Past ChiTaRS Database and Methods:
ChiTaRS 5.0: the comprehensive database of chimeric transcripts matched with druggable fusions and 3D chromatin maps
Deepak Balamurali, Alessandro Gorohovski, Rajesh Detroja, Vikrant Palande, Dorith Raviv-Shay, and Milana Frenkel-Morgenstern
ChiTaRS 5.0: the comprehensive database of chimeric transcripts matched with druggable fusions and 3D chromatin maps
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
ChiTaRS-3.1-the enhanced chimeric transcripts and RNA-seq database matched with protein-protein interactions
ChiTaRS 2.1-an improved database of the chimeric transcripts and RNA-seq data with novel sense-antisense chimeric RNA transcripts
Milana Frenkel-Morgenstern, Alessandro Gorohovski, Dunja Vucenovic, Lorena Maestre, Alfonso Valencia
ChiTaRS 2.1 - an improved database of the chimeric transcripts and RNA-seq data with novel sense - antisense chimeric RNA transcripts
ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data
Milana Frenkel-Morgenstern, Alessandro Gorohovski, Vincent Lacroix, Mark Rogers, Kristina Ibanez, Cesar Boullosa, Eduardo Andres Leon, Asa Ben-Hur, and Alfonso Valencia*
ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data
ChiTaRS 8.0 Database Explanation:
The search results are a tabulated list of Gene Fusions according to their relative occurrence across 934 human cell lines used in cancer research. This is derived from the ChiTaRS database and uses the ChiTaH pipeline to sort through gene fusions based on its junction ID.
(for cell line information please search Cellosaurus - Cell line encyclopedia)
The table appears in Downloads under the name "934CancerCellLines"
Gene Fusion contains 47,445 human chimeras established in human RNA-Seq (both healthy and disease state) made up of gene 1 and gene 2. It is given in a standard pattern unique to the ChiTaRS database. The search results are in tabular format comprising a list of parental gene fusions. The search columns are ChimeraID followed by the parental gene names and the strand of fusion gene partners. It also includes the junction type based on the exon and intron of the parental genes. To begin your search, add the gene fusion by a single parental gene.
It consists of 4,745 gene fusions. This database is correlated to Fusion DB. These are given in the standard ChiTaRS database pattern uniquely established in older records. To search add the gene fusion by a single parental gene.
The table lists 1055 gene fusions with parental genes and the breakpoint type at the molecular level. It also provides information on FDA-approved drugs used against the chimera type. All chimeras given here are druggable fusions provided to target either a single or both parental genes under the Druggable predicted column. The cancer types are also included in the table where the drug is approved and the cancer types for which the breakpoints are applicable. The reference to the article for the druggable fusion is given in the last column for the PubMed breakpoint.
The search results are a tabulated list of druggable fusion genes with the NCBI accession of the parental genes. The gene target for the fusion is mentioned with a list of FDA-approved drugs. It also mentions the cancer types against the given drug and the cancer type breakpoint (table of acronyms is provided below)
The Hi-C search results are a tabulated list of 1055 chimeric breakpoints derived from Hi-C contact maps for the parental genes (with the gene loci of each gene) according to their Chimera ID. It also gives the gene names and type junction (for the exon and intron) with Hi-C points and lib Hi-C (for cell line information please refer to Cellosaurus - Cell line encyclopedia) for the given fusion gene.
The RNA-Seq is a tabulated search tool for RNA sequencing data for patient samples from public and lab databases. It also mentions the disease against GBM (glioblastoma), Psoriasis, Oral Cancer, and 199 EBI (European Bioinformatics Institute) healthy individuals viz added to downloads. Additionally, we have provided the chimera load and the chimera frequency across samples.
The Downloads button is easy access to the collected databases in Excel format for all users. This data is password protected and can be accessed by mailing us a request for the password at:
mfmlab.runi@gmail.com
We will also provide the fasta sequences to the gene fusions upon request.
Acronym table for Cancer type abbreviations:
| Acronym |
Cancer Type |
| LAML | Acute Myeloid Leukemia |
| BLCA | Bladder Urothelial Carcinoma |
| LGG | Brain Lower Grade Glioma |
| BRCA | Breast Invasive Carcinoma |
| CESC | Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma |
| COAD | Colon Adenocarcinoma |
| COADREAD | Colorectal Cancer |
| GBM | Glioblastoma Multiforme |
| HNSC | Head and Neck Squamous Cell Carcinoma |
| KICH | Kidney Chromophobe |
| KIRC | Kidney Renal Clear Cell Carcinoma |
| KIRP | Kidney Renal Papillary Cell Carcinoma |
| LIHC | Liver Hepatocellular Carcinoma |
| LUAD | Lung Adenocarcinoma |
| LUSC | Lung Squamous Cell Carcinoma |
| DLBC | Lymphoid Neoplasm Diffuse Large B-cell Lymphoma |
| MESO | Mesothelioma |
| OV | Ovarian Serous Cystadenocarcinoma |
| PAAD | Pancreatic Adenocarcinoma |
| PRAD | Prostate Adenocarcinoma |
| SARC | Sarcoma |
| SKCM | Skin Cutaneous Melanoma |
| STAD | Stomach Adenocarcinoma |
| TGCT | Testicular Germ Cell Tumor |
| THCA | Thyroid Carcinoma |
| UVM | Uveal Melanoma |
| UCEC | Uterine Corpus Endometrial Carcinoma |
