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Sequence homology in eukaryotes (SHOE): interactive visual tool for promoter analysis

Overview of attention for article published in BMC Genomics, September 2018
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3 tweeters

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Title
Sequence homology in eukaryotes (SHOE): interactive visual tool for promoter analysis
Published in
BMC Genomics, September 2018
DOI 10.1186/s12864-018-5101-3
Pubmed ID
Authors

Natalia Polouliakh, Paul Horton, Kazuhiro Shibanai, Kodai Takata, Vanessa Ludwig, Samik Ghosh, Hiroaki Kitano

Abstract

Microarray and DNA-sequencing based technologies continue to produce enormous amounts of data on gene expression. This data has great potential to illuminate our understanding of biology and medicine, but the data alone is of limited value without computational tools to allow human investigators to visualize and interpret it in the context of their problem of interest. We created a web server called SHOE that provides an interactive, visual presentation of the available evidence of transcriptional regulation and gene co-expression to facilitate its exploration and interpretation. SHOE predicts the likely transcription factor binding sites in orthologous promoters of humans, mice, and rats using the combined information of 1) transcription factor binding preferences (position-specific scoring matrix (PSSM) libraries such as Transfac32, Jaspar, HOCOMOCO, ChIP-seq, SELEX, PBM, and iPS-reprogramming factor), 2) evolutionary conservation of putative binding sites in orthologous promoters, and 3) co-expression tendencies of gene pairs based on 1,714 normal human cells selected from the Gene Expression Omnibus Database. SHOE enables users to explore potential interactions between transcription factors and target genes via multiple data views, discover transcription factor binding motifs on top of gene co-expression, and visualize genes as a network of gene and transcription factors on its native gadget GeneViz, the CellDesigner pathway analyzer, and the Reactome database to search the pathways involved. As we demonstrate here when using the CREB1 and Nf-κB datasets, SHOE can reliably identify experimentally verified interactions and predict plausible novel ones, yielding new biological insights into the gene regulatory mechanisms involved. SHOE comes with a manual describing how to run it on a local PC or via the Garuda platform ( www.garuda-alliance.org ), where it joins other popular gadgets such as the CellDesigner pathway analyzer and the Reactome database, as part of analysis workflows to meet the growing needs of molecular biologists and medical researchers. SHOE is available from the following URL http://ec2-54-150-223-65.ap-northeast-1.compute.amazonaws.com A video demonstration of SHOE can be found here: https://www.youtube.com/watch?v=qARinNb9NtE.

Twitter Demographics

The data shown below were collected from the profiles of 3 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 14 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 14 100%

Demographic breakdown

Readers by professional status Count As %
Professor 1 7%
Other 1 7%
Unknown 12 86%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 2 14%
Unknown 12 86%

Attention Score in Context

This research output has an Altmetric Attention Score of 2. 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 16 June 2021.
All research outputs
#11,978,555
of 18,881,749 outputs
Outputs from BMC Genomics
#5,528
of 9,649 outputs
Outputs of similar age
#166,783
of 289,167 outputs
Outputs of similar age from BMC Genomics
#3
of 8 outputs
Altmetric has tracked 18,881,749 research outputs across all sources so far. This one is in the 34th percentile – i.e., 34% of other outputs scored the same or lower than it.
So far Altmetric has tracked 9,649 research outputs from this source. They receive a mean Attention Score of 4.5. This one is in the 37th percentile – i.e., 37% 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 289,167 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 38th percentile – i.e., 38% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 8 others from the same source and published within six weeks on either side of this one. This one has scored higher than 5 of them.