Journal: Frontiers in Physiology

Article Title: Genome-Wide Analysis of Odorant-Binding Proteins and Chemosensory Proteins in the Bean bug Riptortus pedestris

doi: 10.3389/fphys.2022.949607

Figure Lengend Snippet: The sequences information of RpedOBPs and RpedCSPs.

Article Snippet: We used the protein data of R. pedestris and blasted with different database of Nr (Non-Redundant Protein Sequence), Nt (nucleotide sequence database), UniProt (The Universal Protein Resource), KOG (Clusters of orthologous groups for eukaryotic complete genomes), eggNOG (evolutionary genealogy of genes: No-supervised Orthologous Groups), Interpro (the integrative protein signature), GO (Gene Ontology), and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases , so R. pedestris proteins were annotated based on homology (These data were derived from a previous genome paper).

Techniques: Binding Assay

Journal: Frontiers in Physiology

Article Title: Genome-Wide Analysis of Odorant-Binding Proteins and Chemosensory Proteins in the Bean bug Riptortus pedestris

doi: 10.3389/fphys.2022.949607

Figure Lengend Snippet: The number of OBP and CSP genes in different insect species, obtained from genome (*) or antennal transcriptome (#). The digits by the histogram bars represent number of OBP and CSP genes in different hemipteran species ( Aphis gossypii , Nilaparvata lugens , Sogatella furcifera , Adelphocoris lineolatus , Adelphocoris suturalis , Nysius ericae , R. pedestris ) and phylogenetic tree was built by these hemipteran species COI genes.

Article Snippet: We used the protein data of R. pedestris and blasted with different database of Nr (Non-Redundant Protein Sequence), Nt (nucleotide sequence database), UniProt (The Universal Protein Resource), KOG (Clusters of orthologous groups for eukaryotic complete genomes), eggNOG (evolutionary genealogy of genes: No-supervised Orthologous Groups), Interpro (the integrative protein signature), GO (Gene Ontology), and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases , so R. pedestris proteins were annotated based on homology (These data were derived from a previous genome paper).

Techniques:

Journal: Frontiers in Physiology

Article Title: Genome-Wide Analysis of Odorant-Binding Proteins and Chemosensory Proteins in the Bean bug Riptortus pedestris

doi: 10.3389/fphys.2022.949607

Figure Lengend Snippet: Localization of OBPs and CSPs in the R. pedestris genome. Based on the annotation file of R. pedestris , we acquired the localization of OBP and CSP genes in genome. (A) The RpedOBPs in the R. pedestris genome, they clustered together in 4 chromosomes and one scaffold. (B) The RpedCSPs in the R. pedestris genome, they clustered together in 4 chromosomes.

Article Snippet: We used the protein data of R. pedestris and blasted with different database of Nr (Non-Redundant Protein Sequence), Nt (nucleotide sequence database), UniProt (The Universal Protein Resource), KOG (Clusters of orthologous groups for eukaryotic complete genomes), eggNOG (evolutionary genealogy of genes: No-supervised Orthologous Groups), Interpro (the integrative protein signature), GO (Gene Ontology), and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases , so R. pedestris proteins were annotated based on homology (These data were derived from a previous genome paper).

Techniques:

Journal: Frontiers in Physiology

Article Title: Genome-Wide Analysis of Odorant-Binding Proteins and Chemosensory Proteins in the Bean bug Riptortus pedestris

doi: 10.3389/fphys.2022.949607

Figure Lengend Snippet: Genomic structure of R. pedestris OBPs and CSPs. Based on the annotation file of R. pedestris, we acquired genomic structures of OBP and CSP genes. (A) Numbers of exon/intron and exon/intron structures of RpedOBPs. (B) Numbers of exon/intron and exon/intron structures of RpedCSPs.

Article Snippet: We used the protein data of R. pedestris and blasted with different database of Nr (Non-Redundant Protein Sequence), Nt (nucleotide sequence database), UniProt (The Universal Protein Resource), KOG (Clusters of orthologous groups for eukaryotic complete genomes), eggNOG (evolutionary genealogy of genes: No-supervised Orthologous Groups), Interpro (the integrative protein signature), GO (Gene Ontology), and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases , so R. pedestris proteins were annotated based on homology (These data were derived from a previous genome paper).

Techniques:

Journal: Frontiers in Physiology

Article Title: Genome-Wide Analysis of Odorant-Binding Proteins and Chemosensory Proteins in the Bean bug Riptortus pedestris

doi: 10.3389/fphys.2022.949607

Figure Lengend Snippet: Tissue expression profiles of R. pedestris OBPs by qRT-PCR. The relative expression level is presented as mean ± SE ( n = 3). The heatmap use Log2 and row scale based the relative expression level data. Different capital letters mean a significant difference between tissues ( p < 0.05, ANOVA, LSD). He, heads; Th, thoraxes; Ab, abdomens; Le, legs; Wi, wings; FA, female antennae; MA, male antennae.

Article Snippet: We used the protein data of R. pedestris and blasted with different database of Nr (Non-Redundant Protein Sequence), Nt (nucleotide sequence database), UniProt (The Universal Protein Resource), KOG (Clusters of orthologous groups for eukaryotic complete genomes), eggNOG (evolutionary genealogy of genes: No-supervised Orthologous Groups), Interpro (the integrative protein signature), GO (Gene Ontology), and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases , so R. pedestris proteins were annotated based on homology (These data were derived from a previous genome paper).

Techniques: Expressing, Quantitative RT-PCR

Journal: Frontiers in Physiology

Article Title: Genome-Wide Analysis of Odorant-Binding Proteins and Chemosensory Proteins in the Bean bug Riptortus pedestris

doi: 10.3389/fphys.2022.949607

Figure Lengend Snippet: Tissue expression profiles of R. pedestris CSPs by qRT-PCR. The relative expression level is presented as mean ± SE ( n = 3). The heatmap use Log2 and row scale based the relative expression level data. Different capital letters mean a significant difference between tissues ( p < 0.05, ANOVA, LSD). He, heads; Th, thoraxes; Ab, abdomens; Le, legs; Wi, wings; FA, female antennae; MA, male antennae.

Article Snippet: We used the protein data of R. pedestris and blasted with different database of Nr (Non-Redundant Protein Sequence), Nt (nucleotide sequence database), UniProt (The Universal Protein Resource), KOG (Clusters of orthologous groups for eukaryotic complete genomes), eggNOG (evolutionary genealogy of genes: No-supervised Orthologous Groups), Interpro (the integrative protein signature), GO (Gene Ontology), and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases , so R. pedestris proteins were annotated based on homology (These data were derived from a previous genome paper).

Techniques: Expressing, Quantitative RT-PCR

Journal: Scientific Reports

Article Title: A novel cancer-associated membrane signature predicts prognosis and therapeutic response for lung adenocarcinoma

doi: 10.1038/s41598-025-11105-8

Figure Lengend Snippet: Prognostic model of lung cancer-associated membranes (LCaMPS). ( A ) Forest plot of 13 membrane-associated genes significantly associated with prognosis of LUAD patients. ( B ) Each independent variable’s trajectory and distributions for the lambda. ( C ) Heatmap showing the expression of 9 signatures in high and low-risk groups. ( D ) Kaplan-Meier plot of LCaMPS in the TCGA dataset. ( E ) The ROC curve and area under the curve (AUC) of the 1, 3, 5, and 10-years survival rates based on TCGA dataset. ( F ) Kaplan-Meier plot of LCaMPS in the validation GSE72094 cohort. ( G ) The ROC curve and AUC of the 1, 3, and 5-years survival rates based on GSE72094 cohort. ( H ) Kaplan-Meier plot of LCaMPS in the validation GSE26939 cohort. ( I ) The ROC curve and AUC of the 1, 3, 5, and 10-years survival rates based on GSE26939 cohort.

Article Snippet: Fig. 7 Bulk RNA and protein profiling analysis of LCaMPS targets. ( A ) Boxplot illustrating normalized (log2 (expression + 1)) gene expression of 9 signatures of LCaMPS based on TCGA database. ( B ) Protein expression of the 8 LCaMPS signatures in LUAD and normal lung tissues via the human protein atlas (THPA).

Techniques: Membrane, Expressing, Biomarker Discovery

Journal: Scientific Reports

Article Title: A novel cancer-associated membrane signature predicts prognosis and therapeutic response for lung adenocarcinoma

doi: 10.1038/s41598-025-11105-8

Figure Lengend Snippet: Functional enrichment and immune cell infiltration of LCaMPS. ( A ) GSEA plot depicting KEGG pathway enrichment in high and low-risk groups based on the TCGA database. ( B ) Boxplot showing ESTIMATE score, immune score, stromal score, and tumor purity between high-risk and low-risk groups. ( C ) Boxplot illustrating tissue-infiltrating immune and stromal cell populations based on MCP-counter. ( D ) Boxplot illustrating tissue-infiltrating immune cell types based on Cibersort.

Article Snippet: Fig. 7 Bulk RNA and protein profiling analysis of LCaMPS targets. ( A ) Boxplot illustrating normalized (log2 (expression + 1)) gene expression of 9 signatures of LCaMPS based on TCGA database. ( B ) Protein expression of the 8 LCaMPS signatures in LUAD and normal lung tissues via the human protein atlas (THPA).

Techniques: Functional Assay

Journal: Scientific Reports

Article Title: A novel cancer-associated membrane signature predicts prognosis and therapeutic response for lung adenocarcinoma

doi: 10.1038/s41598-025-11105-8

Figure Lengend Snippet: scRNA and spatial profiling analysis of LCaMPS targets. ( A ) Dotplot illustrating the expression of the 9 signatures of LCaMPS across 2 tissue types (left) and 7 epithelial clusters (right). ( B ) Spatial representation of tumor, LCaMPS signature score and their correlation in 1 LUAD sample HTA1_322_5071604. ( C ) Spatial plot of LCaMPS signature genes, TSPAN8, SLC16A3, BACE2, COX16 and their correlations with tumor in 1 LUAD sample HTA1_322_5071604, respectively.

Article Snippet: Fig. 7 Bulk RNA and protein profiling analysis of LCaMPS targets. ( A ) Boxplot illustrating normalized (log2 (expression + 1)) gene expression of 9 signatures of LCaMPS based on TCGA database. ( B ) Protein expression of the 8 LCaMPS signatures in LUAD and normal lung tissues via the human protein atlas (THPA).

Techniques: Expressing

Journal: Scientific Reports

Article Title: A novel cancer-associated membrane signature predicts prognosis and therapeutic response for lung adenocarcinoma

doi: 10.1038/s41598-025-11105-8

Figure Lengend Snippet: Bulk RNA and protein profiling analysis of LCaMPS targets. ( A ) Boxplot illustrating normalized (log2 (expression + 1)) gene expression of 9 signatures of LCaMPS based on TCGA database. ( B ) Protein expression of the 8 LCaMPS signatures in LUAD and normal lung tissues via the human protein atlas (THPA). The IHC staining levels was categorized as “Not detected”, “Low”, “Medium”, or “High”.

Article Snippet: Fig. 7 Bulk RNA and protein profiling analysis of LCaMPS targets. ( A ) Boxplot illustrating normalized (log2 (expression + 1)) gene expression of 9 signatures of LCaMPS based on TCGA database. ( B ) Protein expression of the 8 LCaMPS signatures in LUAD and normal lung tissues via the human protein atlas (THPA).

Techniques: Expressing, Gene Expression, Immunohistochemistry