EnhancerAtlas 2.0: an updated resource with typical enhancer annotation in 600 tissue/cell types across nine species

Computational resources for enhancers:

Public Databases

Computational Tools


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).