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X Demographics
Mendeley readers
Attention Score in Context
| Title |
An Integrated Pipeline for the Genome-Wide Analysis of Transcription Factor Binding Sites from ChIP-Seq
|
|---|---|
| Published in |
PLOS ONE, February 2011
|
| DOI | 10.1371/journal.pone.0016432 |
| Pubmed ID | |
| Authors |
Eloi Mercier, Arnaud Droit, Leping Li, Gordon Robertson, Xuekui Zhang, Raphael Gottardo |
| Abstract |
ChIP-Seq has become the standard method for genome-wide profiling DNA association of transcription factors. To simplify analyzing and interpreting ChIP-Seq data, which typically involves using multiple applications, we describe an integrated, open source, R-based analysis pipeline. The pipeline addresses data input, peak detection, sequence and motif analysis, visualization, and data export, and can readily be extended via other R and Bioconductor packages. Using a standard multicore computer, it can be used with datasets consisting of tens of thousands of enriched regions. We demonstrate its effectiveness on published human ChIP-Seq datasets for FOXA1, ER, CTCF and STAT1, where it detected co-occurring motifs that were consistent with the literature but not detected by other methods. Our pipeline provides the first complete set of Bioconductor tools for sequence and motif analysis of ChIP-Seq and ChIP-chip data. |
X Demographics
The data shown below were collected from the profile of 1 X user who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| France | 1 | 100% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 1 | 100% |
Mendeley readers
The data shown below were compiled from readership statistics for 175 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United States | 9 | 5% |
| France | 4 | 2% |
| Italy | 2 | 1% |
| Germany | 1 | <1% |
| Austria | 1 | <1% |
| Sweden | 1 | <1% |
| Turkey | 1 | <1% |
| Slovenia | 1 | <1% |
| United Kingdom | 1 | <1% |
| Other | 2 | 1% |
| Unknown | 152 | 87% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 55 | 31% |
| Student > Ph. D. Student | 53 | 30% |
| Student > Master | 16 | 9% |
| Student > Bachelor | 11 | 6% |
| Professor | 9 | 5% |
| Other | 23 | 13% |
| Unknown | 8 | 5% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 95 | 54% |
| Biochemistry, Genetics and Molecular Biology | 38 | 22% |
| Computer Science | 14 | 8% |
| Medicine and Dentistry | 8 | 5% |
| Engineering | 3 | 2% |
| Other | 7 | 4% |
| Unknown | 10 | 6% |
Attention Score in Context
This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 05 September 2013.
All research outputs
#15,278,165
of 22,719,618 outputs
Outputs from PLOS ONE
#130,189
of 193,931 outputs
Outputs of similar age
#83,086
of 105,902 outputs
Outputs of similar age from PLOS ONE
#983
of 1,284 outputs
Altmetric has tracked 22,719,618 research outputs across all sources so far. This one is in the 22nd percentile – i.e., 22% of other outputs scored the same or lower than it.
So far Altmetric has tracked 193,931 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 15.0. This one is in the 24th percentile – i.e., 24% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 105,902 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 12th percentile – i.e., 12% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 1,284 others from the same source and published within six weeks on either side of this one. This one is in the 15th percentile – i.e., 15% of its contemporaries scored the same or lower than it.