Co-expression-based Rice Transcription Factor-Target Prediction Server


Downloadable data



1. Data Information

RTFRD collected 149 rice unique RNA-seq datasets from NCBI GEO database. These datasets are characterized by the absence of biological replicates. For some experimental conditions/stimuli with biological replicates, we only selected RNA-seq sample data from one of the biological replicates to represent that condition/stimulus.
information.txt
TSV-file, 264 KB
information_150.txt
TSV-file, 88 KB

2. Promoter Sequences

Promoter sequence of rice gene
Fasta file header format:
e.g. LOC_Os06g05820 [Chr6 2650068 2652068 + 2000bp]
(gene name [ chromosome start end strand length ])
promoter.fa
FASTA-file, 110 MB

3. TF information

This file mainly corresponds to the information of the BROWSE module
Description:
column 1: Transcription factor ID
column 2: Transcription factor gene ID
column 3: Transcription factor tyle
    type 1 represents a transcription factor with a manually curated, non-redundancy and high-quality motif downloaded directly from PlantTFDB, represented by in BROWSE
    type 2 represents a transcription factor highly homologous to type1 calculated by using blastp. the TF binding motif is the same as the motif of type 1, represented by (e-value < 1e-10) in BROWSE
    type 3 represents a transcription factor generally homologous to type1 calculated by using blastp. the TF binding motif is the same as the motif of type 1, represented by (e-value > 1e-10 and e-value < 1e-4) in BROWSE
    type 4 represents a transcription factor with no homologous to type1 calculated by using blastp. represented by "blank" (e-value > 1e-4) in BROWSE
column 4: Transcription factor family
column 5: Method
column 6: Whether it is homologous TF with type 1(homo OR - )
column 7: the ID of the TF homologous, if it is a TF homologous with type 1
column 8: evalue
TF_list.txt
TSV-file, 152 KB

4. Promoter sequence analysis results

Analyzing Software: FIMO
command: fimo -oc fimo_res Osj_TF_binding_motifs.meme promoter.fa
Osj_TF_binding_motifs.meme: download from PlantTFDB
fimo.tsv.gz
TSV-file, 113 MB

5. Expression matrix of the total datasets

Expression matrix of 150 uniqre samples
Genome and annotation file versions: msu 7.0

6. Expression matrix of the anatomy datasets

Expression matrix of 23 tissues
Genome and annotation file versions: msu 7.0