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sRNAMap? Applications Comparisons Developers References


What is sRNAMap?

     The increased investigations of important regulatory roles for sRNAs encoded far from their targets, acting on multiple targets, or both, has expanded interest in how to find such regulatory RNAs and how they work. Therefore, a resource collects the comprehensive annotation of small non-coding RNAs is crucial. Therefore, we present an integrated database, sRNAMap, to collect the annotations of the sRNAs and the regulatory relationship between transcriptional regulator and sRNA, and between sRNA and its target genes. Additionally, more valuable information of sRNAs, such as the secondary structure of sRNAs, the expressed conditions of sRNAs, the expression profiles of sRNAs, the transcriptional start sites of sRNAs and the cross-links to other biological databases, are provided for further investigation. Besides, various textual and graphical interfaces were designed and implemented to facilitate the data access in sRNAMap.

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Applications

     The database will be developed as follows. (i) It will be made to support sRNA annotations including sRNA genes, sRNA regulators and sRNA targets in Escherichia coli and in other bacteria; (ii) The complete relationship between regulators and sRNAs or sRNAs and targets are contained; (iii) The sRNAMap data will be further analyzed to support the sRNAs expression or their targets expression involved in differential conditions; (iV) We also provide the comparative genomics information which can be used to identify the noncoding RNA genes or targets; (V) The known promoter and adjacent promoter of sRNAs are provided.

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Comparisons




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Developers

Dr.Hsien-Da Huang
Department of Biological Science and Technology, Institute of Bioinformatics National Chiao-Tung University, HsinChu, Taiwan

Heng-Yi Chang
Department of Biological Science and Technology, Institute of Bioinformatics National Chiao-Tung University, HsinChu, Taiwan

Chih-Hung Chou
Department of Biological Science and Technology, Institute of BioMedical Science National Chiao-Tung University, HsinChu, Taiwan

Hsi-Yuan Huang
Department of Biological Science and Technology, Institute of Bioinformatics National Chiao-Tung University, HsinChu, Taiwan
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References

Altschul, S. F., W. Gish, et al. (1990). "Basic local alignment search tool." J Mol Biol 215(3): 403-10.

Baba, T., T. Ara, et al. (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2: 2006 0008.

Barrett, T., D. B. Troup, et al. (2007). "NCBI GEO: mining tens of millions of expression profiles--database and tools update." Nucleic Acids Res 35(Database issue): D760-5.

Chang, T. H., J. T. Horng, et al. (2008). "RNALogo: a new approach to display structural RNA alignment." Nucleic Acids Res.

Gama-Castro, S., V. Jimenez-Jacinto, et al. (2008). "RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation." Nucleic Acids Res 36(Database issue): D120-4.

He, S., C. Liu, et al. (2008). "NONCODE v2.0: decoding the non-coding." Nucleic Acids Res 36(Database issue): D170-2.

Hofacker, I. L. (2003). "Vienna RNA secondary structure server." Nucleic Acids Res 31(13): 3429-31.

Schneider, K. L., K. S. Pollard, et al. (2006). "The UCSC Archaeal Genome Browser." Nucleic Acids Res 34(Database issue): D407-10.

Keseler, I. M., J. Collado-Vides, et al. (2005). "EcoCyc: a comprehensive database resource for Escherichia coli." Nucleic Acids Res 33(Database issue): D334-7.

Marstrand, T. T., J. Frellsen, et al. (2008). "Asap: a framework for over-representation statistics for transcription factor binding sites." PLoS ONE 3(2): e1623.

Misra, R. V., R. S. Horler, et al. (2005). "EchoBASE: an integrated post-genomic database for Escherichia coli." Nucleic Acids Res 33(Database issue): D329-33.

Rudd, K. E. (2000). "EcoGene: a genome sequence database for Escherichia coli K-12." Nucleic Acids Res 28(1): 60-4.

Serres, M. H., S. Goswami, et al. (2004). "GenProtEC: an updated and improved analysis of functions of Escherichia coli K-12 proteins." Nucleic Acids Res 32(Database issue): D300-2.

Wu, T., J. Wang, et al. (2006). "NPInter: the noncoding RNAs and protein related biomacromolecules interaction database." Nucleic Acids Res 34(Database issue): D150-2.

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Department of Biological Science and Technology,

Institute of Bioinformatics National Chiao Tung University, Hsinchu, Taiwan

Contact with: bryan@mail.NCTU.edu.tw