLEDGEMENTS The authors would like to thank MPLabs Ltd for their efforts in making ChiTaRS 5.0 a reality through website design and back-end support.  ... 
doi:10.1093/nar/gkz1025 pmid:31747015 pmcid:PMC7145514 fatcat:bjfnkwc5xvczdchrfiqfq5syky

Fusion Transcripts of Adjacent Genes: New Insights into the World of Human Complex Transcripts in Cancer

Vincenza Barresi, Ilaria Cosentini, Chiara Scuderi, Salvatore Napoli, Virginia Di Bella, Giorgia Spampinato, Daniele Filippo Condorelli
2019 International Journal of Molecular Sciences  
Five databases, containing validated and predicted Fusion Transcripts of Adjacent Genes (FuTAGs), are available for the scientific community.  ...  This kind of transcript was thought to originate only from chromosomal rearrangements, but the discovery of readthrough transcription opens the doors to a new world of fusion RNAs.  ...  Only two of these, namely ChiTaRs v.3.1 and ConjoinG, showed the most matches with the NCBI reported readthrough and they have even shown to have matches between themselves.  ... 
doi:10.3390/ijms20215252 pmid:31652751 pmcid:PMC6862657 fatcat:yamqg4nvlnc75koq7sfe6zafuu

FusionGDB: fusion gene annotation DataBase

Pora Kim, Xiaobo Zhou
2018 Nucleic Acids Research  
We collected 48 117 FGs across pan-cancer from three representative fusion gene resources: the improved database of chimeric transcripts and RNA-seq data (ChiTaRS 3.1), an integrative resource for cancer-associated  ...  Our analyses identified 331, 303 and 667 in-frame FGs with retaining kinase, DNA-binding, and epigenetic factor domains, respectively, as well as 976 FGs lost protein-protein interaction.  ...  ACKNOWLEDGEMENTS We thank the members of the Center for Computational Systems Medicine (CCSM) for valuable discussion. We thank Dr. Weiling Zhao for improving the English of the manuscript.  ... 
doi:10.1093/nar/gky1067 pmid:30407583 pmcid:PMC6323909 fatcat:iry6mve4sfhz7pwepm2yb4xkou

A liquid biopsy platform for detecting gene-gene fusions as glioma diagnostic biomarkers and drug targets [article]

Vikrant Palande, Rajesh Detroja, Alessandro Gorohovski, Rainer Glass, Charlotte Flueh, Marina Kurtz, Shira Perez, Dorith Raviv Shay, Tali Siegal, Milana Frenkel-Morgenstern
2020 bioRxiv   pre-print
These fusions are predicted to alter protein interaction networks, by removing tumour suppressors and adding oncoproteins.  ...  Indeed, several of these fusions are potential drug targets, particularly, NTRK or ROS1 fusions, specifically for crizotinib analogues (like entrectinib and larotrectinib) with enhanced penetration of  ...  ChiTaRS-3.1-the enhanced chimeric transcripts and RNA-seq database matched 553 with protein-protein interactions. Nucleic Acids Res 45, D790-D795 (2017). 554 109.  ... 
doi:10.1101/2020.02.25.963975 fatcat:aut5j2efl5cylogjlyf5u7nope

Characterization of long G4-rich enhancer-associated genomic regions engaging in a novel loop:loop 'G4 Kissing' interaction

Jonathan D Williams, Dominika Houserova, Bradley R Johnson, Brad Dyniewski, Alexandra Berroyer, Hannah French, Addison A Barchie, Dakota D Bilbrey, Jeffrey D Demeis, Kanesha R Ghee, Alexandra G Hughes, Naden W Kreitz (+15 others)
2020 Nucleic Acids Research  
Strikingly, 217 LG4s overlap annotated enhancers, and we find the promoters regulated by these enhancers markedly enriched in G4-capable sequences suggesting G4s facilitate promoter-enhancer interactions  ...  Using a novel computational approach we have identified 301 LG4s in the human genome and find LG4s prone to mutation and significantly associated with chromosomal rearrangements in malignancy.  ...  ACKNOWLEDGEMENTS We thank members of the G.M.B. lab for discussions throughout the course of this work and for comments on the manuscript.  ... 
doi:10.1093/nar/gkaa357 pmid:32383760 fatcat:5ccelen2sfdv5dg4cqofd3fgl4


Junaid Gamieldien
2015 unpublished
with the protein network.  ...  with copy number alteration, and co-expression and transcriptional analysis.  ...  RNA-seq can be used to quantify differential expression of genes and their spliceforms, including chimeric transcripts that are the result of somatic structural genome rearrangements.Microarray technologies  ...