List of databases for the cisTarget family of tools (e.g. RcisTarget, SCENIC/pySCENIC, and cisTopic).
To choose the database appropiate for your analysis, start by selecting the species and ranking type (i.e. What do you want to analyze: genes or regions?).
Note that the download size is typically over 1GB (100GB for mammal region databases), we recommend downloading the files with zsync_curl (see the Help with downloads).
Related files:
sha256sum.txt: To confirm whether the file was succesfuly downloaded
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TF annotation: Annotation to transcripton factors for the motifs or ChIP-seq tracks in each collection (30-100 Mb)
Column info:
Species:
Human(Homo sapiens)Mouse(Mus musculus)Fly(Drosophila melanogaster)
Ranking type:
Region: The ranking contains regions (i.e. for analyses of region-sets from ATAC-seq, ChIP-seq, …)Genes: The ranking contains genes.
Distance: For gene rankings only. Indicates the search space around the TSS of gene in which the motif is scored:
500bpUp: 500bp upstream of TSSTSS+/-10kb: 10kb around the TSS (total: 20kb)TSS+/-5kb: 5kb around the TSS (total: 10kb)5kbUp,FullTx: 5kb upstream TSS and transcript introns500bpUp100Dw: 500bp upstream of TSS, and 100bp downstream.
Motif or track collection:
Motifs - Version 8 (
mc8nr): 20003 motifsMotifs - Version 9 (
mc9nr): 24453 motifs-
TF ChIP-seq - Version 1 (
tc_v1):-
dm6: 1503 tracks -
hg19: 3040 tracks -
hg38: 2993 tracks
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nOrt: Number of orthologous species used to select the regions based on conservation. In case of doubt of which version to use: 7 species is normally appropiate for most analyses.
Genome: Genome version used to construct the ranking. For region-based analyses it is important that this version matches your data! Gene annotation version is shown in parenthesis.
Database name: Database name (add the extensions to obtain specific file names, e.g. .feather or .feather.zsync).
Download URL: Link to the database (.feather file, and its size).
List of databases:
| --- | --- | --- | --- | --- | --- | --- | --- |
| Human | Genes | | tc_v1 | 1 | hg19 (refseq_r45) | encode_20190621__ChIP_seq_transcription_factor.hg19-tss-centered-5kb.max | 128 NAb |
| Human | Genes | | tc_v1 | 1 | hg19 (refseq_r45) | encode_20190621__ChIP_seq_transcription_factor.hg19-500bp-upstream.max | 128 NAb |
| Human | Genes | | tc_v1 | 1 | hg19 (refseq_r45) | encode_20190621__ChIP_seq_transcription_factor.hg19-tss-centered-10kb.max | 128 NAb |
| Human | Genes | | tc_v1 | 1 | hg38 (refseq_r80) | encode_20190621__ChIP_seq_transcription_factor.hg38__refseq-r80__10kb_up_and_down_tss.max | 157 Mb |
| Human | Genes | | tc_v1 | 1 | hg38 (refseq_r80) | encode_20190621__ChIP_seq_transcription_factor.hg38__refseq-r80__500bp_up_and_100bp_down_tss.max | 156 Mb |
| Human | Genes | 500bpUp | mc8nr | 7 | hg19 (refseq_r45) | hg19-500bp-upstream-7species.mc8nr | 852 Mb |
| Human | Genes | 500bpUp | mc9nr | 7 | hg19 (refseq_r45) | hg19-500bp-upstream-7species.mc9nr | 1 Gb |
| Human | Genes | 500bpUp | mc8nr | 10 | hg19 (refseq_r45) | hg19-500bp-upstream-10species.mc8nr | 852 Mb |
| Human | Genes | 500bpUp | mc9nr | 10 | hg19 (refseq_r45) | hg19-500bp-upstream-10species.mc9nr | 1 Gb |
| Human | Genes | 500bpUp100Dw | mc9nr | 9 | hg38 (refseq_r80) | hg38__refseq-r80__500bp_up_and_100bp_down_tss.mc9nr | 1 Gb |
| Human | Genes | TSS+/-10kbp | mc8nr | 7 | hg19 (refseq_r45) | hg19-tss-centered-10kb-7species.mc8nr | 852 Mb |
| Human | Genes | TSS+/-10kbp | mc9nr | 7 | hg19 (refseq_r45) | hg19-tss-centered-10kb-7species.mc9nr | 1 Gb |
| Human | Genes | TSS+/-10kbp | mc9nr | 9 | hg38 (refseq_r80) | hg38__refseq-r80__10kb_up_and_down_tss.mc9nr | 1 Gb |
| Human | Genes | TSS+/-10kbp | mc8nr | 10 | hg19 (refseq_r45) | hg19-tss-centered-10kb-10species.mc8nr | 852 Mb |
| Human | Genes | TSS+/-10kbp | mc9nr | 10 | hg19 (refseq_r45) | hg19-tss-centered-10kb-10species.mc9nr | 1 Gb |
| Human | Genes | TSS+/-5kbp | mc8nr | 7 | hg19 (refseq_r45) | hg19-tss-centered-5kb-7species.mc8nr | 852 Mb |
| Human | Genes | TSS+/-5kbp | mc9nr | 7 | hg19 (refseq_r45) | hg19-tss-centered-5kb-7species.mc9nr | 1 Gb |
| Human | Genes | TSS+/-5kbp | mc8nr | 10 | hg19 (refseq_r45) | hg19-tss-centered-5kb-10species.mc8nr | 852 Mb |
| Human | Genes | TSS+/-5kbp | mc9nr | 10 | hg19 (refseq_r45) | hg19-tss-centered-5kb-10species.mc9nr | 1 Gb |
| Human | Regions | | mc8nr | 9 | hg19 (refseq_r45) | hg19-regions-9species.all_regions.mc8nr | 91 Gb |
| Human | Regions | | mc9nr | 9 | hg19 (refseq_r45) | hg19-regions-9species.all_regions.mc9nr | 112 Gb |
| Mouse | Genes | 500bpUp | mc8nr | 7 | mm9 (refseq_r45) | mm9-500bp-upstream-7species.mc8nr | 844 Mb |
| Mouse | Genes | 500bpUp | mc9nr | 7 | mm9 (refseq_r45) | mm9-500bp-upstream-7species.mc9nr | 1 Gb |
| Mouse | Genes | 500bpUp | mc8nr | 10 | mm9 (refseq_r45) | mm9-500bp-upstream-10species.mc8nr | 844 Mb |
| Mouse | Genes | 500bpUp | mc9nr | 10 | mm9 (refseq_r45) | mm9-500bp-upstream-10species.mc9nr | 1 Gb |
| Mouse | Genes | 500bpUp100Dw | mc9nr | 9 | mm10 (refseq_r80) | mm10__refseq-r80__500bp_up_and_100bp_down_tss.mc9nr | 1 Gb |
| Mouse | Genes | TSS+/-10kbp | mc8nr | 7 | mm9 (refseq_r45) | mm9-tss-centered-10kb-7species.mc8nr | 844 Mb |
| Mouse | Genes | TSS+/-10kbp | mc9nr | 7 | mm9 (refseq_r45) | mm9-tss-centered-10kb-7species.mc9nr | 1 Gb |
| Mouse | Genes | TSS+/-10kbp | mc9nr | 9 | mm10 (refseq_r80) | mm10__refseq-r80__10kb_up_and_down_tss.mc9nr | 1 Gb |
| Mouse | Genes | TSS+/-10kbp | mc8nr | 10 | mm9 (refseq_r45) | mm9-tss-centered-10kb-10species.mc8nr | 844 Mb |
| Mouse | Genes | TSS+/-10kbp | mc9nr | 10 | mm9 (refseq_r45) | mm9-tss-centered-10kb-10species.mc9nr | 1 Gb |
| Mouse | Genes | TSS+/-5kbp | mc8nr | 7 | mm9 (refseq_r45) | mm9-tss-centered-5kb-7species.mc8nr | 844 Mb |
| Mouse | Genes | TSS+/-5kbp | mc9nr | 7 | mm9 (refseq_r45) | mm9-tss-centered-5kb-7species.mc9nr | 1 Gb |
| Mouse | Genes | TSS+/-5kbp | mc8nr | 10 | mm9 (refseq_r45) | mm9-tss-centered-5kb-10species.mc8nr | 844 Mb |
| Mouse | Genes | TSS+/-5kbp | mc9nr | 10 | mm9 (refseq_r45) | mm9-tss-centered-5kb-10species.mc9nr | 1 Gb |
| Mouse | Regions | | mc9nr | 9 | mm9 (refseq_r70) | mm9-regions-9species.all_regions.mc9nr | 125 Gb |
| Fly | Genes | 5kbUp,FullTx | tc_v1 | 1 | dm6 (flybase_r6.02) | encode_modERN_20190621__ChIP_seq.drosophila_melanogaster.dm6.gene_based.max | 98 Mb |
| Fly | Genes | 5kbUp,FullTx | mc8nr | 11 | dm6 (flybase_r6.02) | dm6-5kb-upstream-full-tx-11species.mc8nr | 1 Gb |
| Fly | Regions | | mc9nr | 11 | dm3 (flybase_r5.37) | dm3-regions-11species.mc9nr | 12 Gb |
| Fly | Regions | | mc8nr | 11 | dm6 (flybase_r6.02) | dm6-regions-11species.mc8nr | 10 Gb |
| Fly | Regions | | mc9nr | 11 | dm6 (flybase_r6.02) | dm6-regions-11species.mc9nr | 12 Gb |
