PlantTFDB
Plant Transcriptional Regulatory Map



1. Data Source Back to Top


   1.1 DNase I hypersensitive sites (DHSs, DNase-seq)Back to Top

SpeciesOrganConditionData Source
Arabidopsis thalianaflower14 daysSRR388661
Arabidopsis thalianaopen flowernormalSRR1049812
Arabidopsis thalianainflorescencenormalSRR850512, SRR850513, SRR850514, SRR850515, SRR850516, SRR850517, SRR850518, SRR850519
Arabidopsis thalianaleafnormalSRR2297459
Arabidopsis thalianarootnormalSRR2297460
Arabidopsis thalianaroot7 daysSRR1049804
Arabidopsis thalianaroot hair7 daysSRR1049808
Arabidopsis thalianaroot non hair7 daysSRR2101849, SRR2101856
Arabidopsis thalianaroot non hair10 daysSRR1049805, SRR1049806, SRR1049807
Arabidopsis thalianaseed coat4 days past anthesis rep1SRR2103595
Arabidopsis thalianaseed coat4 days past anthesis rep2SRR1049809, SRR1049810
Arabidopsis thalianaseed coat7 days past anthesisSRR1049811
Arabidopsis thalianaseedlingnormalSRR388658
Arabidopsis thalianaseedling7 day old ControlSRR1049781, SRR1049782
Arabidopsis thalianaseedling7 day old DarkSRR1049775, SRR1049776
Arabidopsis thalianaseedling7 day old Dark 30min lightSRR1049771, SRR1049772
Arabidopsis thalianaseedling7 day old Dark 3hr lightSRR1049773, SRR1049774
Arabidopsis thalianaseedling7 day old Dark 24hrSRR1049769, SRR1049770
Arabidopsis thalianaseedling7 day old Heat ShockSRR1049779, SRR1049780
Arabidopsis thalianaseedlingBay-0 7 day oldSRR1049798, SRR1049799
Arabidopsis thalianaseedlingBur-0 7 day oldSRR1049796, SRR1049797
Arabidopsis thalianaseedlingEst-1 7 day oldSRR1049800, SRR1049801
Arabidopsis thalianaseedlingTsu-1 7 day oldSRR1049802, SRR1049803
Oryza sativa subsp. japonicacallus14 daysSRR094109, SRR094110, SRR094111
Oryza sativa subsp. japonicaseedling14 daysSRR094106, SRR094107, SRR094108

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   1.2 DNase I digital genomic footprinting (DGF, DNase-seq)Back to Top

SpeciesOrganConditionData Source
Arabidopsis thalianaroot7 daysSRR1049804
Arabidopsis thalianaroot non hair7 daysSRR2101849, SRR2101856
Arabidopsis thalianaroot non hair10 daysSRR1049805, SRR1049806, SRR1049807
Arabidopsis thalianaseed coat4 days past anthesisSRR1049809, SRR1049810
Arabidopsis thalianaseedling7 day old ControlSRR1049781, SRR1049782
Arabidopsis thalianaseedling7 day old DarkSRR1049775, SRR1049776
Arabidopsis thalianaseedling7 day old Dark 30min lightSRR1049771, SRR1049772
Arabidopsis thalianaseedling7 day old Dark 3hr lightSRR1049773, SRR1049774
Arabidopsis thalianaseedling7 day old Dark 24hrSRR1049769, SRR1049770
Arabidopsis thalianaseedling7 day old Heat ShockSRR1049779, SRR1049780
Arabidopsis thalianaseedlingBay-0 7 day oldSRR1049798, SRR1049799
Arabidopsis thalianaseedlingBur-0 7 day oldSRR1049796, SRR1049797
Arabidopsis thalianaseedlingEst-1 7 day oldSRR1049800, SRR1049801

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   1.3 Histone modifications (HMs, ChIP-seq)Back to Top

SpeciesOrganConditionTypeData Source
Arabidopsis thalianaaerialtwo-week-oldH3K36me3SRR037786
Arabidopsis thalianaleafnormalH3K23acSRR2046530
Arabidopsis thalianaleafnormalH4K16acSRR2046531
Arabidopsis thalianarosette leafnormalH3K4me1SRR2001270
Arabidopsis thalianarosette leafmature fully-expanded 29dH3K4me3SRR1964977
Arabidopsis thalianarosette leafmature fully-expanded 35dH3K4me3SRR1964979
Arabidopsis thalianarosette leafmature fully-expanded 42dH3K4me3SRR1964981
Arabidopsis thalianarosette leafmature fully-expanded 57dH3K4me3SRR1964983
Arabidopsis thalianarosette leafnormalH3K4me3SRR2001273
Arabidopsis thalianarosette leafnormalH3K9acSRR058387
Arabidopsis thalianarosette leafmature fully-expanded 30dH3K9acSRR1964985
Arabidopsis thalianarosette leafmature fully-expanded 34dH3K9acSRR1964987
Arabidopsis thalianarosette leafmature fully-expanded 42dH3K9acSRR1964989
Arabidopsis thalianarosette leafnormalH3T3phSRR2001292
Arabidopsis thalianaseedling12DAG seedlingsH3K27me3SRR1774027
Arabidopsis thalianaseedlingnormalH3K27me3SRR627962
Arabidopsis thalianaseedlingYoung seedlingsH3K27me3SRR1057651
Arabidopsis thalianaseedling12DAG seedlingsH3K4me3SRR1536272
Arabidopsis thalianashoot28DAG seedlingsH3K9me2SRR3096643
Brassica napusleafnormalH3K4me3SRR1785684
Chlamydomonas reinhardtiiwhole0 hr before starvationH3K27acSRR1521628
Chlamydomonas reinhardtiiwholeNitrogen starvation 1 hrH3K27acSRR1521639
Chlamydomonas reinhardtiiwholeSulfur starvation 1 hrH3K27acSRR1521650
Chlamydomonas reinhardtiiwhole0 hr before starvationH3K36me3SRR1521633
Chlamydomonas reinhardtiiwholeNitrogen starvation 1 hrH3K36me3SRR1521644
Chlamydomonas reinhardtiiwholeSulfur starvation 1 hrH3K36me3SRR1521656
Chlamydomonas reinhardtiiwhole0 hr before starvationH3K4me3SRR1521636
Chlamydomonas reinhardtiiwholeNitrogen starvation 10 minH3K4me3SRR1521608
Chlamydomonas reinhardtiiwholeNitrogen starvation 1 hrH3K4me3SRR1521614
Chlamydomonas reinhardtiiwholeNitrogen starvation 24 hrH3K4me3SRR1521622
Chlamydomonas reinhardtiiwholeNitrogen starvation 2 hrH3K4me3SRR1521616
Chlamydomonas reinhardtiiwholeNitrogen starvation 30 minH3K4me3SRR1521610
Chlamydomonas reinhardtiiwholeNitrogen starvation 48 hrH3K4me3SRR1521624
Chlamydomonas reinhardtiiwholeNitrogen starvation 6 hrH3K4me3SRR1521618
Chlamydomonas reinhardtiiwholeNitrogen starvation 8 hrH3K4me3SRR1521620
Chlamydomonas reinhardtiiwholeSulfur starvation 1 hrH3K4me3SRR1521648
Chlamydomonas reinhardtiiwhole0 hr before starvationH3K9me3SRR1521629
Chlamydomonas reinhardtiiwholeNitrogen starvation 1 hrH3K9me3SRR1521640
Chlamydomonas reinhardtiiwholeSulfur starvation 1 hrH3K9me3SRR1521652
Eucalyptus grandissecondary xylemDevelopingH3K4me3SRR1973564
Oryza sativa subsp. japonicaleafnormalH3K23acSRR2046532
Oryza sativa subsp. japonicaleafnormalH4K16acSRR2046533
Oryza sativa subsp. japonicaseedlingnormalH3K36me3SRR094791
Oryza sativa subsp. japonicaseedlingnormalH3K4me2SRR094790
Oryza sativa subsp. japonicaseedlingnormalH4K12acSRR094792

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   1.4 Nucleosome positioning (NP, MNase-seq)Back to Top

SpeciesOrganConditionData Source
Zea maysrootSeedling Root Heavy Rep 1SRR2542696
Zea maysrootSeedling Root Heavy Rep 2SRR2542697
Zea maysrootSeedling Root Light Rep 1SRR2542694
Zea maysrootSeedling Root Light Rep 2SRR2542695
Zea maysshootSeedling Shoot Heavy Rep 1SRR2542698
Zea maysshootSeedling Shoot Heavy Rep 2SRR2542701
Zea maysshootSeedling Shoot Light Rep 1SRR2542700
Zea maysshootSeedling Shoot Light Rep 2SRR2542699

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   1.5 TF binding sites (TFBSs, ChIP-seq)Back to Top

SpeciesTFOrganConditionData Source
Arabidopsis thalianaAT4G18960inflorescencenormal rep1SRR824573
Arabidopsis thalianaAT4G18960inflorescencenormal rep2SRR824574
Arabidopsis thalianaAT1G24260inflorescence5-7 weeks old rep1SRR016810
Arabidopsis thalianaAT2G46830seedlingnormal rep1SRR1976455
Arabidopsis thalianaAT5G61850seedlingcomplete seedlings rep1SRR070382
Arabidopsis thalianaAT5G61850seedlingcomplete seedlings rep2SRR070383
Arabidopsis thalianaAT5G61850seedlingcomplete seedlings rep3SRR070384
Arabidopsis thalianaAT5G61850seedlingcomplete seedlings rep4SRR070385
Arabidopsis thalianaAT3G10480seedling12 day old rep1SRR1536267
Arabidopsis thalianaAT3G10490seedling12 day old rep1SRR1536268
Arabidopsis thalianaAT2G43010seedlingnormal rep1SRR1988573
Arabidopsis thalianaAT2G43010seedlingnormal rep2SRR1988574
Arabidopsis thalianaAT2G43010seedlingnormal rep3SRR1988575
Arabidopsis thalianaAT2G43010seedlingnormal rep4SRR643947
Arabidopsis thalianaAT2G43010seedlingnormal rep5SRR643949
Arabidopsis thalianaAT3G59060seedlingnormal rep1SRR3040028
Arabidopsis thalianaAT3G59060seedlingnormal rep2SRR3040029
Arabidopsis thalianaAT3G48430seedlingyoung seedlings rep1SRR2243596
Arabidopsis thalianaAT2G01570seedlingnormal rep1SRR1508801
Arabidopsis thalianaAT2G01570seedlingnormal rep2SRR1508802
Arabidopsis thalianaAT2G01570seedlingnormal rep3SRR1508803
Arabidopsis thalianaAT5G18830seedlingnormal rep1SRR776581
Arabidopsis thalianaAT1G49950seedlingnormal rep1SRR2046725, SRR2046726
Arabidopsis thalianaAT1G49950seedlingnormal rep2SRR2046728, SRR2046729
Arabidopsis thalianaAT5G17430somatic embryo24-D induced somatic embryos rep1SRR1029950
Zea maysGRMZM2G017087tasseltassel primordia rep1SRR518975, SRR518976

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2. Methods Back to Top


2.1 Identification of DNase I hypersensitive sites (DHSs) from DNase-seq data

   Reads were mapped to unmasked genomes using Bowtie2 (v2.2.8) with ≤ 1 mismatch in seed alignment allowed. Only uniquely mapped reads were kept for peak calling. The hotspot regions and peaks of DNase I hypersensitive sites were called using Hotspot (v4.1.0) under default settings (threshold: FDR 0.01).

2.2 Identification of genomic TF footprints from DNase-seq data

   Reads were mapped as mentioned above. The genomic TF footprints were identified based on the pipeline and tool (fp2012) described in the paper.

2.3 Identification of peaks of TF binding and histone modification from ChIP-seq data

   Reads were mapped as mentioned above. Macs2 (v2.1.1) was employed to call peaks from ChIP-seq data with options of “--keep-dup all”. For histone modification, “--broad” was added to merge closed peak regions. The top 600 peaks of TF binding in each sample were extracted to discover TF binding motifs using MEME-ChIP with motif length spanning from 7bp to 20bp.

2.4 Mapping nucleosome positions from MNase-seq data

   Reads were mapped as mentioned above. DANPOS (v2.2.2) was employed to search for nucleosome peaks with pair-end mode (-m 1).

2.5 Collection and inference of transcriptional regulatory interactions

   We collected and inferred regulatory interactions in the following ways:
  • Literature mining and manual curation: In our previous study, we mined and manually curated 1 431 functional confirmed transcription regulatory interactions from literature(ATRM), this high-confidence resource were integrated now.
  • Identifying regulatory interactions from ChIP-seq: A potential interaction was assigned between a TF and a gene if there was at least one peak located in the promoter region (TSS +500bp ~ -100bp) of the gene. Only the potential interactions verified in ≥ 2 replications were kept.
  • Motif: FIMO was used to scan the promoter region (TSS +500bp ~ -100bp) of a genes for binding sites using the high-quality binding motifs of a TF with threshold 1e-5, and a potential interaction was assigned if there was at least one binding site in the promoter of the gene.
  • Motif + footprint(DGF): An interaction was assigned only if more than 60% length of a binding site overlapping with the footprints identified above.

3. Introduction of the multiple tools in PlantRegMap Back to Top


3.1 Binding site prediction

   Using the sets of high-quality, non-redundant binding motifs of TFs for 156 species with whole genome sequences (see details), FIMO is employed to scan the input sequences for TF binding sites.

3.2 Regulation prediction

   This tool is used to infer potential regulatory interactions between TF and input genes, and finds the TFs which possess over-represented targets in the input gene set. As described above, the sets of high-quality binding motifs of TFs and FIMO are used to scan TF binding sites in the promoters, and an interaction is assigned if there are one or more binding sites of a TF in the promoter of a gene. The genome assembly and annotation version described in the data source are used to extract promoter sequences when the coordinates of promoters/genes or gene sequences are input. The regulations predicted from the promoter regions (defined by users) of all annotated genes will be used as the background for enrichment analysis. In addition, refined regulation prediction using previous identified footprints is supported now.

3.3 GO enrichment

   Based on the sets of non-redundancy GO annotation for 165 species generated above, topGO (v2.22) is employed and Fisher’s exact tests are performed to find the significant enriched GO terms for the input gene set. Genome annotation IDs, UniProt AC/ID, Entrez Gene IDs and symbols are supported, and a built-in ID mapping tools is used to mapping the input IDs to genome annotation IDs (see id mapping file here).

3.4 TF enrichment

   Based on pre-generated regulatory interactions integrated from literature mining, ChIP-seq, motif combined footprint and motif mentioned above, Fisher’s exact tests are performed to find the TFs possess significantly over-presented target genes in the input gene set.