What is Liver OmixAtlas?
Elucidata’s Liver OmixAtlas is the largest repository of liver tissue-derived data hosted on our data platform, Polly. It contains 9 different types of biomedical molecular data derived from human, mouse and rat from 10 public sources, encompassing normal as well as perturbed (disease, drug treatment, gene knockout/knockdown, etc.) states of liver tissue. Data on Liver OmixAtlas is enriched with metadata annotations to facilitate easy discovery of relevant datasets, and can be accessed on our cloud infrastructure or your existing one.
Why did we build an OmixAtlas?
Every year, vast amounts of biological multi-omics data are being generated and made public by academic labs and organizations worldwide. These data hold tremendous potential for reuse and discovery but are scattered across multiple, disparate sources and lack standardization. Thus, the availability of data does not equate to its easy usability, making the need for an efficient means of exploring molecular data an immediate necessity.
Additionally, biological systems and processes are intrinsically complex. No single type of data, be it metabolomic, proteomic, or genomic, will be sufficient to capture the complexity of biological phenomena. Adopting an integrated approach could significantly aid the ability to gain a holistic and more accurate understanding of physiology and disease pathology at the molecular level.
Elucidata’s Liver OmixAtlas addresses the above issues by ensuring that the metadata across different public resources has been curated and harmonized and made ready for downstream machine learning and analytical applications.
Why start with ‘Liver’ OmixAtlas?
Polly is primarily geared towards multi-disciplinary drug discovery teams in the pharmaceutical industry. A significant hurdle during drug development is the prediction of the safety and metabolic characteristics of a novel drug prior to clinical trials. Since the liver is the major site of metabolism and detoxification, various types of molecular data derived from liver tissue can play an important role in predicting the safety of drugs.
A deep dive into Liver OmixAtlas:
|Public Source||Type of Data|
|1.||The Cancer Cell Line Encyclopedia (CCLE)|
Bulk Transcriptomics (Microarray and RNA Seq)
|2.||The Cancer Genome Atlas (TCGA)||RNA Seq|
|3.||The Human Protein Atlas (HPA)||RNA Seq|
|4.||The Cancer Dependency Map Project (DepMap)||Gene dependency|
|5.||Other public sources||Single-cell|
|8.||Library of Integrated Network-based Cellular Signatures||L1000 RNA Seq|
|9.||Genotype-Tissue Expression Portal(GTEx)||RNA Seq|
|10.||Gene Expression Omnibus (GEO)||Bulk Transcriptomics (Microarray and RNA Seq)|
|11.||Clinical Proteomic Tumor Analysis Consortium (CPTAC)||Proteomics|
How are the data available in Liver OmixAtlas different from the data available in public resources?
The data in Liver OmixAtlas are curated through Polly’s ML-based curation workflow that structures different types of data, harmonizes metadata, and makes the data analysis ready. All data available in Liver OmixAtlas can be queried and directly used in downstream statistical or ML-based analyses.
Data available in LiverOmix Atlas have the following harmonized metadata:
- Data descriptors
- data type
- dataset source
- Metadata to identify the biological system and samples being studied:
- cell line
- cell type
- Metadata to identify specific perturbations:
- genetic modification – type and gene
- Metadata to understand experiment design
- experimental factors (*only applicable for GEO, LINCS, Metabolights, metabolomics workbench)
- total number of samples
- total number of cells (only applicable for single cell data)