Bioinformatic Analysis of Differentially Expressed Genes (DEGs) Detected from RNA-Sequence Profiles of Mouse Striatum

Background/Aims: The mouse is widely used as an animal model for studying human embryo implantation. However, the mouse is unique in that both ovarian progesterone and estrogen are critical to implantation, whereas in the majority of species (e.g. human and hamster) implantation can occur in the presence of progesterone alone. Methods: In this study, we analyzed embryo-induced transcriptomic changes in the hamster uterus during embryo implantation by using RNA-seq. Differentially expressed genes were characterized by bioinformatic analysis. Results: We identified a total of 781 differentially expressed genes, of which 367 genes were up-regulated and 414 genes were down-regulated at the implantation site compared to the inter-implantation site. Functional clustering and gene network analysis highlighted the cell cycle process in uterus upon embryo implantation. By examining of the promoter regions of differentially expressed genes, we identified 7 causal transcription factors. Additionally, through connectivity map (CMap) analysis, multiple compounds were identified to have potential anti-implantation effects due to their ability to reverse embryo-induced transcriptomic changes. Conclusion: Our study provides a valuable resource for in-depth understanding of the mechanism underlying embryo implantation.

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Bioinformatic Analysis of Differentially Expressed Genes and Screening of Hub Genes in Uveal Melanoma Cells with BRCA1-Associated Protein 1 Related Protein 1 Depletion

Journal of Biomedical Nanotechnology ◽

10.1166/jbn.2020.2968 ◽

2020 ◽

Vol 16 (8) ◽

pp. 1205-1218

Author(s):

Wei Li ◽

Aiqin Nie ◽

Qiang Li ◽

He Cao ◽

Yinwei Song ◽

...

Keyword(s):

Cell Adhesion ◽

Differentially Expressed Genes ◽

Uveal Melanoma ◽

Wnt Signaling Pathway ◽

Tumor Development ◽

Bioinformatic Analysis ◽

Melanoma Cells ◽

Differentially Expressed ◽

Data Sets ◽

And Migration

Recent studies have found that chromosome 3 is frequently mutated in metastatic uveal melanoma (UVM), which leads to the loss of BAP1 expression or the weakening of BRCA1-associated protein 1 (BAP1) function and promotes metastasis of uveal melanoma cells. However, the specific signaling pathways that are affected by BAP1 depletion in uveal melanoma remain unclear. Our aim in this study was to verify the effect and regulatory mechanism of BAP1 on uveal melanoma. RT-qPCR and western blotting results showed that BAP1 was significantly down-regulated in OCM-1A cells treated with a BAP1 shRNA vector. MTT, cell scratch and transwell migration assays showed that low expression of BAP1 significantly promoted the proliferation and migration of UVM cells. A total of 269 up-regulated and 807 down-regulated genes were identified from the combined GSE110193 and GSE48863 data sets. These differentially expressed genes are mainly involved in the composition of extracellular matrix and the regulation of the Wnt signaling pathway and are closely related to the cell adhesion pathway. CXCL8, COL5A3, COL11A1, and COL12A1 were among the differentially expressed genes and are closely related to the prognosis of UVM. Therefore, the deletion of BAP1 is closely related to poor prognosis of UVM and is a risk factor for UVM metastasis. The potential targets of BAP1 include CXCL8, COL5A3, COL11A1, and COL12A1. It is believed that BAP1 regulates UVM cell adhesion through these four genes and ultimately regulates tumor development and migration.

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Differentially expressed genes and interacting pathways in bladder cancer revealed by bioinformatic analysis

Molecular Medicine Reports ◽

10.3892/mmr.2014.2396 ◽

2014 ◽

Vol 10 (4) ◽

pp. 1746-1752 ◽

Cited By ~ 5

Author(s):

YINZHOU SHEN ◽

XUELEI WANG ◽

YONGCHAO JIN ◽

JIASUN LU ◽

GUANGMING QIU ◽

...

Keyword(s):

Bladder Cancer ◽

Differentially Expressed Genes ◽

Bioinformatic Analysis ◽

Differentially Expressed

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Bioinformatic analysis of differentially expressed genes and pathways in idiopathic pulmonary fibrosis

Annals of Translational Medicine ◽

10.21037/atm-21-4224 ◽

2021 ◽

Vol 0 (0) ◽

pp. 0-0

Author(s):

Nana Li ◽

Lingxiao Qiu ◽

Cheng Zeng ◽

Zeming Fang ◽

Shanshan Chen ◽

...

Keyword(s):

Idiopathic Pulmonary Fibrosis ◽

Pulmonary Fibrosis ◽

Differentially Expressed Genes ◽

Bioinformatic Analysis ◽

Differentially Expressed

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Identification and bioinformatic analysis of differentially expressed genes in pancreatic cancer stem cells

World Chinese Journal of Digestology ◽

10.11569/wcjd.v21.i13.1218 ◽

2013 ◽

Vol 21 (13) ◽

pp. 1218

Author(s):

Jian-Xin Jiang ◽

Shan Gao ◽

Min Wang ◽

Xu Li ◽

Cheng-Yi Sun

Keyword(s):

Pancreatic Cancer ◽

Stem Cells ◽

Cancer Stem Cells ◽

Differentially Expressed Genes ◽

Bioinformatic Analysis ◽

Differentially Expressed ◽

Pancreatic Cancer Stem Cells

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Bioinformatic Analysis: Screening and Identification of Differentially Expressed Genes Modified by m6A in Ovarian Cancer

10.21203/rs.3.rs-111366/v1 ◽

2020 ◽

Author(s):

Huidong Liu ◽

Wen-wen Zhang ◽

Ge Lou

Keyword(s):

Ovarian Cancer ◽

Differentially Expressed Genes ◽

Clinical Sample ◽

Therapeutic Targets ◽

Enrichment Analysis ◽

Underlying Mechanism ◽

Bioinformatic Analysis ◽

Gene Expression Omnibus ◽

Differentially Expressed ◽

Kegg Pathways

Abstract Background: N6-methyladenosine(m6A) is one of the most common RNA modifications that occurs at the nitrogen-6 position of adenine. Emerging evidence has revealed that regulatory functions of m6A play an essential role in the development of cancer. However the study of m6A in ovarian cancer(OC) is still in our infancy. In this work ,we aimed to identify and analysis the differentially expressed genes(DEGs） modified by m6A which can provide new therapeutic targets and key biomarkers in OC.Methods: We downloaded Microarray datasets GSE146553 and GSE124766 from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were identified by GEO2R analysis tools. Subsequently, The DAVID database was used to construct Enrichment analysis of GO and KEGG pathways. Next, the DEGs modified by m6A were identified by m6AVar database. Finally, the functional analysis and clinical sample validation of these genes were verified by ONCOMINE, GEPIA, cBioPortal online platform and Kaplan-Meier Plotter.Results:152 DEGs were selected ,and the DEGs were mainly enriched in extracellular exosome, spindle microtubule, response to hypoxia and cell cycle .And we identified 15 DEGs which were modified by m6A:MAPK10、MXRA5、CHD7、MECOM、SCN7A、GREB、PRUNE2、MX2、TOP2A、JAM2、DST、LAPTM5、CDKN2A、GATM and ANGPTL1. After statistical analysis, two DEGs (SCN7A and GAMT) were selected for detailed study. We revealed that SCN7A and GAMT were expressed at a low level in OC. Afterwards, Survival analysis showed that SCN7A and GAMT expression were correlated with OC overall survival. And the expression of SCN7A and GAMT mRNA decreasing in different TNM stages. Finally, we presumed that the modification of m6A spongs GAMT via EIF4A3 or FUS to participate in the occcurrence and the development of OC.Conclusion: Altogether, the current study identified and analysised the DEGs modified by m6A in OC. It will help us to investigate the underlying mechanism and progression of OC. In addition, it can provide new diagnostic markers and potential therapeutic targets in OC.

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