Spatiotemporal expression profile of embryonic and adult ankyrin repeat and EF-hand domain containing protein 1-encoding genes ankef1a and ankef1b in zebrafish

Daniel, Jeffrey G.; Panizzi, Jennifer R.

doi:10.1016/j.gep.2019.119069

Cited by 7 publications

(11 citation statements)

References 42 publications

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“…In eukaryotic cells, Ankyrins are intracellular adaptor proteins critical for the expression and targeting of cytoskeletal elements that serve as the interface between the plasma membrane and cytoskeleton (El Refaey and Mohler, 2017). Previous studies have suggested an important role for Ankyrin protein during embryonic development (Daniel et al, 2019). Similar to our results, Daniel et al (2019) have been showed that both forms of Ankyrin were ubiquitously expressed early in development stages.…”

Section: Skeletal Muscle Proteinssupporting

confidence: 93%

Identifying candidate genes involved in the regulation of growth using comparative transcriptome analysis (Androctonus crassicauda)

Salabi

Jafari

2022

Preprint

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BackgroundScorpions are venomous arthropod belonging to the arachnida, which considered as living fossils. Recently, transcriptomic analyses of scorpion venom gland were carried out by high-throughput sequencing and further analysis, but so far, the transcriptional analysis of venom gland of scorpion in different growth stages (adult and juvenile) have not been examined. Here, an Illumina-based sequencing study was designed to detect the candidate genes associated with growth development of scorpions of A. crassicauda. ResultsA total of 209951 mRNA transcripts were identified from total RNA-seq data, of which 963 transcripts were differentially expressed (DE) in adult and juvenile scorpions (p<0.01). Overall, we identified 397 out of 558 up-regulated transcripts and 269 out of 405 down-regulated transcripts with sequence similarity to annotated genes from various animals. GO and KEGG enrichment analyses indicated that the metabolic, thermogenesis, cytoskeleton, estrogen signaling, GnRH signaling, growth hormone signaling and melanogenesis pathways were affected by two different growth conditions and the results suggested that the DE genes related to those pathways are important biomarker genes associated with scorpions development and maturation, in which they may be important in future studies, including Chs, Elovl, MYH, RDX, ACTN, VCL, PIP5K, PP1C, FGFR, GNAS, EGFR, CREB, CoA, PLCB, CALM, CACNA, PKA and CAMK genes. ConclusionsThese findings broadened our knowledge about the differences between adult and juvenile scorpion’s venom and opens new perspectives about the application of comparative transcriptome analysis to identify the special biomarkers.

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Section: Skeletal Muscle Proteinssupporting

confidence: 93%

Identifying candidate genes involved in the regulation of growth using comparative transcriptome analysis (Androctonus crassicauda)

Salabi

Jafari

2022

Preprint

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“…instance, GRHL2 reduces the invasion and migration through the inhibition of TGF-βinduced EMT in gastric cancer [26]; GRHL2 leads to mesenchymal-epithelial transition (MET) through the inhibition of ZEB1 [13]. ANKRD5 plays roles in protocadherin-mediated cell protrusion and adhesion, and participates in cell adhesion [18]. FOXF2 was identified as a novel TF related to EMT-suppressing in basal-like breast cancer (BLBC) FOXF2 negatively targets TWIST1 in the EMT programming and metastasis progress of BLBC [22].…”

Section: Plos Onementioning

confidence: 99%

Global gene network exploration based on explainable artificial intelligence approach

et al. 2020

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In recent years, personalized gene regulatory networks have received significant attention, and interpretation of the multilayer networks has been a critical issue for a comprehensive understanding of gene regulatory systems. Although several statistical and machine learning approaches have been developed and applied to reveal sample-specific regulatory pathways, integrative understanding of the massive multilayer networks remains a challenge. To resolve this problem, we propose a novel artificial intelligence (AI) strategy for comprehensive gene regulatory network analysis. In our strategy, personalized gene networks corresponding specific clinical characteristic are constructed and the constructed network is considered as a second-order tensor. Then, an explainable AI method based on deep learning is applied to decompose the multilayer networks, thus we can reveal all-encompassing gene regulatory systems characterized by clinical features of patients. To evaluate the proposed methodology, we apply our method to the multilayer gene networks under varying conditions of an epithelial–mesenchymal transition (EMT) process. From the comprehensive analysis of multilayer networks, we identified novel markers, and the biological mechanisms of the identified genes and their reciprocal mechanisms are verified through the literature. Although any biological knowledge about the identified genes was not incorporated in our analysis, our data-driven approach based on AI approach provides biologically reliable results. Furthermore, the results provide crucial evidences to reveal biological mechanism related to various diseases, e.g., keratinocyte proliferation. The use of explainable AI method based on the tensor decomposition enables us to reveal global and novel mechanisms of gene regulatory system from the massive multiple networks, which cannot be demonstrated by existing methods. We expect that the proposed method provides a new insight into network biology and it will be a useful tool to integrative gene network analysis related complex architectures of diseases.

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“…In eukaryotic cells, Ankyrins are intracellular adaptor proteins critical for the expression and targeting of cytoskeletal elements that serve as the interface between the plasma membrane and cytoskeleton [ 48 ]. Previous studies have suggested an important role for Ankyrin protein during embryonic development [ 49 ]. Similar to our results, Daniel et al [ 49 ] showed that both forms of Ankyrin were ubiquitously expressed early in development stages.…”

Section: Discussionmentioning

confidence: 99%

“…Previous studies have suggested an important role for Ankyrin protein during embryonic development [ 49 ]. Similar to our results, Daniel et al [ 49 ] showed that both forms of Ankyrin were ubiquitously expressed early in development stages.…”

Section: Discussionmentioning

confidence: 99%

Differential venom gland gene expression analysis of juvenile and adult scorpions Androctonus crassicauda

Salabi

Jafari

2022

BMC Genomics

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Background The Androctonus crassicauda, belonging to the genus Androctonus of the family Buthidae, is the most venomous scorpion in Middle East countries. However, the venom gland transcriptome profile of A. crassicauda scorpion has not yet been studied. In this study, we elucidated and compared the venom gland gene expression profiles of adult and juvenile male scorpion A. crassicauda using high-throughput transcriptome sequencing. This is the first report of transcriptional analysis of the venom glands of scorpions in different growth stages, with insights into the identification of the key genes during venom gland development. Results A total of 209,951 mRNA transcripts were identified from total RNA-seq data, of which 963 transcripts were differentially expressed (DE) in adult and juvenile scorpions (p < 0.01). Overall, we identified 558 up-regulated and 405 down-regulated transcripts in the adult compared to the juvenile scorpions, of which 397 and 269 unique unigenes were annotated, respectively. GO and KEGG enrichment analyses indicated that the metabolic, thermogenesis, cytoskeleton, estrogen signaling, GnRH signaling, growth hormone signaling, and melanogenesis pathways were affected by two different growth conditions and the results suggested that the DE genes related to those pathways are important genes associated with scorpion venom gland development, in which they may be important in future studies, including Chs, Elovl, MYH, RDX, ACTN, VCL, PIP5K, PP1C, FGFR, GNAS, EGFR, CREB, CoA, PLCB, CALM, CACNA, PKA and CAMK genes. Conclusions These findings broadened our knowledge of the differences between adult and juvenile scorpion venom and opened new perspectives on the application of comparative transcriptome analysis to identify the special key genes.

show abstract

Spatiotemporal expression profile of embryonic and adult ankyrin repeat and EF-hand domain containing protein 1-encoding genes ankef1a and ankef1b in zebrafish

Cited by 7 publications

References 42 publications

Identifying candidate genes involved in the regulation of growth using comparative transcriptome analysis (Androctonus crassicauda)

Identifying candidate genes involved in the regulation of growth using comparative transcriptome analysis (Androctonus crassicauda)

Global gene network exploration based on explainable artificial intelligence approach

Differential venom gland gene expression analysis of juvenile and adult scorpions Androctonus crassicauda

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