Find the Links of Databases
Epigenetic modifications in the mitochondrial genome has been an emerging area of interest in the recent years in field of mitochondrial biology. The renewed interest in the area has been largely fuelled by a number of reports in the recent years suggesting the presence of epigenetic modifications in human mitochondrial genome and their associations with exposure to environmental factors and human diseases and or traits. Nevertheless there has been no systematic effort to curate, organise this information to enable cross-comparison between studies and datasets.
We compiled 62 datasets from 9 studies on the epigenetic modifications in human mitochondrial genome to create a comprehensive catalog. This catalog is available as a user friendly interface - mitoepigenomeKB, where the data could be searched, browsed or visualised.
URL : http://clingen.igib.res.in/mitoepigenome
almena is a comprehensive resource of genetic variants in Middle East and North Africa. The present version of the database provides information on over 26 million variants derived from integration of multiple whole genome and whole exome studies from the region. Apart from providing the allele frequencies for the genetic variants, this unique resource also provides relevant annotations for clinically relevant genetic variants.
URL : http://clingen.igib.res.in/almena
SAGE is a comprehensive repertoire of genome and exome information from South Asians. We have integrated 6 datasets encompassing 1213 human genome and exome data to create a compendium of 154 million genetic variants. The resource has immense applications in understanding the allelic frequencies, carrier rates for rare genetic diseases and genetic traits including pharmacogenetics, apart from prioritising and discovering novel disease associated variants. The variants were systematically annotated, integrated with other public databases and and allele frequencies are available in this browsable resource. To know more please look in to the FAQ section.
URL : http://clingen.igib.res.in/sage
The Arab world encompassing Middle East and North Africa is home to over 350 million people. This approximately represents over 5% of the world population and is characterized by significant ethnic, linguistic and genetic diversity, while encompassing similarities in language, traditions, cultural practices as well as geographic proximity. The Disease Alleles in Arabs (dalia) is a unique venture to systematically characterize evidence from literature to build a comprehensive catalog of disease associated variants in the region.
URL : http://clingen.igib.res.in/dalia
Ataxia LSDB is a Locus Specific Variant Database for ataxia genes ATN1, ATXN1, ATXN2, ATXN3, ATXN7, CACNA1A, and PPP2R2B. The resource can be searched using the gene names or using the links as below.
URL : http://clingen.igib.res.in/AtaxiaLSDB
NutriGenDB is a comprehensive database of nutrigenetic markers mined and curated from peer-reviewed literature. This resource fulfills the unmet need for a systematically curated resource and ready reference for nutrigenetic variants to enable functional analysis, genomic interpretation and enable epidemiological studies. The present resource includes over 400 annotations from over 250 publications in the field encompassing a wide variety of nutritional traits and molecules . The database is accessible for academic use, and may not be used for clinical interpretation.
URL : http://clingen.igib.res.in/NutriGenDB
Circular RNAs (circRNAs) are unique transcript isoforms characterised by back splicing of exon ends to form a covalently closed loop or circular conformation. These transcript isoforms are now known to be expressed in a variety of organisms across the kingdoms of life. Recent studies have shown the role of circRNAs in a number of diseases and increasing evidence points to their potential application as biomarkers in these diseases. We have created a comprehensive manually curated database of circular RNAs associated with diseases.The database is unique in many ways. Firstly it provides standard disease nomenclature as per the ICD codes. It additionally lists the assay and PCR primer details including experimentally validated ones as a ready reference to researchers. To the best of our knowledge, circad is the most comprehensive and updated database of disease associated circular RNAs.
URL : http://clingen.igib.res.in/circad
Circular RNAs (circRNAs) are a novel group of recently discovered class of non-coding RNAs which are formed by back-splicing of pre-RNA transcript. In recent years, studies have published genome-wide circRNA-transcriptome in a number of organisms including human, cell lines, plants and animals. We have created a manually curated database, CircRNome, which is a compiled database for both animal and plants comprising predicted as well as validated cirRNAs for each organism. This serves the most updated database created for circRNAs.
URL : http://clingen.igib.res.in/circRNome/
Circular RNAs (circRNAs) are transcript isoforms generated by back-splicing of exons and circularisation of the transcript. Recent genome-wide maps created for circular RNAs in humans and other model organisms have motivated us to explore the repertoire of circular RNAs in zebrafish, a popular model organism. We generated RNA-seq data for five major zebrafish tissues- Blood, Brain, Heart, Gills and Muscle. Our analysis revealed 3,428 novel circRNAs in zebrafish. Expression analysis using quantitative real time PCR recapitulate selected tissue specificity in the candidates studied. This study provides a comprehensive genome-wide map of circular RNAs in zebrafish tissues.
URL : http://clingen.igib.res.in/zfcircdb
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WilsonGen is a comprehensive resource of genetic variants in ATP7B gene manually curated from literature and data resources and systematically annotated using the ACMG & AMP guidelines for assessing pathogenicity of genetic variants. The resource therefore serves as a central point for clinicians and geneticists working on Wilson Disease
URL : http://clingen.igib.res.in/WilsonGen/
The IndiGenomes resource encompasses the genomic data from over 1000 whole genome sequences sequenced from across India as part of the IndiGen programme and represents diverse geographies and ethnicities. The resource provides access to over 55 million genetic variants comprising of single nucleotide variants and indels. The variants are systematically annotated according to the recent Genome Reference Consortium Human Build 38 (GRCh38). Clinically relevant annotations as well as allele frequencies from global populations have also been integrated.
URL : http://clingen.igib.res.in/indigen/
IndiCoV is a comprehensive resource for SARS-CoV genomes and variants from India. The resource provides a searchable interface for genomes, genomic variants and variant annotations for the SARS-CoV-2 isolates from India. The variant positions are based on the SARS-nCoV-2 reference genome (Wuhan-Hu-1 reference genome ; Genbank NC_045512)
URL : https://clingen.igib.res.in/indicov/
DystoGen is a comprehensive resource, which encompasses genetic variants from 124 dystonia-associated genes. The resource provides access to 30510 variants, which have been manually curated from published literature and open access public databases, and have been systematically annotated and classified according to ACMG & AMP (American College of Medical Genetics and the Association of Molecular Pathologists) guidelines.
URL : https://clingen.igib.res.in/dystogen/
ATP7Agen is a comprehensive resource of genetic variants in the ATP7A gene. This resource systematically compiles genetic variants in ATP7A gene from literature as well as variant datasets and is further systematically annotated as per the ACMG & AMP guidelines for assessing pathogenicity of genetic variants.
URL : https://clingen.igib.res.in/ATP7Agen/
FaviCov is a comprehensive resource for functionally relevant SARS-CoV genetic variants. The resource provides a searchable interface for genomic variants and corresponding variant annotations. The variant positions are based on the SARS-nCoV-2 reference genome (Wuhan-Hu-1 reference genome ; Genbank NC_045512)
URL : https://clingen.igib.res.in/favicov/
BGvar is a comprehensive compilation of human blood group alleles belonging to International Society of Blood Transfusion (ISBT) approved human blood group systems. The resource integrates relevant data from a range of public sources, encompassing a total of 43 human group systems (updated till August, 2021), 345 antigens, 1700 approved alleles.
URL : https://clingen.igib.res.in/bgvar/
Esc (Immune escape variants in SARS-CoV-2) is a comprehensive and manually curated compendium of genetic variants in SARS-CoV-2 associated with immune escape. The data on variants and associations have been compiled from published literature as well as preprints and includes a variety of antibodies ranging from monoclonal as well as oligoclonal and convalescent plasma panels.
The ESC resource provides a user friendly and searchable interface to query and understand the variants and their functional annotations in detail. This resource may not be used for clinical decision making or intervention.
URL : https://clingen.igib.res.in/esc/
alnasab is a user friendly online search engine, presenting a comprehensive collection of blood group related variations mined from various population scale datasets of the Greater Middle Eastern region. The resource encompasses a total of 2149 blood group related variants fetched from about 47 blood genes. The compiled variants are systematically annotated for their HGVS nomenclature, Global Allele Frequencies and frequencies of various Middle Eastern subpopulations.
URL : https://clingen.igib.res.in/alnasab/
- 20. Indian Covid-19 Genome Surveillance