Image_1_m6A-related lncRNAs are potential biomarkers for the prognosis of COAD patients.jpeg

BackgroundColon adenocarcinoma (COAD) is the most common subtype of colon cancer. However, the 5-year survival rate of COAD patients remains unsatisfactory. N6-methyladenosine (m6A) and long noncoding RNAs (lncRNAs) play essential roles in the occurrence and development of COAD. Herein, we are committed to establish and validate a prognostic m6A-related lncRNA signature.MethodsWe obtained m6A-related lncRNAs by coexpression. The m6A-related lncRNA risk signature (m6ALncSig) was developed via univariate, LASSO, and multivariate Cox regression analyses. Kaplan-Meier (KM) survival curves, gene set enrichment analysis (GSEA), and nomogram generation were conducted to assess m6ALncSig. In addition, the potential immunotherapeutic signatures were also discussed. Real-time PCR and CCK8 analysis were performed to evaluate the expression and functions of lncRNA UBA6-AS1, which was selected.ResultsThe risk signature comprising 14 m6A-related lncRNAs (m6ALncSig) was established, which possessed a superior predictive ability of prognosis. Meanwhile, m6ALncSig was linked to immune cell infiltration. The level of UBA6-AS1 expression was validated in 17 pairs of COAD samples. In cell function experiments, UBA6-AS1 knockdown attenuated cell proliferation capacity.ConclusionsCollectively, m6ALncSig could serve as an independent predictive factor for COAD and accurately estimate the outcome for COAD patients. Importantly, UBA6-AS1 was first identified as an oncogene in COAD.</p

Dynamic evolutionary procedure of a predicted temporal protein complex.

<p>The red proteins are unchanged in this procedure; the blue ones shown in (A) are absent in (B), and then reappear in (C); and the green protein shown in (A) is absent in both (B) and (C).</p

The properties of TEPIN, DPIN and SPIN.

<p>The properties of TEPIN, DPIN and SPIN.</p

Function enrichment analysis of predicted protein complexes detected from WTEPIN and WDPIN.

<p>Function enrichment analysis of predicted protein complexes detected from WTEPIN and WDPIN.</p

Percentage comparison of known protein complexes matched by the predicted protein complexes detected from various kinds of networks.

<p>Percentage comparison of known protein complexes matched by the predicted protein complexes detected from various kinds of networks.</p

Performance comparison of SPIN, DPIN and TEPIN.

<p>Performance comparison of SPIN, DPIN and TEPIN.</p

Some examples of the predicted protein complexes with small p-values detected from WTEPIN.

<p>Some examples of the predicted protein complexes with small p-values detected from WTEPIN.</p

Comparative Transcriptome Analysis between the Cytoplasmic Male Sterile Line NJCMS1A and Its Maintainer NJCMS1B in Soybean (<i>Glycine max</i> (L.) Merr.)

<div><p>Background</p><p>The utilization of soybean heterosis is probably one of the potential approaches in future yield breakthrough as was the situation in rice breeding in China. Cytoplasmic male sterility (CMS) plays an important role in the production of hybrid seeds. However, the molecular mechanism of CMS in soybean remains unclear.</p><p>Results</p><p>The comparative transcriptome analysis between cytoplasmic male sterile line NJCMS1A and its near-isogenic maintainer NJCMS1B in soybean was conducted using Illumina sequencing technology. A total of 88,643 transcripts were produced in Illumina sequencing. Then 56,044 genes were obtained matching soybean reference genome. Three hundred and sixty five differentially expressed genes (DEGs) between NJCMS1A and NJCMS1B were screened by threshold, among which, 339 down-regulated and 26 up-regulated in NJCMS1A compared to in NJCMS1B. Gene Ontology (GO) annotation showed that 242 DEGs were annotated to 19 functional categories. Clusters of Orthologous Groups of proteins (COG) annotation showed that 265 DEGs were classified into 19 categories. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that 46 DEGs were assigned to 33 metabolic pathways. According to functional and metabolic pathway analysis combined with reported literatures, the relations between some key DEGs and the male sterility of NJCMS1A were discussed. qRT-PCR analysis validated that the gene expression pattern in RNA-Seq was reliable. Finally, enzyme activity assay showed that energy supply was decreased in NJCMS1A compared to in NJCMS1B.</p><p>Conclusions</p><p>We concluded that the male sterility of NJCMS1A might be related to the disturbed functions and metabolism pathways of some key DEGs, such as DEGs involved in carbohydrate and energy metabolism, transcription factors, regulation of pollen development, elimination of reactive oxygen species (ROS), cellular signal transduction, and programmed cell death (PCD) etc. Future research will focus on cloning and transgenic function validation of possible candidate genes associated with soybean CMS.</p></div

Distribution of the number of proteins with varying amount of active time points in TEPIN.

<p>Distribution of the number of proteins with varying amount of active time points in TEPIN.</p

The protein complexes labeled as 550.1.213 predicted from WTEPIN and WDPIN.

<p>(A) shows the real complex labeled as 550.1.213 in the known protein complex set. (B) and (C) are the protein complexes with the identical label predicted from WTEPIN and WDPIN by CAMSE algorithm respectively. For each predicted protein complex, the proteins shown in red are involved in the real complex, while those shown in blue are not.</p