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a catalog of biological databases

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Database information

HumCFS (Human chromosmal fragile sites)

General information

Description: HumCFS provides comprehensive information about experimentally identified chromosomal fragile sites/regions (CFS) at a single source.
Year founded: 2019
Last update:
Version:
Accessibility:
Manual:
Accessible
Real time : Checking...
Country/Region: India
Data type:
DNA
Data object:
Database category:
Major organism:
Keywords:

Contact information

University/Institution: Indraprastha Institute of Information Technology
Address:
City:
Province/State:
Country/Region: India
Contact name (PI/Team): Gajendra P. S. Raghava
Contact email (PI/Helpdesk): raghava@iiitd.ac.in

Related Database

Record metadata

Created on: 2019-05-29
Curated by:
Lina Ma [2019-05-29]

Ranking

All databases:
3290/4549 (27.698%)
Gene genome and annotation:
941/1211 (22.378%)
3290
Total Rank
1
Citations
1
z-index

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Publications

30999860
HumCFS: a database of fragile sites in human chromosomes. [PMID: 30999860]
Kumar R, Nagpal G, Kumar V, Usmani SS, Agrawal P, Raghava GPS.

BACKGROUND:Fragile sites are the chromosomal regions that are susceptible to breakage, and their frequency varies among the human population. Based on the frequency of fragile site induction, they are categorized as common and rare fragile sites. Common fragile sites are sensitive to replication stress and often rearranged in cancer. Rare fragile sites are the archetypal trinucleotide repeats. Fragile sites are known to be involved in chromosomal rearrangements in tumors. Human miRNA genes are also present at fragile sites. A better understanding of genes and miRNAs lying in the fragile site regions and their association with disease progression is required. RESULT:HumCFS is a manually curated database of human chromosomal fragile sites. HumCFS provides useful information on fragile sites such as coordinates on the chromosome, cytoband, their chemical inducers and frequency of fragile site (rare or common), genes and miRNAs lying in fragile sites. Protein coding genes in the fragile sites were identified by mapping the coordinates of fragile sites with human genome Ensembl (GRCh38/hg38). Genes present in fragile sites were further mapped to DisGenNET database, to understand their possible link with human diseases. Human miRNAs from miRBase was also mapped on fragile site coordinates. In brief, HumCFS provides useful information about 125 human chromosomal fragile sites and their association with 4921 human protein-coding genes and 917 human miRNA's. CONCLUSION:User-friendly web-interface of HumCFS and hyper-linking with other resources will help researchers to search for genes, miRNAs efficiently and to intersect the relationship among them. For easy data retrieval and analysis, we have integrated standard web-based tools, such as JBrowse, BLAST etc. Also, the user can download the data in various file formats such as text files, gff3 files and Bed-format files which can be used on UCSC browser. Database URL: http://webs.iiitd.edu.in/raghava/humcfs/.

BMC Genomics. 2019:19(Suppl 9) | 1 Citations (from Europe PMC, 2020-05-23)