Analysis of functional genomic signals using the XOR gate.
Modeling gene regulatory networks requires recognition of active transcriptional sites in the genome. For this reason, we present a novel approach for inferring active transcriptional regulatory modules in a genome using an established systems model of bit encoded DNA sequences. Our analysis showed...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2009-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC2680033?pdf=render |
| _version_ | 1828788047698722816 |
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| author | Mahesh Yaragatti Qi Wen |
| author_facet | Mahesh Yaragatti Qi Wen |
| author_sort | Mahesh Yaragatti |
| collection | DOAJ |
| description | Modeling gene regulatory networks requires recognition of active transcriptional sites in the genome. For this reason, we present a novel approach for inferring active transcriptional regulatory modules in a genome using an established systems model of bit encoded DNA sequences. Our analysis showed variations in several properties between random and functional sequences. Cross correlation within random and functional groups uncovered a wave pattern associated with functional sequences. Using the exclusive-OR (XOR) logic gate, we formulated a scheme to threshold signals that may correlate to putative active transcriptional modules from a population of random genomic fragments. It is our intent to use this as a basis for identifying novel regulatory sites in the genome. |
| first_indexed | 2024-12-12T00:44:11Z |
| format | Article |
| id | doaj.art-fb948eccbe404f408682aaeff32e59b1 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-12T00:44:11Z |
| publishDate | 2009-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-fb948eccbe404f408682aaeff32e59b12022-12-22T00:44:11ZengPublic Library of Science (PLoS)PLoS ONE1932-62032009-01-0145e560810.1371/journal.pone.0005608Analysis of functional genomic signals using the XOR gate.Mahesh YaragattiQi WenModeling gene regulatory networks requires recognition of active transcriptional sites in the genome. For this reason, we present a novel approach for inferring active transcriptional regulatory modules in a genome using an established systems model of bit encoded DNA sequences. Our analysis showed variations in several properties between random and functional sequences. Cross correlation within random and functional groups uncovered a wave pattern associated with functional sequences. Using the exclusive-OR (XOR) logic gate, we formulated a scheme to threshold signals that may correlate to putative active transcriptional modules from a population of random genomic fragments. It is our intent to use this as a basis for identifying novel regulatory sites in the genome.http://europepmc.org/articles/PMC2680033?pdf=render |
| spellingShingle | Mahesh Yaragatti Qi Wen Analysis of functional genomic signals using the XOR gate. PLoS ONE |
| title | Analysis of functional genomic signals using the XOR gate. |
| title_full | Analysis of functional genomic signals using the XOR gate. |
| title_fullStr | Analysis of functional genomic signals using the XOR gate. |
| title_full_unstemmed | Analysis of functional genomic signals using the XOR gate. |
| title_short | Analysis of functional genomic signals using the XOR gate. |
| title_sort | analysis of functional genomic signals using the xor gate |
| url | http://europepmc.org/articles/PMC2680033?pdf=render |
| work_keys_str_mv | AT maheshyaragatti analysisoffunctionalgenomicsignalsusingthexorgate AT qiwen analysisoffunctionalgenomicsignalsusingthexorgate |