PUBLICATION
Comparative transcriptomic characterization of a new mib mutant allele, mibnn2002, in zebrafish.
- Authors
- Lai, K.P., Li, J.W., Hsu, C.H., You, M.S., Chan, T.F., Tse, W.K.F., Jiang, Y.J.
- ID
- ZDB-PUB-171113-8
- Date
- 2017
- Source
- Gene 642: 51-57 (Journal)
- Registered Authors
- Hsu, Chia-Hao, Jiang, Yun-Jin, Tse, Ka Fai William, You, May-su
- Keywords
- Bioinformatics analysis, Next generation sequencing, Zebrafish
- MeSH Terms
-
- Zebrafish Proteins/genetics*
- Gene Expression Profiling/methods*
- Animals
- High-Throughput Nucleotide Sequencing
- Gene Regulatory Networks
- Gene Ontology
- Gene Expression Regulation, Developmental
- Somites/abnormalities*
- Ubiquitin-Protein Ligases/genetics*
- Computational Biology/methods
- Sequence Analysis, RNA
- Zebrafish/embryology*
- Zebrafish/genetics
- Sequence Deletion*
- PubMed
- 29126925 Full text @ Gene
Citation
Lai, K.P., Li, J.W., Hsu, C.H., You, M.S., Chan, T.F., Tse, W.K.F., Jiang, Y.J. (2017) Comparative transcriptomic characterization of a new mib mutant allele, mibnn2002, in zebrafish.. Gene. 642:51-57.
Abstract
mibnn2002, identified from an allele screen, shows early segmentation defect and severe cell death phenotypes, which are different from those of other described mib mutant alleles. We have previously reported its defects in somitogenesis and identified its origin of mutation, a large deletion in LG2. The report here is a continuous study, where we applied the bioinformatics analysis to profile the genetic background of mibnn2002 mutants. By comparing the transcriptomic data of mibnn2002 mutants with those of AB wild-type, a total of 1945 differentially expressed genes were identified, including 685 up- and 1260 down-regulated genes. The Database for Annotation, Visualization and Integrated Discovery (DAVID) analysis and Ingenuity Pathway Analysis (IPA) identified the enriched pathways and their related biological functions. Our data further demonstrated that the defects in the somitogenesis were related to the down-regulated segmentation genes, such as foxc1a, smyhc1, myod1 and mylpfa.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping