Table 2 Data sources for each PLAIDOH default file. Data names, sources and descriptions for all of the metrics utilized by PLAIDOH to annotate lncRNA and gene function
Data source | Data Type | Description | URL |
|---|---|---|---|
Enhancer Atlas [104] | Enhancer boundaries | Chromosomal positions for enhancer boundaries from all available tissue samples were downloaded in May 2018. | |
Super Enhancer Archive [105] | Super-enhancer boundaries | Chromosomal positions for super enhancer boundaries from all available tissue samples were downloaded in May 2018. | |
ENCODE [106] | Histone ChIP-seq (p-value of peaks) | H3K4ME3, H3K4ME1, and H3K27AC ChIP-seq experiment bed files for all available cell lines were downloaded from the ENCODE experiment database in May 2018. All bed files were modified to contain the cell line, histone modification and peak p-value as a column entry. | |
ENCODE [1] | Cell Fraction Expression (proportion of total RPKM), | FPKMs for all transcripts in nuclear and cytoplasmic RNA-seq for GM12878 cells were downloaded in March 2018. The fraction of total reads in the nuclear fraction for each transcript was calculated. | |
ENCODE [107] | RNA-Binding Protein (eCLIP) (interacting partners, number RBP bound, number RBP binding sites), | eCLIP experiment bed files for replicates 01 and 02 from K562 and HepG2 cells for all available RBPs were downloaded from the ENCODE experiment database in May 2018. All bed files were modified to contain the RBP gene name, replicate number and cell line as column entries. | |
ENCODE [49] | ChIA-PET (boundaries of interacting fragments, score) | POL2RA ChIA-PET interactions from K562 and MCF-7 cells were downloaded in April 2018. | |
ENSEMBL BIOMART [108] | Gene Ontology, Transcript strand, Transcript Name | A biomart query was performed in May 2018. “Gene description”, “Strand”, and “Gene name” were selected and downloaded for all hg19 transcripts. | |
Ren Lab Hi-C Project [40] | Topologically Associating Domain (TAD) Boundaries | Chromosomal positions were downloaded from two combined replicates of Human ES Cells. | |
RBP Image Database [82] | Sub-cellular localization of RNA Binding Proteins | Localization of all RBPs in HepG2 cells was downloaded and pruned to show only Nuclear and Cytoplasmic compartments. |