liver-disease-atlas-app
Science Score: 57.0%
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Found 5 DOI reference(s) in README -
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Low similarity (10.0%) to scientific vocabulary
Last synced: 7 months ago
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Repository
Basic Info
- Host: GitHub
- Owner: saezlab
- License: mit
- Language: R
- Default Branch: master
- Homepage: https://saezlab.shinyapps.io/liverdiseaseatlas/
- Size: 277 KB
Statistics
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Created about 5 years ago
· Last pushed over 4 years ago
Metadata Files
Readme
Changelog
License
Citation
README.Rmd
---
output: github_document
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# Welcome to the Liver disease atlas
The prevalence of chronic liver diseases (CLD) has increased during the last decades. Mouse models are frequently used to study the pathophysiology of liver diseases, identify therapeutic targets, and test drug candidates.
To allow a better assessment of translational relevance from mouse models to human CLD we analyzed genome-wide transcriptome data from seven mouse models (one with chronic and six with acute liver damage) comprising 227 mice and five studies of human CLD with a total of 372 patients.
See the corresponding publication for more details: [_Transcriptomic cross-species analysis of chronic liver disease reveals consistent regulation between humans and mice_](https://doi.org/10.1002/hep4.1797).
## About
This application informs for any gene of interest on:
* mean expression changes in the chronic and acute mouse models and in patients of different liver disease etiologies. Users may choose to show the log-fold changes or the t-statistic both derived from a differential gene expression analysis.
* the categorization into genes that are altered exclusively during acute or chronic damage or commonly deregulated in both acute and chronic mouse models. See the _chronicity_ box. This classification is not available for any gene. For a complete list please visit the `data` tab.
* the associated cell type in which we found the gene also significantly deregulated between cirrhotic and healthy patients. This information was inferred from from single-cell RNA-seq data.
* if the gene is consistently altered in mice and humans. If this is true, the rank is displayed. See the _consistency_ box. The better the displayed rank (from low to high) the stronger the gene is consistently altered in human and mice. Please visit the `data` tab to see the full list of genes.
### How to cite?
>Holland CH, Ramirez Flores RO, Myllys M, Hassan R, Edlund K, Hofmann U, Marchan R, Cadenas C, Reinders J, Hoehme S, Seddek A, Dooley S, Keitel V, Godoy P, Begher-Tibbe B, Trautwein C, Rupp C, Mueller S, Longerich T, Hengstler JG^#^, Saez-Rodriguez J^#^, Ghallab A^#^. "Transcriptomic cross-species analysis of chronic liver disease reveals consistent regulation between humans and mice." _Hepatology Communications_. 2021. DOI: [10.1002/hep4.1797](https://doi.org/10.1002/hep4.1797).
^#^ _Shared senior authorship_
Owner
- Name: Saez Lab
- Login: saezlab
- Kind: organization
- Email: pub.saez@uni-heidelberg.de
- Location: Germany
- Website: saezlab.org
- Repositories: 241
- Profile: https://github.com/saezlab
Institute for Computational Biomedicine - Julio Saez-Rodriguez's group
Citation (CITATION.cff)
cff-version: 1.2.0
message: "If you use this app please cite as below."
authors:
- family-names: "Holland"
given-names: "Christian H."
orcid: "https://orcid.org/0000-0002-3060-5786"
- family-names: "Ramirez Flores"
given-names: "Ricardo O."
- family-names: "Myllys"
given-names: "Maiju"
- family-names: "Hassan"
given-names: "Reham"
- family-names: "Edlund"
given-names: "Karolina"
- family-names: "Hofmann"
given-names: "Ute"
- family-names: "Marchan"
given-names: "Rosemarie"
- family-names: "Cadenas"
given-names: "Cristina"
- family-names: "Reinders"
given-names: "Jörg"
- family-names: "Seddek,"
given-names: "Abdel-latif "
- family-names: "Hoehme"
given-names: "Stefan"
- family-names: "Dooley"
given-names: "Steven"
- family-names: "Keitel"
given-names: "Verena"
- family-names: "Godoy"
given-names: "Patricio"
- family-names: "Begher-Tibbe"
given-names: "Brigitte"
- family-names: "Trautwein"
given-names: "Christian"
- family-names: "Rupp"
given-names: "Christian"
- family-names: "Mueller"
given-names: "Sebastian"
- family-names: "Longerich"
given-names: "Thomas"
- family-names: "Hengstler"
given-names: "Jan G."
- family-names: "Saez-Rodriguez"
given-names: "Julio"
- family-names: "Ghallab"
given-names: "Ahmed"
doi: 10.1002/hep4.1797
title: "Transcriptomic Cross-Species Analysis of Chronic Liver Disease Reveals Consistent Regulation Between Humans and Mice"
year: 2021
month: August
url: "https://doi.org/10.1002/hep4.1797"
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- christianholland (2)