3.4. Datasets

This page enumerates the datasets used and integrated by RicePilaf.

Note to Page Maintainers:

1. The links under the project and source columns should point to the actual download links (not the homepage of the project or source).
2. The links under the publication column should point to the DOI to ensure persistence.

1️⃣ Gene List and Lift-Over

Dataset Type	Project	Publication	Save Location
Genome sequences, annotation, gene descriptions, and orthology maps of rice varieties	Rice Gene Index	Molecular Plant	static/app_data/genomes, static/app_data/annotations, static/app_data/gene_descriptions, static/raw_data/gene_ID_mapping_fromRGI [1]
Protein, protein domain, and protein family information from UniProt, InterPro, and Pfam	Obtained via automatic queries using PyRice	Bioinformatics	static/raw_data/iric_data/iric_data_original.pkl
QTL from published literature	QTARO (Accessed June 2016)	Rice	static/raw_data/qtaro/Qtaro_Mar2016_convMSU_1849.csv

Mapping	Source	Save Location
InterPro Accession to Name	InterPro	static/raw_data/iric_data/interpro2name.txt
Pfam Accession to Name	InterPro [2]	static/raw_data/iric_data/pfam2name.json

^[1] We thank Jianwei Zhang and Zhichao Yu for providing orthology maps from the Rice Gene Index.
^[2] Pfam is now hosted by InterPro. Choose the "Export to JSON" option to download the file.

2️⃣ Gene Retrieval by Text Mining

Dataset Type	Project (URL)	Publication	Save Location
Related PubMed articles	In-house text-mined dataset	–	static/app_data/text_mining/annotated_abstracts.tsv

3️⃣ Co-Expression Network Analysis

Dataset Type	Project	Publication	Save Location
Co-expression network	RiceNet	Nucleic Acids Research	static/app_data/networks/OS-CX.txt
Co-expression network	Rice Combined Mutual Ranked Network (RCRN)	Frontiers in Plant Science	static/app_data/networks/RCRN.txt
Gene ontology annotations	Rice Annotation Project Database (RAP-DB)	Plant & Cell Physiology	static/raw_data/enrichment_analysis/rap_db/IRGSP-1.0_representative_annotation_2023-03-15.tsv [3]
Gene ontology annotations	agriGO v2.0	Nucleic Acids Research	static/raw_data/enrichment_analysis/go/agrigo.tsv
Gene, plant, and trait ontology annotations	Oryzabase	Plant Physiology	static/raw_data/enrichment_analysis/go/OryzabaseGeneListAll_20230322010000.txt
Pathway maps	Fetched from the Kyoto Encyclopedia of Genes and Genomes (KEGG) via KEGGREST	Nucleic Acids Research	static/raw_data/enrichment_analysis/kegg_dosa/geneset/kegg-dosa-geneset.tsv

Mapping	Source	Save Location
MSU to RAP-DB accessions	RAP-DB	static/raw_data/enrichment_analysis/rap_db/RAP-MSU_2023-03-15.txt [4]
RAP-DB accessions to KEGG transcript IDs	RAP-DB	static/raw_data/enrichment_analysis/rap_db/IRGSP-1.0_representative_annotation_2023-03-15.tsv [3]

^[3] Text file is obtained by running gzip -dv IRGSP-1.0_representative_annotation_2023-03-15.tsv.gz
^[4] Text file is obtained by running gzip -dv RAP-MSU_2023-03-15.txt.gz

4️⃣ Regulatory Feature Enrichment

Dataset Type	Project	Publication	Save Location
Transcription factor binding sites	PlantRegMap	Nucleic Acids Research	static/raw_data/tf_enrichment

5️⃣ Epigenomic Information

Dataset Type	Project	Publication	Save Location
Open chromatin	RiceENCODE	Molecular Plant	static/app_data/open_chromatin