Public Databases
Computational Tools
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Public Databases:
1. dbSUPER:
an integrated database of super-enhancers in mouse and human genome (Aziz Khan,
et al., 2015).
2. EMAGE:
a freely available database of in situ gene expression patterns that allows users to perform online queries of mouse developmental gene expression (Richardson L,
et al., 2014).
3. cis-Decoder:
a Drosophila genome-wide conserved sequence database to identify functionally related cis-regulatory enhancers (Thomas Brody,
et al., 2012).
4. ZETRAP 2.0:
an updated online database of novel Zebrafish Enhancer TRAP transgenic lines (Kondrychyn I,
et al., 2011).
5. zTrap:
a database of zebrafish gene trap and enhancer traps (Kawakami K,
et al., 2010).
6. PEDB:
a mammalian promoter/enhancer database (Kumaki Y,
et al., 2008).
7. VISTA Enhancer Browser:
a central resource for experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice (Visel A,
et al., 2007).
8. EI cENHs:
a resource of candidate tissue-speicific enhancers in human and mouse (Pennacchio LA,
et al., 2007).
9. ZETRAP:
a database of Zebrafish transgenic Enhancer TRAP lines (Choo BG,
et al., 2006).
10. GETDB:
a database compiling expression patterns and molecular locations of a collection of gal4 enhancer traps (Hayashi S,
et al., 2002).
Computational Tools:
1. DEEP:
a general computational framework for predicting enhancers (Kleftogiannis D,
et al., 2015).
2. DELTA:
A Distal Enhancer Locating Tool Based on AdaBoost Algorithm and Shape Features of Chromatin Modifications (Lu Y, et al., 2015).
3. IM-PET:
A useful tool using integrated methods for predicting enhancer targets (He B, et al., 2014).
4. EnhancerFinder:
a tool with a two-step method for distinguishing developmental enhancers from the genomic background and then predicting their tissue specificity (Erwin GD,
et al., 2014). The
tool is not available.
5. RFECS:
Predicting protein sumoylation sites from sequence features (Rajagopal N,
et al., 2013).
6. EMdeCODE:
a novel predictor capable of reading words of epigenetic code to predict enhancers. (Santoni FA,
2013).
7. WashU Epigenome Browser:
a next-generation genomic data visualization system for human and model organisms to support multiple types of long-range genome interaction data (Xin Z,
et al., 2013).
8. ChromaGenSVM:
a tool with optimum combinations of specific histone epigenetic marks to predict enhancers (Fernandez M,
et al., 2012).
9. ReLA:
a local alignment search tool for the identification of distal and proximal gene regulatory regions and their conserved transcription factor binding sites (Gonzalez S,
et al., 2012).
10. p300enhancer:
A predictor of EP300-bound enhancers using only genomic sequence and an unbiased set of general sequence features (Lee D,
et al., 2011).
11. CSI-ANN:
A tool to identify regulatory DNA elements using chromatin signatures and artificial neural network (Firpi HA,
et al., 2010).
