ArticleDatabase : the journal of biological databases and curation2013
Nencki Genomics Database--Ensembl funcgen enhanced with intersections, user data and genome-wide TFBS motifs.
Article in Database : the journal of biological databases and curation, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed.
- Challenges in mimicking hypoxia: insights into HIF-regulated MiRNA expression induced by DMOG and CoClCell communication and signaling : CCS · 2025Article
- A dynamic model of gene activation in response to hypoxia accounting for both HIF-1 and HIF-2.Briefings in functional genomics · 2025Article
- The hypoxia-induced changes in miRNA-mRNA in RNA-induced silencing complexes and HIF-2 induced miRNAs in human endothelial cells.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2022Article
- Genome-wide mRNA profiling identifies X-box-binding protein 1 (XBP1) as an IRE1 and PUMA repressor.Cellular and molecular life sciences : CMLS · 2021Article
- Transcription factors Krüppel-like factor 4 and paired box 5 regulate the expression of the Grainyhead-like genes.PloS one · 2021Article
- Exploring the possibility of predicting human head hair greying from DNA using whole-exome and targeted NGS data.BMC genomics · 2020Article
- Search for novel STAT3-dependent genes reveals SERPINA3 as a new STAT3 target that regulates invasion of human melanoma cells.Laboratory investigation; a journal of technical methods and pathology · 2019Article
- FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2019Article
- Primary endothelial cell-specific regulation of hypoxia-inducible factor (HIF)-1 and HIF-2 and their target gene expression profiles during hypoxia.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2019Article
- PIWI proteins contribute to apoptosis during the UPR in human airway epithelial cells.Scientific reports · 2018Article
- Coordinated expression and genetic polymorphisms in Grainyhead-like genes in human non-melanoma skin cancers.BMC cancer · 2018Article
- The embryonic type of SPP1 transcriptional regulation is re-activated in glioblastoma.Oncotarget · 2017Article
- Increased phosphorylation of eIF2α in chronic myeloid leukemia cells stimulates secretion of matrix modifying enzymes.Oncotarget · 2016Article
- Adult Deletion of SRF Increases Epileptogenesis and Decreases Activity-Induced Gene Expression.Molecular neurobiology · 2016Article
- Emerging role of transcription factor-microRNA-target gene feed-forward loops in cancer.Biomedical reports · 2015Article
- Optimally choosing PWM motif databases and sequence scanning approaches based on ChIP-seq data.BMC bioinformatics · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present the Nencki Genomics Database, which extends the functionality of Ensembl Regulatory Build (funcgen) for the three species: human, mouse and rat. The key enhancements over Ensembl funcgen include the following: (i) a user can add private data, analyze them alongside the public data and manage access rights; (ii) inside the database, we provide efficient procedures for computing intersections between regulatory features and for mapping them to the genes. To Ensembl funcgen-derived data, which include data from ENCODE, we add information on conserved non-coding (putative regulatory) sequences, and on genome-wide occurrence of transcription factor binding site motifs from the current versions of two major motif libraries, namely, Jaspar and Transfac. The intersections and mapping to the genes are pre-computed for the public data, and the result of any procedure run on the data added by the users is stored back into the database, thus incrementally increasing the body of pre-computed data. As the Ensembl funcgen schema for the rat is currently not populated, our database is the first database of regulatory features for this frequently used laboratory animal. The database is accessible without registration using the mysql client: mysql -h database.nencki-genomics.org -u public. Registration is required only to add or access private data. A WSDL webservice provides access to the database from any SOAP client, including the Taverna Workbench with a graphical user interface.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.