Epigenetic Regulations, Motif and Pathway Identification of Gabaergic Neurotransmitter’s Chip Sequence

DOI

10.2991/978-94-6463-164-7_10How to use a DOI?

Keywords

Chromatin immunoprecipitation (ChiP); Gamma-Amino Butyric Acid (GABA); Neurotransmission; PCR duplicates; MACS2 callpeak; ChiP peak; KEGG pathway; motif

Abstract

Background: The next generation techniques has revolutionalized the biology era. In this work we are using Chromatin immunoprecipitation (ChiP) technique on the ChIP–seq of Gamma-Amino Butyric Acid (GABA). GABA is a brain-made chemical. It also found in some foods. The effect of GABA in brain is anti-seizure and anti-anxiety. GABA blocks the brain signals, the neurotransmissions and hence there is interest in using GABA as a dietary supplement. But it is taken by mouth, it is able to cross the blood-brain barrier. Hence the effects of GABA supplements on the brain is unknown.

Methodology: GABA is implicated in several neurological disorders like alzheimers, rett symdrome, schizophrenia, etc. In this work, the chip sequence of GABA is retrieved from SRA database, removed the PCR duplicates and finally identified the genome enriched region using the MAC2 call peak tool.

Results: Peak table was annotated to identify the genes and the corresponding pathways was identified from the KEGG pathway. This annotated peak table was used to identify the motifs present in the chip-seq of GABA.

Copyright

© 2023 The Author(s)

Open Access

Open Access This chapter is licensed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International License (http://creativecommons.org/licenses/by-nc/4.0/), which permits any noncommercial use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license and indicate if changes were made.

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TY  - CONF
AU  - I. A. Shylesh Murthy
AU  - Preenon Bagchi
PY  - 2023
DA  - 2023/06/05
TI  - Epigenetic Regulations, Motif and Pathway Identification of Gabaergic Neurotransmitter’s Chip Sequence
BT  - Proceedings of the Joint 3rd International Conference on Bioinformatics and Data Science (ICBDS 2022)
PB  - Atlantis Press
SP  - 121
EP  - 131
SN  - 2468-5739
UR  - https://doi.org/10.2991/978-94-6463-164-7_10
DO  - 10.2991/978-94-6463-164-7_10
ID  - Murthy2023
ER  -