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Bidirectional gene pairs are highly abundant and mostly co-regulated in eukaryotic genomes. The structural features of bidirectional promoters (BDPs) have been well studied in yeast, humans and plants. However, the underlying mechanisms responsible for the coexpression of BDPs remain understudied, especially in plants.
Pubmed ID: 27716056
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Genome wide map of putative transcription factor binding sites in Arabidopsis thaliana genome.Data in AthaMap is based on published transcription factor (TF) binding specificities available as alignment matrices or experimentally determined single binding sites.Integrated transcriptional and post transcriptional data.Provides web tools for analysis and identification of co-regulated genes. Provides web tools for database assisted identification of combinatorial cis-regulatory elements and the display of highly conserved transcription factor binding sites in Arabidopsis thaliana.
View all literature mentionsSoftware tool for transcriptome assembly and differential expression analysis for RNA-Seq. Includes script called cuffmerge that can be used to merge together several Cufflinks assemblies. It also handles running Cuffcompare as well as automatically filtering a number of transfrags that are likely to be artifacts. If the researcher has a reference GTF file, the researcher can provide it to the script to more effectively merge novel isoforms and maximize overall assembly quality.
View all literature mentionsThe TIGR database is a collection of plant transcript sequences. Transcript assemblies are searchable using BLAST and accession number. The construction of plant transcript assemblies (TAs) is similar to the TIGR gene indices. The sequences that are used to build the plant TAs are expressed transcripts collected from dbEST (ESTs) and the NCBI GenBank nucleotide database (full length and partial cDNAs). "Virtual" transcript sequences derived from whole genome annotation projects are not included. All plant species for which more than 1,000 ESTs or cDNA sequences are available are included in this project. TAs are clustered and assembled using the TGICL tool (Pertea et al., 2003), Megablast (Zhang et al., 2000) and the CAP3 assembler (Huang and Madan, 1999). TGICL is a wrapper script which invokes Megablast and CAP3. Sequences are initially clustered based on an all-against-all comparisons using Megablast. The initial clusters are assembled to generate consensus sequences using CAP3. Assembly criteria include a 50 bp minimum match, 95% minimum identity in the overlap region and 20 bp maximum unmatched overhangs. Any EST/cDNA sequences that are not assembled into TAs are included as singletons. All singletons retain their GenBank accession numbers as identifiers. Plant TA identifiers are of the form TAnumber_taxonID, where number is a unique numerical identifier of the transcript assembly and taxonID represents the NCBI taxon id. In order to provide annotation for the TAs, each TA/singleton was aligned to the UniProt Uniref database. For release 1 TAs, a masked version of the Uniref90 database was used. For release 2 and onwards, a masked version of the UniRef100 database is used. Alignments were required to have at least 20% identity and 20% coverage. The annotation for the protein with the best alignment to each TA or singleton was used as the annotation for that sequence. Additionally, the relative orientation of each TA/singleton to the best matching protein sequence was used to determine the orientation of each TA/singleton. Some sequences did not have alignments to the protein database that met our quality criteria, and those sequences have neither annotation nor orientation assignments. The release number for the plant TAs refers to the release version for a particular species. For the initial build, all TA sets are of version 1. Subsequent TA updates for new releases will be carried out when the percentage increase of the EST and cDNA counts exceeds 10% of the previous release and when the increase contains more than 1,000 new sequences. New releases will also include additional plant species with more than 1,000 EST or cDNA sequences that have become publicly available.
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