Arabidopsis tf database

Author: rjxc

August undefined, 2024

WebSCENIC’s main approach is to search the putative regulatory regions of target genes for TF motif enrichment. This approach can be supplemented by the use of ChIP-seq track databases, which are based on direct experimental evidence of TF binding. Both direct and indirect binding are taken into account when generating pruned regulons. WebFull name: Plant Transcription Factor Database. Description: PlantTFDB provides genomic TF repertoires across Viridiplantae. Based on the family assignment rules, we identified …

Identification of potential transcriptional regulators of actinorhizal ...

WebAAtDB, An Arabidopsis thaliana Database. The latest version of AAtDB is available for UNIX and Macintosh operating systems. To get your own copy of the software, connect … Web29 ott 2024 · The quality of ReMap data is illustrated in the latest version of the JASPAR database , for which peaks were used to calculate TF link profiles. We believe that our … henkin model

Cell lineage-specific transcriptome analysis for interpreting

Web12 ott 2007 · Several Arabidopsis TF online databases such as AtTFDB and RARTF are available over the Internet (3,4). In previous work, we have systematically predicted and annotated the transcription factors in Arabidopsis, rice and poplar based on their genome sequences, and constructed three distinct TF databases ( 5–7 ). http://planttfdb.gao-lab.org/aboutus.php Web24 ott 2016 · After the first attempt to identify the TF repertoire in Arabidopsis thaliana genome in 2000 , several dedicated TF databases for either individual or multiple … henkiparantajat

:: AGRIS AtTFDB : Transcription Factor Families::

Bioinformatic landscapes for plant transcription factor …

Web10 feb 2024 · Salt stress inhibits normal plant growth and development by disrupting cellular water absorption and metabolism. Therefore, understanding plant salt tolerance mechanisms should provide a theoretical basis for developing salt-resistant varieties. Here, we cloned ThTrx5 from Tamarix hispida, a salt-resistant woody shrub, and generated … Web11 set 2024 · As mentioned above, we used the DAP-seq Arabidopsis database for the initial validation of EAT-UpTF. However, the EAT-UpTF analysis is not limited to the use … henkin knivesWebTo create a comprehensive catalog of Arabidopsis motifs and genomic TF binding locations, DAP-seq experiments were carried out on 1,812 TFs comprising 80 families … henkin stanislav

"Web14 giu 2024 · Several databases 15,24,25,26,27,28 were recently established for ... Extensive TF co-associations and regulatory loops in Arabidopsis. We investigated TF co-associations and TF-targets gene ... " - Arabidopsis tf database

Arabidopsis tf database

Identification of potential transcriptional regulators of actinorhizal ...

Websis of Arabidopsis.TheArabidopsis TF database (RARTF) hosted by the RIKEN BioResource Center in Japan applies PSI-BLAST and InterProScan to the identiﬁcation of all putative TFs in Ara-bidopsis (7). WebHere, we report on the TRANSPLANTA collection of Arabidopsis lines, each expressing one of 949 TFs under the control of a β-estradiol-inducible promoter. Thus far, 1636 independent homozygous lines, representing an average of 2.6 lines for every TF, have been produced for the inducible expression of 634 TFs.

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Web10 dic 2014 · Identification of C. glauca and A. glutinosatranscription factors. To identify transcription factors in actinorhizal plants, tBLASTn searches of the C. glauca and A. glutinosa unigene databases were performed using the DNA-binding domain from the TF database of Arabidopsis thaliana as query sequences. These databases contain … Web8 dic 2024 · Arabidopsis thaliana. Heat stress transcription factors (Hsfs) are the major regulators of the plant heat stress (hs) response. Sequencing of the Arabidopsis genome revealed the existence of 21 open-reading frames (ORFs) encoding putative Hsfs assigned to classes A-C. Here we present results of a functional genomics approach to the …

WebAbout Arabidopsis thaliana. Arabidopsis thaliana is a small flowering plant that is widely used as a model organism in plant biology. Arabidopsis is a member of the mustard (Brassicaceae) family, which includes cultivated species such as cabbage and radish. Arabidopsis is not of major agronomic significance, but its small genome size and ease ... Web2 giu 2024 · The SeqEnrich program contains the most extensive database of TFs, TF-DNA sequence motif interactions, ... we compared its output to previously published Arabidopsis TF networks from publicly available datasets [8,32]. A total of 661 genes co-expressed in the chalazal endosperm of the mature seed ...

WebAbout TAIR The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana.Data … WebPlantTribes -- a gene and gene family resource for comparative genomics in plants. A plant gene family database based on the inferred proteomes of five sequenced plant species: …

WebSeveral Arabidopsis TF online databases such as AtTFDB and RARTF are available over the Internet (3,4). In previous work, we have systematically predicted and annotated the

WebOverall, we found that TF ChIP–seq data confirmed 39% of predicted interactions in the iGRN, demonstrating that a large fraction of iGRN interactions are supported by in vivo TF binding. henkioppiWebTF_MADSbox:IPR002100 1-61: PANTHER. PTHR48019:SF101 1-237: PANTHER. PTHR48019 1-237: CDD. CD00265. MADS_MEF2-like:IPR033896 2-77: PATTERNSCAN. PS00350. ... The Subcellular Location of Proteins in Arabidopsis Database (SUBA) Arabidopsis Protein Phosphorylation Site Database (PhosPhAt) Community Comments … henkin testWeb8 dic 2024 · Plant transcription factor database, ... Arabidopsis thaliana, Glycine max, Oryza sativa, Populus trichocarpa, ... Couldn't find the species interested? Please try the … Plant transcription factor database, ... Arabidopsis thaliana, Glycine max, … Plant Transcription Factor Database. Previous version: v3.0 v4.0: Home … BLAST - PlantTFDB - Plant Transcription Factor Database @ CBI, PKU Plant transcription factor database, ... TF binding site prediction, Regulation … Plant transcription factor database, ... Arabidopsis halleri: download: … Plant Transcription Factor Database. Previous version: v3.0 v4.0: Home … An Arabidopsis transcriptional regulatory map reveals distinct functional and … ©2010-2024, Center for Bioinformatics, Peking University Last Modified: 2024 … henkiopas meditaatioWeb11 apr 2024 · Adenosine methylation in Arabidopsis mRNA is associated with the 3â€² end and reduced levels cause developmental defects. Front. Plant Sci. 3:48. Boccaletto, P., and BagiÅ„ski, B. (2024). MODOMICS: An operational guide to the use of the RNA modification pathways database. Methods Mol. Biol. 2284:481â€“505. henkiopasWeb31 ott 2024 · To provide an example of how regulators can be used in PlantCADB to retrieve the putative corresponding regulatory network, the basic helix-loop-helix (bHLH) TF family transcription factor myelocytomatosis 2 (MYC2, AT1G32640.1) in Arabidopsis thaliana is used as input to our database for ‘search ACR by TF’. henkiparannusWeb7 dic 2015 · Several ArabidopsisTF online databases such as AtTFDB and RARTFare available over the Internet (3,4). In previous work,we have systematically predicted and annotated thetranscription factors in Arabidopsis, rice and poplarbased on their genome sequences, and constructed threedistinct TF databases (5–7). henkin setsWebWe started to construct the database of Arabidopsis TFs in 2005 and developed a pipeline for systematic identification of plant TFs from genomic and transcript ... domain … henkiparantaja