EpiDB is a platform for sharing processed NGS data useful as reference
information and data reuse to link genotype to phenotype in domestic
food animal species.
Started in 2014, the EpiDB
has been undergoing active developments, which is aimed for a smart, interactive
repository and platform for searching and analyzing domestic food animal
epigenetic and gene expression data. The main idea of this web-based resource
was to make functional next-generation sequencing (NGS) data for chicken, cattle,
pig, horse, and sheep available as pre-processed and summarized genomic
information to the scientific community, as well as to promote the re-use of
existing data.
Functions already available are (legacy data):
- Querying the meta data database to facilitate data re-use;
- Downloads available for tissue specific, whole transcriptome expression baseline levels;
- Access to a dynamic gene expression atlas;
- Datasets for cattle, pig, chicken, sheep, and horse.
Future:
- Add new data from cattle FAANG project;
- Provide tissue-specific allele specific expression;
- Provide full epigenetic expression levels, as miRNA and methylation;
- Facilitate all livestock species;
- Incorporate ChIPseq and regulation information;
- Expand to additional species and data types.
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Data counts in current EpiDB version
Species | Tissues | Genes | Data set | Expression counts |
Cattle | 72 | 45,060 | 4 | 101,898,860 |
Chicken | 0 | 0 | 0 | 0 |
Horse | 0 | 0 | 0 | 0 |
Pig | 0 | 0 | 0 | 0 |
Sheep | 0 | 0 | 0 | 0 |
Most recent data updates
Data realm | Last updates |
count types | 2023-06-27 15:44:22 |
data src | 2023-12-04 17:03:06 |
exp types | 2023-06-27 15:35:02 |
expr counts | 2023-12-04 17:03:06 |
gene info | 2023-07-21 02:57:48 |
miRBase | 2023-11-10 21:08:12 |
sample conditions | 2023-09-06 11:17:30 |
species info | 2022-12-18 18:18:18 |
tissue link | 2024-08-17 23:12:30 |
tissue linksrc | 2023-07-18 22:40:59 |
users | 2023-04-06 21:43:50 |
Recent web tools developments
- EpiDB.animalgenome.org/freqct (Jun 26, 2024)
- EpiDB.animalgenome.org/data (Mar 14, 2024)
- EpiDB.animalgenome.org/dev/login (Mar 14, 2024)
- EpiDB.animalgenome.org/dev/maptrait (Mar 04, 2024)
- EpiDB.animalgenome.org/resource (Dec 01, 2023)
- EpiDB.animalgenome.org/index (Dec 01, 2023)
- EpiDB.animalgenome.org/dev/entry (Dec 01, 2023)
- EpiDB.animalgenome.org/atlas (Dec 01, 2023)
- EpiDB.animalgenome.org/tools (Dec 01, 2023)
- EpiDB.animalgenome.org/dev/userset (Nov 01, 2023)
- EpiDB.animalgenome.org/exprcounts (Sep 26, 2023)
- EpiDB.animalgenome.org/dev/index (May 19, 2023)
- EpiDB.animalgenome.org/pubSeqSum (Feb 21, 2019)
- EpiDB.animalgenome.org/test_dataQuery (Jul 21, 2016)
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