Dataset Information

Ppdb: plant promoter database version 3.0.

ABSTRACT: ppdb (http://ppdb.agr.gifu-u.ac.jp) is a plant promoter database that provides information on transcription start sites (TSSs), core promoter structure (TATA boxes, Initiators, Y Patches, GA and CA elements) and regulatory element groups (REGs) as putative and comprehensive transcriptional regulatory elements. Since the last report in this journal, the database has been updated in three areas to version 3.0. First, new genomes have been included in the database, and now ppdb provides information on Arabidopsis thaliana, rice, Physcomitrella patens and poplar. Second, new TSS tag data (34 million) from A. thaliana, determined by a high throughput sequencer, has been added to give a ?200-fold increase in TSS data compared with version 1.0. This results in a much higher coverage of ?27,000 A. thaliana genes and finer positioning of promoters even for genes with low expression levels. Third, microarray data-based predictions have been appended as REG annotations which inform their putative physiological roles.

SUBMITTER: Hieno A

PROVIDER: S-EPMC3965062 | biostudies-literature | 2014 Jan

REPOSITORIES: biostudies-literature

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ppdb: plant promoter database version 3.0.

Hieno Ayaka A Naznin Hushna Ara HA Hyakumachi Mitsuro M Sakurai Tetsuya T Tokizawa Mututomo M Koyama Hiroyuki H Sato Naoki N Nishiyama Tomoaki T Hasebe Mitsuyasu M Zimmer Andreas D AD Lang Daniel D Reski Ralf R Rensing Stefan A SA Obokata Junichi J Yamamoto Yoshiharu Y YY

Nucleic acids research 20131104 Database issue

ppdb (http://ppdb.agr.gifu-u.ac.jp) is a plant promoter database that provides information on transcription start sites (TSSs), core promoter structure (TATA boxes, Initiators, Y Patches, GA and CA elements) and regulatory element groups (REGs) as putative and comprehensive transcriptional regulatory elements. Since the last report in this journal, the database has been updated in three areas to version 3.0. First, new genomes have been included in the database, and now ppdb provides information ...[more]

PMID: 24194597

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Project description:BackgroundThe Chicago Classification version 4.0 (CCv4.0) of ineffective esophageal motility (IEM) is more stringent than the Chicago Classification version 3.0 (CCv3.0) definition. We aimed to compare the clinical and manometric features of patients meeting CCv4.0 IEM criteria (group 1) versus patients meeting CCv3.0 IEM but not CCv4.0 criteria (group 2).MethodsWe collected retrospective clinical, manometric, endoscopic, and radiographic data on 174 adults diagnosed with IEM from 2011 to 2019. Complete bolus clearance was defined as evidence of exit of the bolus by impedance measurement at all distal recording sites. Barium studies included barium swallow, modified barium swallow, and barium upper gastrointestinal series studies, and collected data from these reports include abnormal motility and delay in the passage of liquid barium or barium tablet. These data along with other clinical and manometric data were analyzed using comparison and correlation tests. All records were reviewed for repeated studies and the stability of the manometric diagnoses.ResultsMost demographic and clinical variables were not different between the groups. A lower mean lower esophageal sphincter pressure was correlated with greater percent of ineffective swallows in group 1 (n = 128) (r = -0.2495, P = 0.0050) and not in group 2. In group 1, increased percent of failed contractions on manometry was associated with increased incomplete bolus clearance (r = 0.3689, P = 0.0001). No such association was observed in group 2. A lower median integrated relaxation pressure was correlated with greater percent of ineffective contractions in group 1 (r = -0.1825, P = 0.0407) and not group 2. Symptom of dysphagia was more prevalent (51.6% versus 69.6%, P = 0.0347) in group 2. Dysphagia was not associated with intrabolus pressure, bolus clearance, barium delay, or weak or failed contractions in either group. In the small number of subjects with repeated studies, a CCv4.0 diagnosis appeared more stable over time.ConclusionsCCv4.0 IEM was associated with worse esophageal function indicated by reduced bolus clearance. Most other features studied did not differ. Symptom presentation cannot predict if patients are likely to have IEM by CCv4.0. Dysphagia was not associated with worse motility, suggesting it may not be primarily dependent on bolus transit.

Dataset Information

Ppdb: plant promoter database version 3.0.

Publications

ppdb: plant promoter database version 3.0.

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