Journal: International Journal of Molecular Sciences

Article Title: Integrated Analysis of Microarray, Small RNA, and Degradome Datasets Uncovers the Role of MicroRNAs in Temperature-Sensitive Genic Male Sterility in Wheat

doi: 10.3390/ijms23158057

Figure Lengend Snippet: Differentially expressed miRNAs between cold and control conditions at the respective stages. ( a ) Venn diagram of the differentially expressed miRNAs at stages 1.5, 2.2, and 3.0 (left); Venn diagram of the differentially expressed miRNAs in cold and control conditions, and the DEMs between the cold and control conditions. ( b ) The up- and downregulation of DEMs between cold and control conditions. ( c ) Expression heatmap for all DEMs in/between cold and control conditions. ( d ) Heatmap of the conserved known DEMs mentioned. ( e ) GO analysis of the predicted targets for the DEMs between cold and control conditions. A and E in ( a ) represent cold and control; C, F, and P in ( e ) indicate cellular component, molecular function, and biological process, respectively.

Article Snippet: Reads that did not annotate to any category were used to predict novel miRNAs using the miRNA prediction program MIREAP ( http://sourceforge.net/projects/mireap/ , accessed on 15 August 2020).

Techniques: Control, Expressing

Journal: International Journal of Molecular Sciences

Article Title: Integrated Analysis of Microarray, Small RNA, and Degradome Datasets Uncovers the Role of MicroRNAs in Temperature-Sensitive Genic Male Sterility in Wheat

doi: 10.3390/ijms23158057

Figure Lengend Snippet: The predicted opposite miRNA–mRNA pairs and functional analysis. ( a ) Differentially expressed miRNA–target pairs identified in the array and miRNA sequencing data. ( b ) Heatmap of the differentially expressed miRNA–target pairs with opposite expression patterns. miRNAs and genes with opposite expression patterns were framed using the same color in the heatmap for miRNAs and genes. The purple, red, and black frames represent opposite miRNAs and target genes at stages 1.5, 2.2, and 3.0, respectively. ( c ) Venn diagram of the predicted opposite miRNA–mRNA pairs at three developmental stages. ( d ) GO analysis of the target genes from the opposite miRNA–mRNA pairs.

Article Snippet: Reads that did not annotate to any category were used to predict novel miRNAs using the miRNA prediction program MIREAP ( http://sourceforge.net/projects/mireap/ , accessed on 15 August 2020).

Techniques: Functional Assay, Sequencing, Expressing

Journal: International Journal of Molecular Sciences

Article Title: Integrated Analysis of Microarray, Small RNA, and Degradome Datasets Uncovers the Role of MicroRNAs in Temperature-Sensitive Genic Male Sterility in Wheat

doi: 10.3390/ijms23158057

Figure Lengend Snippet: The predicted opposite miRNA–mRNA pairs for known DEMs between the cold and control conditions. Red V-shape represents miRNAs; green circle represents genes; purple triangle represents transcription factors.

Article Snippet: Reads that did not annotate to any category were used to predict novel miRNAs using the miRNA prediction program MIREAP ( http://sourceforge.net/projects/mireap/ , accessed on 15 August 2020).

Techniques: Control

Journal: International Journal of Molecular Sciences

Article Title: Integrated Analysis of Microarray, Small RNA, and Degradome Datasets Uncovers the Role of MicroRNAs in Temperature-Sensitive Genic Male Sterility in Wheat

doi: 10.3390/ijms23158057

Figure Lengend Snippet: Expression of conserved miRNAs and target genes at different developmental stages between cold and control conditions. F indicates control conditions, S indicates cold conditions. Asterisks indicate significant differences between cold and control conditions (Student’s t -test, * p -value < 0.05, ** p -value < 0.01). PMC, pollen mother cell stage; ME, meiosis stage; UN, uninucleate stage; MUN, middle uninucleate stage; VA, vacuolated stage.

Article Snippet: Reads that did not annotate to any category were used to predict novel miRNAs using the miRNA prediction program MIREAP ( http://sourceforge.net/projects/mireap/ , accessed on 15 August 2020).

Techniques: Expressing, Control

Journal: International Journal of Molecular Sciences

Article Title: Integrated Analysis of Microarray, Small RNA, and Degradome Datasets Uncovers the Role of MicroRNAs in Temperature-Sensitive Genic Male Sterility in Wheat

doi: 10.3390/ijms23158057

Figure Lengend Snippet: T-plots of representative miRNA targets under cold and control conditions. ( a ) The T-plots of ARF17 targeted by miR160. ( b ) The T-plots of MYB65 targeted by tae-159a. ( c ) The T-plots of HB - HD - ZIP targeted by miR166a. Upper panel, cold conditions; lower panel, control conditions. The red line represents the sliced target transcripts and is indicated by an arrow. The alignments show the miRNA with a portion of its target sequence (middle panel).

Article Snippet: Reads that did not annotate to any category were used to predict novel miRNAs using the miRNA prediction program MIREAP ( http://sourceforge.net/projects/mireap/ , accessed on 15 August 2020).

Techniques: Control, Sequencing

Journal: International Journal of Molecular Sciences

Article Title: Integrated Analysis of Microarray, Small RNA, and Degradome Datasets Uncovers the Role of MicroRNAs in Temperature-Sensitive Genic Male Sterility in Wheat

doi: 10.3390/ijms23158057

Figure Lengend Snippet: T-plots of representative miRNA targets under cold conditions. ( a ) The T-plots of ARF17 targeted by miR160a. ( b ) The T-plots of NF-YA targeted by miR169a. ( c ) The T-plots of ARF17 targeted by miR160a. ( d ) The T-plots of TaAP2 - A targeted by miR172. ( e ) The T-plots of TIR1 targeted by miR393. ( f ) The T-plots of HD-ZIP targeted by miR66a. The red line represents the sliced target transcripts and is indicated by an arrow. The alignments show the miRNA with a portion of its target sequence.

Article Snippet: Reads that did not annotate to any category were used to predict novel miRNAs using the miRNA prediction program MIREAP ( http://sourceforge.net/projects/mireap/ , accessed on 15 August 2020).

Techniques: Sequencing

Journal: Molecular Medicine Reports

Article Title: Expression and clinical significance of circular RNA hsa_circ_0079787 in the peripheral blood of patients with axial spondyloarthritis

doi: 10.3892/mmr.2020.11520

Figure Lengend Snippet: Snippet of the detailed annotation for circRNA/miRNA interactions. Interactions of hsa_circ_0079787/hsa-miR-580-3p, hsa_circ_0079787/hsa-miR-125b-5p, hsa_circ_0079787/hsa-miR-5191, hsa_circ_0079787/hsa-miR-6830-5p and hsa_circ_0079787/hsa-miR-4694-3p are displayed. UTR, untranslated region; miRNA/miR, microRNA; circRNA/circ, circular RNA; hsa, Homo sapiens ; M, circRNA/miRNA interaction target from Arraystar's home-made miRNA target prediction software based on miRanda; T, circRNA/miRNA interaction target from Arraystar's home-made miRNA target prediction software based on TargetScan.

Article Snippet: The circRNA/miRNA interactions were predicted using Arraystar's home-made miRNA target prediction software (version 1; KangChen Bio-tech, Inc.) ( , ) based on TargetScan (version 6) ( ) and miRanda (version 3.3a) , and the differentially expressed circRNAs within all the comparisons were annotated in detail with the circRNA/miRNA interaction information.

Techniques: Software

Journal: Oncotarget

Article Title: Screening circular RNA expression patterns following focal cerebral ischemia in mice

doi: 10.18632/oncotarget.21238

Figure Lengend Snippet: The vertical axis represents the miRNA targeting pathways associated with the circRNAs, and the horizontal axis represents the –LgP pathway values. LgP was the logarithm of p-value, and p < 0.05 was considered significant.

Article Snippet: We then predicted the potential interactions between circRNAs and their target miRNAs using the Arraystar software for miRNA targets, according to the TargetScan and miRanda databases.

Techniques:

Journal: Oncotarget

Article Title: Screening circular RNA expression patterns following focal cerebral ischemia in mice

doi: 10.18632/oncotarget.21238

Figure Lengend Snippet: The network consists of the 3 circRNAs, mmu_circRNA_40001, mmu_circRNA_013120, and mmu_circRNA_40806; (green nodes), miRNAs (red) and their target genes (yellow).

Article Snippet: We then predicted the potential interactions between circRNAs and their target miRNAs using the Arraystar software for miRNA targets, according to the TargetScan and miRanda databases.

Techniques:

Journal: Poultry Science

Article Title: Exosomal circ_CCDC7/gga-miR-6568-3p/Pax7 axis accelerates the differentiation of chicken embryonic stem cells infected with subgroup J avian leukosis virus

doi: 10.1016/j.psj.2024.103898

Figure Lengend Snippet: circRNA/miRNA/mRNA network. (A) circRNA-targeted miRNA network. Green color represents the top 5 differential expressed circRNAs. Grape color represents circRNA-targeted miRNA. Orange color represents co-targeted miRNA of circRNAs. (B) miRNA-targeted mRNA network. Deep blue color represents 3 major ESC marker genes. Blue color represents gene-targeted miRNA. Orange color represents co-targeted miRNA of genes.

Article Snippet: Potential miRNA response elements for the 71 differentially expressed circRNAs were identified using customized Arraystar miRNA target prediction software based on the Targetscan algorithms and miRanda ( ).

Techniques: Marker

Journal: International Journal of Molecular Medicine

Article Title: Microarray analysis of circular RNA expression patterns in polarized macrophages

doi: 10.3892/ijmm.2017.2852

Figure Lengend Snippet: A snippet of the detailed annotation for circRNA-010231/miRNA interaction. The circRNA/miRNA interaction was predicted with Arraystar's home-made miRNA target prediction software based on TargetScan and miRanda, and the most differentially expressed circRNAs within all the comparisons were annotated in detail with the circRNA/miRNA interaction information. Binding sites of conserved miRNAs with good mirSVR scores are represented.

Article Snippet: To further facilitate the implication of our research study, we used the Arraystar's home-made miRNA target prediction software based on TargetScan ( ) and miRanda ( ) to predict circRNA/microRNA interaction.

Techniques: Software, Binding Assay

Journal: Oncotarget

Article Title: Circular RNA alterations are involved in resistance to avian leukosis virus subgroup-J-induced tumor formation in chickens

doi: 10.18632/oncotarget.16442

Figure Lengend Snippet: Yellow represents circRNAs, green represents miRNAs and pink represents miRNA target genes.

Article Snippet: CircRNA and miRNA interactions were predicted using customized Arraystar miRNA target prediction software based on TargetScan and miRanda [ , ]; the top five putative target miRNAs were identified for upregulated circRNAs in ALV-J-resistant chickens.

Techniques: