REMAP statistics

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REMAP specifications

Information


Unique identifier OMICS_23427
Name REMAP
Alternative name the Remote Ecosystem Monitoring and Assessment Pipeline
Interface Web user interface
Restrictions to use None
Input data A region of interest and a vector file.
Input format KML
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


  • person_outline Nicholas Murray
  • person_outline David Keith
  • person_outline Daniel Simpson
  • person_outline John Wilshire
  • person_outline Richard Lucas

Publication for the Remote Ecosystem Monitoring and Assessment Pipeline

REMAP citations

 (11)
library_books

Genome wide association study of self reported food reactions in Japanese identifies shrimp and peach specific loci in the HLA DR/DQ gene region

2018
Sci Rep
PMCID: 5773682
PMID: 29348432
DOI: 10.1038/s41598-017-18241-w

[…] ranscription factor binding sites (TFBS), we created a .bed file for our variants, moved the genome-build coordinates from hg19 to hg38 using the UCSC liftOver tool, and then annotated them using the ReMap 2018 Annotation Tool. […]

library_books

The 2018 Nucleic Acids Research database issue and the online molecular biology database collection

2017
Nucleic Acids Res
PMCID: 5753253
PMID: 29316735
DOI: 10.1093/nar/gkx1235

[…] ranscription factors (TF) and transcriptional regulation are represented by a number of databases. The popular returning database of TF binding profiles, JASPAR (), is published back to back with the ReMAP database () of TF ChIP-seq data: data from ReMAP contributed directly to JASPAR’s improved coverage. With recent intense interest in the role of 3D chromatin structure in gene regulation, the 3D […]

library_books

DNA methylation at enhancers identifies distinct breast cancer lineages

2017
Nat Commun
PMCID: 5680222
PMID: 29123100
DOI: 10.1038/s41467-017-00510-x

[…] ological functions of Clusters 1 and 2.Next, we focused on the TF binding regions obtained from the MCF7 cell line and mined 71 ChIP-seq experiments from ENCODE and 40 available at GEO retrieved from ReMap; we performed enrichment analyses using hypergeometric tests. We observed that emQTL-CpGs were most strongly enriched at ERα, FOXA1, and GATA3 binding sites and to a lesser extend at GREB1, FOS, […]

library_books

Integrative whole genome sequence analysis reveals roles of regulatory mutations in BCL6 and BCL2 in follicular lymphoma

2017
Sci Rep
PMCID: 5539289
PMID: 28765546
DOI: 10.1038/s41598-017-07226-4

[…] T complex have similar but distinct PWMs (Supplementary Figure ), are predicted to be both positively and negatively affected ones. Nevertheless, according to the in vivo experiments that reported in ReMap, ARNT usually does not bind to ±1000 bp of BCL2 TSS, and the predicted negative binding affinity change may be neglected.Based on an in silico study of genome-wide sequencing data of both test ( […]

library_books

DNA methylation at the mu 1 opioid receptor gene (OPRM1) promoter predicts preoperative, acute, and chronic postsurgical pain after spine fusion

2017
PMCID: 5432115
PMID: 28533693
DOI: 10.2147/PGPM.S132691

[…] To identify potential regulatory mechanisms in the OPRM1 promoter, a large collection of functional genomics data sets from various sources, including ENCODE, Road-map Epigenomics, Cistrome, and ReMap-ChIP, was compiled. The genomic coordinates of the OPRM1 promoter were intersected against the genomic coordinates contained in each data set. In total, this database contains 4,953 data sets pe […]

library_books

CHD1 regulates cell fate determination by activation of differentiation induced genes

2017
Nucleic Acids Res
PMCID: 5570082
PMID: 28475736
DOI: 10.1093/nar/gkx377

[…] 5409 regions). Averaged ChIP-seq signals at these regions were calculated by scale-region mode over computeMatrix. Analysis of additional transcription factor binding was further performed using the ReMap tool (). […]

Citations

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REMAP institution(s)
Centre for Ecosystem Science, School of Biological, Earth and Environmental Science, University of New South Wales, Sydney, NSW, Australia; New South Wales Office of Environment and Heritage, Hurstville, NSW, Australia
REMAP funding source(s)
Supported by a Google Earth Engine Research Award and an Australian Research Council Linkage Grant LP130100435, co-funded by the International Union for the Conservation of Nature, MAVA Foundation, NSW Office of Environment and Heritage, and the South Department of Environment, Water and Natural Resources.

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