Genome-Wide Characterization of Fennel (Anethum foeniculum) MiRNome and Identification of its Potential Targets in Homo sapiens and Arabidopsis thaliana: An Inter and Intra-species Computational Scrutiny
MicroRNAs could be promising biomarkers for various diseases, and small RNA drugs have already been FDA approved for clinical use. This area of research is rapidly expanding and has significant potential for the future. Fennel ( Anethum foeniculum ) is a highly esteemed spice plant with economic and...
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| Veröffentlicht in: | Biochemical genetics 2024-08, Vol.62 (4), p.2766-2795 |
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| description | MicroRNAs could be promising biomarkers for various diseases, and small RNA drugs have already been FDA approved for clinical use. This area of research is rapidly expanding and has significant potential for the future. Fennel (
Anethum foeniculum
) is a highly esteemed spice plant with economic and medicinal benefits, making it an invaluable asset in the pharmaceutical industry. To characterize the fennel miRNAs and their
Arabidopsis thaliana
and
Homo sapience
targets with functional enrichment analysis and human disease association. A homology-based computational approach characterized the MiRnome of the
Anethum foeniculum
genome and assessed its impact on
Arabidopsis thaliana
and
Homo sapience
transcriptomes. In addition, functional enrichment analysis was evaluated for both species’ targets. Moreover, PPI network analysis, hub gene identification, and MD simulation analysis of the top hub node with fennel miRNA were incorporated. We have identified 100 miRNAs of fennel and their target genes, which include 2536 genes in
Homo sapiens
and 1314 genes in
Arabidopsis thaliana
. Functional enrichment analysis reveals 56
Arabidopsis thaliana
targets of fennel miRNAs showed involvement in metabolic pathways. Highly enriched human KEGG pathways were associated with several diseases, especially cancer. The protein–protein interaction network of human targets determined the top ten nodes; from them, seven hub nodes, namely
MAPK1
, PIK3R1, STAT3, EGFR, KRAS, CDC42, and SMAD4,
have shown their involvement in the pancreatic cancer pathway. Based on the Blast algorithm, 21 fennel miRNAs are homologs to 16 human miRNAs were predicted; from them, the
CSPP1
target was a common target for afo-miR11117a-3p and has-miR-6880-5p homologs miRNAs. Our results are the first to report the 100 fennel miRNAs, and predictions for their endogenous and human target genes provide a basis for further understanding of
Anethum foeniculum
miRNAs and the biological processes and diseases with which they are associated. |
| doi_str_mv | 10.1007/s10528-023-10575-7 |
| format | Article |
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Anethum foeniculum
) is a highly esteemed spice plant with economic and medicinal benefits, making it an invaluable asset in the pharmaceutical industry. To characterize the fennel miRNAs and their
Arabidopsis thaliana
and
Homo sapience
targets with functional enrichment analysis and human disease association. A homology-based computational approach characterized the MiRnome of the
Anethum foeniculum
genome and assessed its impact on
Arabidopsis thaliana
and
Homo sapience
transcriptomes. In addition, functional enrichment analysis was evaluated for both species’ targets. Moreover, PPI network analysis, hub gene identification, and MD simulation analysis of the top hub node with fennel miRNA were incorporated. We have identified 100 miRNAs of fennel and their target genes, which include 2536 genes in
Homo sapiens
and 1314 genes in
Arabidopsis thaliana
. Functional enrichment analysis reveals 56
Arabidopsis thaliana
targets of fennel miRNAs showed involvement in metabolic pathways. Highly enriched human KEGG pathways were associated with several diseases, especially cancer. The protein–protein interaction network of human targets determined the top ten nodes; from them, seven hub nodes, namely
MAPK1
, PIK3R1, STAT3, EGFR, KRAS, CDC42, and SMAD4,
have shown their involvement in the pancreatic cancer pathway. Based on the Blast algorithm, 21 fennel miRNAs are homologs to 16 human miRNAs were predicted; from them, the
CSPP1
target was a common target for afo-miR11117a-3p and has-miR-6880-5p homologs miRNAs. Our results are the first to report the 100 fennel miRNAs, and predictions for their endogenous and human target genes provide a basis for further understanding of
Anethum foeniculum
miRNAs and the biological processes and diseases with which they are associated.</description><identifier>ISSN: 0006-2928</identifier><identifier>ISSN: 1573-4927</identifier><identifier>EISSN: 1573-4927</identifier><identifier>DOI: 10.1007/s10528-023-10575-7</identifier><identifier>PMID: 38017284</identifier><language>eng</language><publisher>New York: Springer US</publisher><subject>Algorithms ; Anethum ; Arabidopsis - genetics ; Arabidopsis thaliana ; assets ; Biochemistry ; Biological activity ; Biological effects ; Biomarkers ; Biomedical and Life Sciences ; Biomedicine ; Cancer ; Cdc42 protein ; Chromosome 5 ; Computational Biology - methods ; Computer applications ; Enrichment ; fennel ; Foeniculum ; Foeniculum - genetics ; Foeniculum vulgare var. vulgare ; Gene Expression Regulation, Plant ; Gene set enrichment analysis ; Genes ; Genome, Plant ; Genomes ; Genomic analysis ; Homo ; Homo sapiens ; Homology ; human diseases ; Human Genetics ; Humans ; Impact analysis ; Medical Microbiology ; Medicinal plants ; Metabolic pathways ; microRNA ; MicroRNAs ; MicroRNAs - genetics ; miRNA ; Network analysis ; Nodes ; Original Article ; Pancreatic cancer ; pancreatic neoplasms ; Pharmaceutical industry ; Protein Interaction Maps ; protein-protein interactions ; Proteins ; RNA, Plant - genetics ; Simulation analysis ; simulation models ; Smad4 protein ; species ; spices ; Stat3 protein ; transcriptome ; Transcriptomes ; Zoology</subject><ispartof>Biochemical genetics, 2024-08, Vol.62 (4), p.2766-2795</ispartof><rights>The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2023. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.</rights><rights>2023. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c359t-2f96eb3f66bc19a1b8a452bdd95a0d42e2b873bd63d6d5d35b82c6d82bec22503</cites><orcidid>0000-0003-4919-1322 ; 0000-0003-0882-3995 ; 0000-0002-7985-1187 ; 0000-0002-7040-3003 ; 0009-0001-6433-1840</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s10528-023-10575-7$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s10528-023-10575-7$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,777,781,27905,27906,41469,42538,51300</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/38017284$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Trivedi, Tithi S.</creatorcontrib><creatorcontrib>Shaikh, Aafrinbanu M.</creatorcontrib><creatorcontrib>Mankad, Archana U.</creatorcontrib><creatorcontrib>Rawal, Rakesh M.</creatorcontrib><creatorcontrib>Patel, Saumya K.</creatorcontrib><title>Genome-Wide Characterization of Fennel (Anethum foeniculum) MiRNome and Identification of its Potential Targets in Homo sapiens and Arabidopsis thaliana: An Inter and Intra-species Computational Scrutiny</title><title>Biochemical genetics</title><addtitle>Biochem Genet</addtitle><addtitle>Biochem Genet</addtitle><description>MicroRNAs could be promising biomarkers for various diseases, and small RNA drugs have already been FDA approved for clinical use. This area of research is rapidly expanding and has significant potential for the future. Fennel (
Anethum foeniculum
) is a highly esteemed spice plant with economic and medicinal benefits, making it an invaluable asset in the pharmaceutical industry. To characterize the fennel miRNAs and their
Arabidopsis thaliana
and
Homo sapience
targets with functional enrichment analysis and human disease association. A homology-based computational approach characterized the MiRnome of the
Anethum foeniculum
genome and assessed its impact on
Arabidopsis thaliana
and
Homo sapience
transcriptomes. In addition, functional enrichment analysis was evaluated for both species’ targets. Moreover, PPI network analysis, hub gene identification, and MD simulation analysis of the top hub node with fennel miRNA were incorporated. We have identified 100 miRNAs of fennel and their target genes, which include 2536 genes in
Homo sapiens
and 1314 genes in
Arabidopsis thaliana
. Functional enrichment analysis reveals 56
Arabidopsis thaliana
targets of fennel miRNAs showed involvement in metabolic pathways. Highly enriched human KEGG pathways were associated with several diseases, especially cancer. The protein–protein interaction network of human targets determined the top ten nodes; from them, seven hub nodes, namely
MAPK1
, PIK3R1, STAT3, EGFR, KRAS, CDC42, and SMAD4,
have shown their involvement in the pancreatic cancer pathway. Based on the Blast algorithm, 21 fennel miRNAs are homologs to 16 human miRNAs were predicted; from them, the
CSPP1
target was a common target for afo-miR11117a-3p and has-miR-6880-5p homologs miRNAs. Our results are the first to report the 100 fennel miRNAs, and predictions for their endogenous and human target genes provide a basis for further understanding of
Anethum foeniculum
miRNAs and the biological processes and diseases with which they are associated.</description><subject>Algorithms</subject><subject>Anethum</subject><subject>Arabidopsis - genetics</subject><subject>Arabidopsis thaliana</subject><subject>assets</subject><subject>Biochemistry</subject><subject>Biological activity</subject><subject>Biological effects</subject><subject>Biomarkers</subject><subject>Biomedical and Life Sciences</subject><subject>Biomedicine</subject><subject>Cancer</subject><subject>Cdc42 protein</subject><subject>Chromosome 5</subject><subject>Computational Biology - methods</subject><subject>Computer applications</subject><subject>Enrichment</subject><subject>fennel</subject><subject>Foeniculum</subject><subject>Foeniculum - genetics</subject><subject>Foeniculum vulgare var. vulgare</subject><subject>Gene Expression Regulation, Plant</subject><subject>Gene set enrichment analysis</subject><subject>Genes</subject><subject>Genome, Plant</subject><subject>Genomes</subject><subject>Genomic analysis</subject><subject>Homo</subject><subject>Homo sapiens</subject><subject>Homology</subject><subject>human diseases</subject><subject>Human Genetics</subject><subject>Humans</subject><subject>Impact analysis</subject><subject>Medical Microbiology</subject><subject>Medicinal plants</subject><subject>Metabolic pathways</subject><subject>microRNA</subject><subject>MicroRNAs</subject><subject>MicroRNAs - genetics</subject><subject>miRNA</subject><subject>Network analysis</subject><subject>Nodes</subject><subject>Original Article</subject><subject>Pancreatic cancer</subject><subject>pancreatic neoplasms</subject><subject>Pharmaceutical industry</subject><subject>Protein Interaction Maps</subject><subject>protein-protein interactions</subject><subject>Proteins</subject><subject>RNA, Plant - genetics</subject><subject>Simulation analysis</subject><subject>simulation models</subject><subject>Smad4 protein</subject><subject>species</subject><subject>spices</subject><subject>Stat3 protein</subject><subject>transcriptome</subject><subject>Transcriptomes</subject><subject>Zoology</subject><issn>0006-2928</issn><issn>1573-4927</issn><issn>1573-4927</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkstu1DAUhiMEotPCC7BAltiURcCXOInZjUa0HalcBEUsI19OOq4SO9jOorxiXwrPpBSJBaxsH3__f86R_qJ4QfAbgnHzNhLMaVtiysp8a3jZPCpWhDesrARtHhcrjHFdUkHbo-I4xpv8FLiqnhZHrMWkoW21Ku7OwfkRyu_WANrsZJA6QbA_ZbLeId-jM3AOBnS6dpB284h6D87qeZjH1-iD_fIxi5F0Bm0NuGR7qx-UNkX02ad9WQ7oSoZryBXr0IUfPYpysuDiQbsOUlnjp2gjSjs5WOnkO7R2aOvyMIu9S0GWcQJtIaKNH6c5HTpl6686zMm622fFk14OEZ7fnyfFt7P3V5uL8vLT-Xazviw14yKVtBc1KNbXtdJESKJaWXGqjBFcYlNRoKptmDI1M7XhhnHVUl2blirQlHLMTorTxXcK_scMMXWjjRqGQTrwc-wY4axhjNf8vyhtBadcMCwy-uov9MbPIe-XDXFbk5pi0WSKLpQOPsYAfTcFO8pw2xHc7VPRLanociq6Qyq6vejlvfWsRjAPkt8xyABbgJi_3DWEP73_YfsLSY_Few</recordid><startdate>202408</startdate><enddate>202408</enddate><creator>Trivedi, Tithi S.</creator><creator>Shaikh, Aafrinbanu M.</creator><creator>Mankad, Archana U.</creator><creator>Rawal, Rakesh M.</creator><creator>Patel, Saumya K.</creator><general>Springer US</general><general>Springer Nature B.V</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7SS</scope><scope>7TK</scope><scope>7U7</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>K9.</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>7S9</scope><scope>L.6</scope><orcidid>https://orcid.org/0000-0003-4919-1322</orcidid><orcidid>https://orcid.org/0000-0003-0882-3995</orcidid><orcidid>https://orcid.org/0000-0002-7985-1187</orcidid><orcidid>https://orcid.org/0000-0002-7040-3003</orcidid><orcidid>https://orcid.org/0009-0001-6433-1840</orcidid></search><sort><creationdate>202408</creationdate><title>Genome-Wide Characterization of Fennel (Anethum foeniculum) MiRNome and Identification of its Potential Targets in Homo sapiens and Arabidopsis thaliana: An Inter and Intra-species Computational Scrutiny</title><author>Trivedi, Tithi S. ; Shaikh, Aafrinbanu M. ; Mankad, Archana U. ; Rawal, Rakesh M. ; Patel, Saumya K.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c359t-2f96eb3f66bc19a1b8a452bdd95a0d42e2b873bd63d6d5d35b82c6d82bec22503</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Algorithms</topic><topic>Anethum</topic><topic>Arabidopsis - genetics</topic><topic>Arabidopsis thaliana</topic><topic>assets</topic><topic>Biochemistry</topic><topic>Biological activity</topic><topic>Biological effects</topic><topic>Biomarkers</topic><topic>Biomedical and Life Sciences</topic><topic>Biomedicine</topic><topic>Cancer</topic><topic>Cdc42 protein</topic><topic>Chromosome 5</topic><topic>Computational Biology - methods</topic><topic>Computer applications</topic><topic>Enrichment</topic><topic>fennel</topic><topic>Foeniculum</topic><topic>Foeniculum - genetics</topic><topic>Foeniculum vulgare var. vulgare</topic><topic>Gene Expression Regulation, Plant</topic><topic>Gene set enrichment analysis</topic><topic>Genes</topic><topic>Genome, Plant</topic><topic>Genomes</topic><topic>Genomic analysis</topic><topic>Homo</topic><topic>Homo sapiens</topic><topic>Homology</topic><topic>human diseases</topic><topic>Human Genetics</topic><topic>Humans</topic><topic>Impact analysis</topic><topic>Medical Microbiology</topic><topic>Medicinal plants</topic><topic>Metabolic pathways</topic><topic>microRNA</topic><topic>MicroRNAs</topic><topic>MicroRNAs - genetics</topic><topic>miRNA</topic><topic>Network analysis</topic><topic>Nodes</topic><topic>Original Article</topic><topic>Pancreatic cancer</topic><topic>pancreatic neoplasms</topic><topic>Pharmaceutical industry</topic><topic>Protein Interaction Maps</topic><topic>protein-protein interactions</topic><topic>Proteins</topic><topic>RNA, Plant - genetics</topic><topic>Simulation analysis</topic><topic>simulation models</topic><topic>Smad4 protein</topic><topic>species</topic><topic>spices</topic><topic>Stat3 protein</topic><topic>transcriptome</topic><topic>Transcriptomes</topic><topic>Zoology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Trivedi, Tithi S.</creatorcontrib><creatorcontrib>Shaikh, Aafrinbanu M.</creatorcontrib><creatorcontrib>Mankad, Archana U.</creatorcontrib><creatorcontrib>Rawal, Rakesh M.</creatorcontrib><creatorcontrib>Patel, Saumya K.</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Neurosciences Abstracts</collection><collection>Toxicology Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>AGRICOLA</collection><collection>AGRICOLA - Academic</collection><jtitle>Biochemical genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Trivedi, Tithi S.</au><au>Shaikh, Aafrinbanu M.</au><au>Mankad, Archana U.</au><au>Rawal, Rakesh M.</au><au>Patel, Saumya K.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genome-Wide Characterization of Fennel (Anethum foeniculum) MiRNome and Identification of its Potential Targets in Homo sapiens and Arabidopsis thaliana: An Inter and Intra-species Computational Scrutiny</atitle><jtitle>Biochemical genetics</jtitle><stitle>Biochem Genet</stitle><addtitle>Biochem Genet</addtitle><date>2024-08</date><risdate>2024</risdate><volume>62</volume><issue>4</issue><spage>2766</spage><epage>2795</epage><pages>2766-2795</pages><issn>0006-2928</issn><issn>1573-4927</issn><eissn>1573-4927</eissn><abstract>MicroRNAs could be promising biomarkers for various diseases, and small RNA drugs have already been FDA approved for clinical use. This area of research is rapidly expanding and has significant potential for the future. Fennel (
Anethum foeniculum
) is a highly esteemed spice plant with economic and medicinal benefits, making it an invaluable asset in the pharmaceutical industry. To characterize the fennel miRNAs and their
Arabidopsis thaliana
and
Homo sapience
targets with functional enrichment analysis and human disease association. A homology-based computational approach characterized the MiRnome of the
Anethum foeniculum
genome and assessed its impact on
Arabidopsis thaliana
and
Homo sapience
transcriptomes. In addition, functional enrichment analysis was evaluated for both species’ targets. Moreover, PPI network analysis, hub gene identification, and MD simulation analysis of the top hub node with fennel miRNA were incorporated. We have identified 100 miRNAs of fennel and their target genes, which include 2536 genes in
Homo sapiens
and 1314 genes in
Arabidopsis thaliana
. Functional enrichment analysis reveals 56
Arabidopsis thaliana
targets of fennel miRNAs showed involvement in metabolic pathways. Highly enriched human KEGG pathways were associated with several diseases, especially cancer. The protein–protein interaction network of human targets determined the top ten nodes; from them, seven hub nodes, namely
MAPK1
, PIK3R1, STAT3, EGFR, KRAS, CDC42, and SMAD4,
have shown their involvement in the pancreatic cancer pathway. Based on the Blast algorithm, 21 fennel miRNAs are homologs to 16 human miRNAs were predicted; from them, the
CSPP1
target was a common target for afo-miR11117a-3p and has-miR-6880-5p homologs miRNAs. Our results are the first to report the 100 fennel miRNAs, and predictions for their endogenous and human target genes provide a basis for further understanding of
Anethum foeniculum
miRNAs and the biological processes and diseases with which they are associated.</abstract><cop>New York</cop><pub>Springer US</pub><pmid>38017284</pmid><doi>10.1007/s10528-023-10575-7</doi><tpages>30</tpages><orcidid>https://orcid.org/0000-0003-4919-1322</orcidid><orcidid>https://orcid.org/0000-0003-0882-3995</orcidid><orcidid>https://orcid.org/0000-0002-7985-1187</orcidid><orcidid>https://orcid.org/0000-0002-7040-3003</orcidid><orcidid>https://orcid.org/0009-0001-6433-1840</orcidid></addata></record> |
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| ispartof | Biochemical genetics, 2024-08, Vol.62 (4), p.2766-2795 |
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| source | MEDLINE; Springer Nature - Complete Springer Journals |
| subjects | Algorithms Anethum Arabidopsis - genetics Arabidopsis thaliana assets Biochemistry Biological activity Biological effects Biomarkers Biomedical and Life Sciences Biomedicine Cancer Cdc42 protein Chromosome 5 Computational Biology - methods Computer applications Enrichment fennel Foeniculum Foeniculum - genetics Foeniculum vulgare var. vulgare Gene Expression Regulation, Plant Gene set enrichment analysis Genes Genome, Plant Genomes Genomic analysis Homo Homo sapiens Homology human diseases Human Genetics Humans Impact analysis Medical Microbiology Medicinal plants Metabolic pathways microRNA MicroRNAs MicroRNAs - genetics miRNA Network analysis Nodes Original Article Pancreatic cancer pancreatic neoplasms Pharmaceutical industry Protein Interaction Maps protein-protein interactions Proteins RNA, Plant - genetics Simulation analysis simulation models Smad4 protein species spices Stat3 protein transcriptome Transcriptomes Zoology |
| title | Genome-Wide Characterization of Fennel (Anethum foeniculum) MiRNome and Identification of its Potential Targets in Homo sapiens and Arabidopsis thaliana: An Inter and Intra-species Computational Scrutiny |
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