Here, AraPPISite, a database that presents fine-grained interaction details for A. thaliana PPIs is established. First, the experimentally determined 3D structures of 27 A. thaliana PPIs are collected from the Protein Data Bank database and the predicted 3D structures of 3023 A. thaliana PPIs ...
The SUBcellular location database for Arabidopsis proteins (SUBA4, http://suba.live) is a comprehensive collection of manually curated published data sets of large-scale subcellular proteomics, fluorescent protein visualization, protein-protein interaction (PPI) as well as subcellular targeting calls from...
The IQD1-KLCR1 interaction in yeast (Fig. 5) is supported by querying the Arabidopsis interactome database, which points to interactions between IQD and KLCR protein, i.e. IQD2 with At4g10840 (KLCR1) and At3g27960 (KLCR2) and IQD23 with At3g27960 (KLCR2) (43). The Arabidopsis KL...
Protein-protein interactions (PPIs) constitute the regulatory network that coordinates diverse cellular functions. There are growing needs in plant research for creating protein interaction maps behind complex cellular processes and at a systems biology level. However, only a few approaches have been succ...
We generated an extended PPI network to have a complete view of the protein interaction landscape of TFs directing gynoecium development (Figure 6C). For this, we retrieved reported interactions (IntAct database; Orchard et al., 2014) between the GYN-TF set of proteins (this study) and other...
and presents an overview of the database of these genes, and highlights some aspects of the distribution of mutants in different pathways and protein classes. The database provides information on the phenotypes of mutants, pathways, and enzymes/proteins associated with the mutants and allows rapid ...
Histone modifications can regulate transcription epigenetically by marking specific genomic loci, which can be mapped using chromatin immunoprecipitation sequencing (ChIP-seq). Here we present QHistone, a predictive database of 1534 ChIP-seqs from 27 his
(Basic Local Alignment Search Tool) search of theArabidopsisprotein database. However, anotherArabidopsisgene (AT1G15200,AtPININ) encodes a protein with an RSB domain and is considered a homolog of mammalian Pinin14. AtACINUS and AtPININ share 12 amino acids within the 15-amino acid region ...
Histone modifications can regulate transcription epigenetically by marking specific genomic loci, which can be mapped using chromatin immunoprecipitation sequencing (ChIP-seq). Here we present QHistone, a predictive database of 1534 ChIP-seqs from 27 his
Fig. 5. Interaction networks of the identified circadian-regulated phosphoproteins. Network mapping performed by the STRING protein interaction algorithm based on the STRING database (51). A, Photosynthesis. B, Ribosomal proteins network. C, Circadian regulated. D, ABA pathway. E, Chaperones. F,...