ZFIN ID: ZDB-PUB-171113-8
Comparative transcriptomic characterization of a new mib mutant allele, mibnn2002, in zebrafish.
Lai, K.P., Li, J.W., Hsu, C.H., You, M.S., Chan, T.F., Tse, W.K.F., Jiang, Y.J.
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:
  • Animals
  • Computational Biology/methods
  • Gene Expression Profiling/methods*
  • Gene Expression Regulation, Developmental
  • Gene Ontology
  • Gene Regulatory Networks
  • High-Throughput Nucleotide Sequencing
  • Sequence Analysis, RNA
  • Sequence Deletion*
  • Somites/abnormalities*
  • Ubiquitin-Protein Ligases/genetics*
  • Zebrafish/embryology*
  • Zebrafish/genetics
  • Zebrafish Proteins/genetics*
PubMed: 29126925 Full text @ Gene
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.