Data description
Inflammatory Bowel Disease example data description
NIHMS1510763-supplement-Dataset_1.xlsx: The Metabolomic Abundance Raw Matrix was downloaded from https://doi.org/10.1038/s41564-018-0306-4.
NIHMS1510763-supplement-Dataset_2.xlsx: The Metabolite Original ID and Metabolite Name Conversion Table was downloaded from https://doi.org/10.1038/s41564-018-0306-4.
NIHMS1510763-supplement-Dataset_6.xlsx: The Metagenomic Original Gene Abundance Matrix File was downloaded from https://doi.org/10.1038/s41564-018-0306-4.
enzyme_ko.txt: The ID mapping file (mapping enzymes to KEGG K-Numbers) was downloaded from https://github.com/YuLab-SMU/Supplemental-MMINP/blob/main/data/20220924_kegg/enzyme_ko.txt.
metabolwasm_expr.csv: The processed metabolomic abundance matrix file was derived from https://doi.org/10.1038/s41564-018-0306-4.
metabolwasm_meta.csv: The processed metabolomic experimental grouping information file was derived from https://doi.org/10.1038/s41564-018-0306-4.
mg.expr.csv: The processed metagenomic abundance matrix file was derived from https://doi.org/10.1038/s41564-018-0306-4.
mg.meta.csv: The processed metabolomic experimental grouping information file was derived from https://doi.org/10.1038/s41564-018-0306-4.
name_map.csv: The ID mapping file(mapping metabolites to KEGG C-Numbers) was downloaded from https://www.metaboanalyst.ca/MetaboAnalyst/resources/users/guest7299843510837833804tmp/name_map.csv.
Phyllostachys Edulis example data description:
Phe_GO_annotation.txt: The Phyllostachys Edulis gene GO annotation data was downloaded from https://plantregmap.gao-lab.org/download_ftp.php?filepath=08-download/Phyllostachys_heterocycla/GO/Phe_GO_annotation.gz.
Phe_TF_list.txt: The Phyllostachys Edulis transcription factor family annotation data was downloaded from https://planttfdb.gao-lab.org/download/TF_list/Phe_TF_list.txt.gz.
regulation_from_motif_CE_Phe.txt: The Predicted Phyllostachys Edulis transcription factor target gene was downloaded from https://plantregmap.gao-lab.org/download_ftp.php?filepath=08-download/Phyllostachys_heterocycla/binding/regulation_from_motif_CE_Phe.txt.
counts.txt: The counts.txt was processed Phyllostachys Edulis gene count matrix derived from https://db.cngb.org/search/project/CNP0002243/.
group_info.txt: The Phyllostachys Edulis sample group infomation was derived from https://onlinelibrary.wiley.com/doi/10.1111/jipb.13357.
PBMC single cell example data description:
c8.all.v2023.1.Hs.symbols.gmt: The C8 gene set was downloaded from https://www.gsea-msigdb.org/gsea/msigdb.
barcodes.tsv, genes.tsv, matrix.mtx: The single-cell transcriptomic data used in this study was derived from PBMC (Peripheral Blood Mononuclear Cell) samples and can be obtained from the following source: https://cf.10xgenomics.com/samples/cell/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz.