Applications

 

CBRC Applications List

Secuence Analysis Tools

​Knoweldgebases and Detabases

Text Mining and Data Mining Tools

​Internal
Apps

 

 

An INtegrated Data warehouse of mIcrobial GenOmes (INDIGO)

INDIGO enables the integration of annotations for the exploration and analysis of newly sequenced microbial genomes.It provides keyword search or Query builder for more complex queries for data mining and allows for saving or exporting results. INDIGO is developed in CBRC.

INDIGO - INtegrated data warehouse of microbial genomes with examples from the red sea extremophiles. Alam I, Antunes A, Kamau AA, Ba Alawi W, Kalkatawi M, Stingl U, Bajic VB. PLoS One. 2013 Dec 6;8(12):e82210. doi: 10.1371/journal.pone.0082210.



Dragon Database for Methylated Genes and Diseases (DDMGD)

Dragon Database for Methylated Genes and Diseases (DDMGD) can provide associations between methylated genes and diseases. The associations were extracted automatically from PubMed abstracts using Dragon Extractor of Methylated Genes in Diseases (DEMGD) tool. You can search using the gene, diseases and/or species

DDMGD: the database of text-mined associations between genes methylated in diseases from different species. Bin Raies A, Mansour H, Incitti R, Bajic VB. Nucleic Acids Res. 2015 Jan;43(Database issue):D879-86. doi: 10.1093/nar/gku1168.

Dragon Database of Genes Implicated in Prostate Cancer (DDPC)

This knowledgebase resource efficiently and conveniently integrates expert reviewed information summary about the genes implicated in prostate cancer, including comprehensive information about every specific gene. A centralized resource for researchers to support functional characterization and analysis of molecular processes related to prostate cancer. It is compiled based on extensive text-mining and data-mining.

DDPC: Dragon Database of Genes associated with Prostate Cancer. Maqungo M, Kaur M, Kwofie SK, Radovanovic A, Schaefer U, Schmeier S, Oppon E, Christoffels A,Bajic VB. Nucleic Acids Res. 2011 Jan;39(Database issue):D980-5. doi: 10.1093/nar/gkq849.

Dragon Database of Transcription Co-Factors and Transcription Factor Interacting Proteins (TcoF)

Database is a resource for systems biology studies that facilitate exploration of transcription regulation networks and include information about proteins involved in the regulation of transcription in humans. It contains hand-curated information about transcription factor (TF) proteins (those that directly bind to DNA and affect transcription initiation) and transcription co-factor (TcoF) regulatory proteins that bind to TFs and affect transcription initiation but not to bind DNA directly.

TcoF-DB: dragon database for human transcription co-factors and transcription factor interacting proteins. Schaefer U, Schmeier S, Bajic VB. Nucleic Acids Res. 2011 Jan;39(Database issue):D106-10. doi: 10.1093/nar/gkq945.

Dragon Database on Polymorphic Regulation of Human miRNA Genes (dPORE - miRNA)

Database is a resource for systems biology studies that facilitate exploration of transcription regulation networks and include information about promoter regions of human miRNA genes, SNPs, and predicted TFBSs in the promoter regions. The web-interface allows to explore the effect of SNPs on the transcriptional regulation of miRNA genes.

dPORE-miRNA: polymorphic regulation of microRNA genes. Schmeier S, Schaefer U, MacPherson CR, Bajic VB. PLoS One. 2011 Feb 4;6(2):e16657. doi: 10.1371/journal.pone.0016657.

Dragon ENhancers database (DENdb)

DENdb is a centralized on-line repository of predicted enhancers derived from multiple human cell-lines. DENdb integrates enhancers predicted by five different methods (ChromHMM, Segway, RFECS, CSI-ANN, and ENCODE integrated annotation) generating an enriched catalogue of enhancers for each of the analyzed cell-lines.

Dragon Exploration System for Marine Sponge Compounds Interactions (DESMSCI)

DESMSCI is a complex knowledgebase that provides information about the associations of the sponge compounds with the different biological entities like human genes, proteins, diseases and pathways based on the scientific literature available in the PubMed and information deposited in the other databases. It is compiled based on extensive text-mining and data-mining.

Dragon exploration system on marine sponge compounds interactions. Sagar S, Kaur M, Radovanovic A, Bajic VB. J Cheminform. 2013 Feb 16;5(1):11. doi: 10.1186/1758-2946-5-11.

Dragon Exploration System for Sickle-cell disease (DESSCD)

Specialized knowledgebase resource specifically aimed at researchers investigating Sickle-cell disease. A centralized resource that support functional characterization and analysis of molecular processes related to Sickle-cell disease. It is compiled based on extensive text-mining and data-mining.

Information exploration system for sickle cell disease and repurposing of hydroxyfasudil. Essack M, Radovanovic A, Bajic VB. PLoS One. 2013 Jun 10;8(6):e65190. doi: 10.1371/journal.pone.0065190.

Dragon Exploration System for Toxicants and Fertility (DESTAF)

This knowledgebase is a resource aimed to facilitate research in reproductive toxicity. It is a complex information system that conveniently and efficiently integrates various information related to reproductive toxicity. Its primary goal is to enable researchers to efficiently and rapidly query the human reproductive toxicity literature in an innovative manner and on a deeper level than articles and from differing gene/protein-, protein-, metabolite / enzyme-, biological- and chemical/toxin-, disease- and human anatomical-centric perspectives.

DESTAF: a database of text-mined associations for reproductive toxins potentially affecting human fertility. Dawe AS, Radovanovic A, Kaur M, Sagar S, Seshadri SV, Schaefer U, Kamau AA, Christoffels A, Bajic VB. Reprod Toxicol. 2012 Jan;33(1):99-105. doi: 10.1016/j.reprotox.2011.12.007.

Dragon Exploratory System on Hepatitis C Virus (DESHCV)

This is a comprehensive knowledgebase on Hepatitis C Virus (HCV) based on extensive text-mining and data-mining. It integrates in an efficient and convenient manner information using specified concepts, keywords and phrases. Each concept search generates text-derived association networks and hypotheses which could be tested to identify potentially novel relationship between different concepts.

If you are using this resource in your research please cite:

Kwofie SK, Radovanovic A, Sundararajan VS, Maqungo M, Christoffels A, Bajic VB (June 2011) Dragon Exploratory System on Hepatitis C Virus (DESHCV). Infect Genet Evol 11(4):734-9. doi:10.1016/j.meegid.2010.12.006.

Dragon Explorer of Enzymes and Compounds Of Industrial Importance (DEECOII)

Dragon Explorer of Enzymes and Compounds Of Industrial Importance (DEECOII) is an online resource that highlights industrially important biological entities (enzymes, microorganisms or chemical compounds).

Dragon Explorer of Osmoprotection Pathways (DEOP)

Dragon Explorer of Osmoprotection Pathways (DEOP) is a unique web system focused on the exploration of manually-curated information related to the production of osmoprotectants captured from species and includes pathways, genes/enzymes, compounds and reactions. The system allows the user to test their genomic sequences in relation to osmoprotectant pathways.

DEOP: a database on osmoprotectants and associated pathways. Bougouffa S, Radovanovic A, Essack M, Bajic VB. Database (Oxford). 2014 Oct 17;2014. pii: bau100. doi: 10.1093/database/bau100.

FARNA: Database of Function Annotation of human non-coding RNA transcripts

FARNA is a database that contains functional annotations (GO terms, pathways, disease information) for human non-coding RNA (ncRNA) transcripts. Two classes of ncRNAs are included: microRNA (miRNA) and long ncRNA (lncRNA). Functional annotation of transcripts is obtained based on the novel method we developed for function inference that relies on the regulatory network of the transcript.

Hepatitis C Virus Protein Interaction Database (HCVpro)

Comprehensive and integrated knowledgebase on Hepatitis C Virus (HCV) protein interactions. It contains manually verified information from literature and databases on curated interactions comprising of HCV and host human cellular proteins.

HCVpro: hepatitis C virus protein interaction database. Kwofie SK, Schaefer U, Sundararajan VS, Bajic VB, Christoffels A. Infect Genet Evol. 2011 Dec;11(8):1971-7. doi: 10.1016/j.meegid.2011.09.001.

Homo Sapiens Comprehensive Model Collection (HOCOMOCO)

We present the Homo Sapiens Comprehensive Model Collection (HOCOMOCO) of transcription factor (TF) binding models obtained by careful integration of data from different sources. HOCOMOCO contains 426 non-redundant curated binding models for 401 human TFs.

HOCOMOCO: a comprehensive collection of human transcription factor binding sites models. Kulakovskiy IV, Medvedeva YA, Schaefer U, Kasianov AS, Vorontsov IE, Bajic VB, Makeev VJ. Nucleic Acids Res. 2013 Jan;41(Database issue):D195-202. doi: 10.1093/nar/gks1089.

metaINDIGO: An integratred data warehouse of metagenomes

Meta-INDIGO enables the integration of annotations for the exploration and analysis of newly sequenced microbial genomes.

Microbial Knowledge Exploration Systems

Portal for Microbial Knowledge Exploration Systems is a platform for discovery, analysis and exploration of information from a number of topic-specific microbial knowledgebases. The knowledgebases include up to date information from published scientific literature and a number of major databases from biology fields.