AnnoLnc: a web server for systematically annotating novel human lncRNAs

Hou, Mei; Tang, Xing; Tian, Feng; Shi, Fang-Yuan; Liu, Fenglin; Gao, Ge

doi:10.1186/s12864-016-3287-9

Cited by 51 publications

(26 citation statements)

References 52 publications

(55 reference statements)

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“…Prediction and expression of candidate miRNA with AnnoLnc and starBase database AnnoLnc (http://annolnc.cbi.pku.edu.cn) [23] is a web interface to systematically annotate newly identi ed human lncRNAs based on more than 700 data sources. The systematic annotation of lncRNAs cover a wide range of functions, including genome location, secondary structure, expression pattern, transcriptional regulation, miRNA interaction, protein interaction, genetic association and evolution.…”

Section: Methodsmentioning

confidence: 99%

Identification of long noncoding RNA RP11-89K21.1 and RP11-357H14.17 as prognostic signature of endometrial carcinoma via integrated bioinformatics analysis

Gao

Nie

Zhang

et al. 2020

Preprint

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Background: Endometrial carcinoma (EC) is one of the most common malignant tumors in gynecology. The potential functions and mechanisms of long noncoding RNAs (lncRNAs) in the occurrence and progression of EC remains unclear. It’s meaningful to explore lncRNAs signature for providing prognostic value of EC. Methods：The differentially expressed lncRNAs and their prognostic values in EC were investigated based on The Cancer Genome Atlas (TCGA) database; the transcriptional factors (TFs), the competing endogenous RNA (ceRNA) mechanism, functional regulatory network and immune infiltration of RP11-89K21.1 and RP11-357H14.17 were further explored by various bioinformatics tools and databases. Results: We firstly identified high expression of RP11-89K21.1 and RP11-357H14.17 were closely associated with shorten overall survival (OS) and poor prognosis in patients with EC. We also elucidated the networks of transcription factor and co-expression genes associated with RP11-89K21.1 and RP11-357H14.17. Furthermore, the ceRNA network mechanism was successfully constructed through 2 lncRNAs (RP11-89K21.1 and RP11-357H14.17), 11 miRNAs and 183 mRNAs. Functional enrichment analysis revealed that the targeting genes of RP11-89K21.1 and RP11-357H14.17 were strongly associated with microRNAs in cancer, vessel development, growth regulation, growth factor and cell differentiation, and involved in pathways including pathways in cancer, microRNAs in cancer and apoptotic signaling pathway. Conclusions: We demonstrated for the first time that RP11-89K21.1 and RP11-357H14.17 may play crucial roles in the occurrence, development and malignant biological behavior of EC, and can be regarded as potential prognostic biomarkers for EC.

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Section: Methodsmentioning

confidence: 99%

Identification of long noncoding RNA RP11-89K21.1 and RP11-357H14.17 as prognostic signature of endometrial carcinoma via integrated bioinformatics analysis

Gao

Nie

Zhang

et al. 2020

Preprint

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“…Since the study of lncRNAs is an emerging but growing field, and some lncRNAs can be functionally identified as new transcripts, a consensus for indexing the different aliases needs to be established, a mission covered by several databases, such as LNCipedia [162], NONCODE [163], AnnoLnc [164], lncRNAdb [165] or lncRBase [166], containing annotations and gene information.…”

Section: Bioinformatics Resources For Lncrna Researchmentioning

confidence: 99%

The Challenges and Opportunities of LncRNAs in Ovarian Cancer Research and Clinical Use

Salamini-Montemurri

Lamas-Maceiras

Barreiro-Alonso

et al. 2020

Cancers

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Ovarian cancer is one of the most lethal gynecological malignancies worldwide because it tends to be detected late, when the disease has already spread, and prognosis is poor. In this review we aim to highlight the importance of long non-coding RNAs (lncRNAs) in diagnosis, prognosis and treatment choice, to make progress towards increasingly personalized medicine in this malignancy. We review the effects of lncRNAs associated with ovarian cancer in the context of cancer hallmarks. We also discuss the molecular mechanisms by which lncRNAs become involved in cellular physiology; the onset, development and progression of ovarian cancer; and lncRNAs' regulatory mechanisms at the transcriptional, post-transcriptional and post-translational stages of gene expression. Finally, we compile a series of online resources useful for the study of lncRNAs, especially in the context of ovarian cancer. Future work required in the field is also discussed along with some concluding remarks.

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“…AnnoLnc (http://annolnc.cbi.pku.edu.cn) [22] is a web interface to systematically annotate newly identified human lncRNAs based on more than 700 data sources. The systematic annotation of lncRNAs cover a wide range of functions, including genome location, secondary structure, expression pattern, transcriptional regulation, miRNA interaction, protein interaction, genetic association and evolution.…”

Section: Prediction and Expression Of Candidate Mirna With Annolnc Anmentioning

confidence: 99%

Identification of long noncoding RNA RP11-89K21.1 and RP11-357H14.17 as prognostic signature of endometrial carcinoma via integrated bioinformatics analysis

Gao

Nie

Zhang

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: Endometrial carcinoma (EC) is one of the most common malignant tumors in gynecology. The potential functions and mechanisms of long noncoding RNAs (lncRNAs) in the occurrence and progression of EC remains unclear. It’s meaningful to explore lncRNAs signature for providing prognostic value of EC. Methods：The differentially expressed lncRNAs and their prognostic values in EC were investigated based on The Cancer Genome Atlas (TCGA) database; the transcriptional factors (TFs), the competing endogenous RNA (ceRNA) mechanism, functional regulatory network and immune infiltration of RP11-89K21.1 and RP11-357H14.17 were further explored by various bioinformatics tools and databases. Results: We first identified high expression of RP11-89K21.1 and RP11-357H14.17 were closely associated with shorten overall survival (OS) and poor prognosis in patients with EC. We also elucidated the networks of transcription factor and co-expression genes associated with RP11-89K21.1 and RP11-357H14.17. Furthermore, the ceRNA network mechanism was successfully constructed through 2 lncRNAs (RP11-89K21.1 and RP11-357H14.1), 11 miRNAs and 183 mRNAs. Functional enrichment analysis revealed that the targeting genes of RP11-89K21.1 and RP11-357H14.17 were strongly associated with microRNAs in cancer, vessel development, growth regulation, growth factor and cell differentiation, and involved in pathways including cytokine-mediated signaling pathway, transmembrane receptor protein tyrosine kinase signaling pathway and apoptotic signaling pathway. Moreover, RP11-89K21.1 and RP11-357H14.17 were correlated with immune infiltration including CD8_T cell, CD4_Tcell, Macrophage and Neutrophil. Conclusions: We demonstrated for the first time that RP11-89K21.1 and RP11-357H14.17 may play crucial roles in the occurrence, development and malignant biological behavior of EC, and can be regarded as potential prognostic biomarkers for EC.

show abstract

AnnoLnc: a web server for systematically annotating novel human lncRNAs

Cited by 51 publications

References 52 publications

Identification of long noncoding RNA RP11-89K21.1 and RP11-357H14.17 as prognostic signature of endometrial carcinoma via integrated bioinformatics analysis

Identification of long noncoding RNA RP11-89K21.1 and RP11-357H14.17 as prognostic signature of endometrial carcinoma via integrated bioinformatics analysis

The Challenges and Opportunities of LncRNAs in Ovarian Cancer Research and Clinical Use

Identification of long noncoding RNA RP11-89K21.1 and RP11-357H14.17 as prognostic signature of endometrial carcinoma via integrated bioinformatics analysis

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