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Citations per year

Number of citations per year for the bioinformatics software tool my5C
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Tool usage distribution map

This map represents all the scientific publications referring to my5C per scientific context
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Protocols

my5C specifications

Information


Unique identifier OMICS_15677
Name my5C
Interface Web user interface
Restrictions to use None
Input data The 5C region file, the region name, the restriction site, the optimal primer length, the optimal TM, the primer set options, the primer pool description
Input format FASTA
Computer skills Basic
Stability No
Maintained No

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Publication for my5C

my5C citations

 (6)
library_books

5C analysis of the Epidermal Differentiation Complex locus reveals distinct chromatin interaction networks between gene rich and gene poor TADs in skin epithelial cells

2017
PLoS Genet
PMCID: 5599062
PMID: 28863138
DOI: 10.1371/journal.pgen.1006966

[…] ction of the spatial chromatin looping contacts and identification of TADs [, ]. For the 5C analysis, 381 forward and 382 reverse 5C probes were designed in an alternating scheme using the tools from my5C software suite [] to interrogate HindIII sites with the unique anchoring regions at the EDC and its flanking regions (mm9, chromosome 3: 89.9–95.2 Mbp) (, ). The designed probe pool interrogated […]

call_split

Software tools for visualizing Hi C data

2017
Genome Biol
PMCID: 5290626
PMID: 28159004
DOI: 10.1186/s13059-017-1161-y
call_split See protocol

[…] olutions that strike a balance between sparsity and detail. We found that Juicebox, the Epigenome Browser and the 3D Genome Browser process user data in binary formats in a few seconds. Hi-Browse and my5C do not support loading of a complete dataset at these resolutions, instead the user must upload the Hi-C contact matrix corresponding to the region of interest. The average times required to visu […]

library_books

Analysis of long range interactions in primary human cells identifies cooperative CFTR regulatory elements

2015
Nucleic Acids Res
PMCID: 4824072
PMID: 26615198
DOI: 10.1093/nar/gkv1300

[…] instance of Galaxy as previously described (,). This analysis generates an excel sheet containing interaction frequency lists (IFL) as well as a text file, which was used to visualize results using ‘my5C-heatmap’ ().Normalization between different libraries was done first by read count and then using the compaction profiles for the ERCC3 region and the gene desert region ENr313, setting one sampl […]

library_books

Clustering of Tissue Specific Sub TADs Accompanies the Regulation of HoxA Genes in Developing Limbs

2013
PLoS Genet
PMCID: 3873244
PMID: 24385922
DOI: 10.1371/journal.pgen.1004018

[…] ds which do not contain EcoRI restriction sites. This analysis generates an excel sheet containing interaction frequency lists (IFL) as well as a text file, which was used to visualize results using ‘my5C-heatmap’ . Limb-enriched 5C interactions were obtained by subtracting limb and head 5C-seq data. Data was normalized by dividing the number of reads of each 5C contact by the total number of read […]

library_books

Hox in motion: tracking HoxA cluster conformation during differentiation

2013
Nucleic Acids Res
PMCID: 3919592
PMID: 24174538
DOI: 10.1093/nar/gkt998

[…] We used this new analysis platform to obtain normalized interaction frequency values for all pairwise interactions in the HoxA locus and control gene desert region, and visualized the data with the ‘my5C’ heatmap tool (). Figure 2.A shows the HoxA 5C maps from our main time course (biological 1) and from a biological replicate (biological 2) in heatmap form where pairwise IFs are color-coded acco […]

library_books

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

2011
PLoS Biol
PMCID: 3079585
PMID: 21526222
DOI: 10.1371/journal.pbio.1001046

[…] start sites across chromosome 21 and selected domains throughout the genome. Special interfaces have been developed to visualize these 3-dimensional genomic data and are publicly available at http://my5C.umassmed.edu . […]


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my5C institution(s)
Program in Gene Function and Expression and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
my5C funding source(s)
This work was supported by The National Institutes of Health (HG003143, HG004592) and the Keck Foundation.

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