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Screening key lncRNAs for human rectal adenocarcinoma based on lncRNA-mRNA functional synergistic network

ABSTRACT: Screening key lncRNAs for human rectal adenocarcinoma based on lncRNA-mRNA functional synergistic network

PROVIDER: PRJNA529589 | ENA |

REPOSITORIES: ENA

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Screening key lncRNAs for human rectal adenocarcinoma based on lncRNA-mRNA functional synergistic network

Project description:The purpose of this project was to find key long non-coding RNAs and mRNAs in rectal adenocarcinoma. RNA-sequencing was performed to identify the differentially expressed mRNAs (DEmRNAs) and lncRNAs (DElncRNAs) in rectal adenocarcinoma compared to normal tissue.

2020-04-13 | GSE128969 | GEO

Screening key lncRNAs for human rectal adenocarcinoma based on lncRNA-mRNA functional synergistic network.

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Identification of differentially expressed key-lncRNAs in lung adenocarcinoma

Project description:Lung cancer is a heterogeneous disease with high mortality rate globally. Lung adenocarcinoma (ADC) is the most common histological subtype of lung cancer. Multiple studies indicate that lncRNAs emerge as a novel class of critical regulators of cancer. However, the expression of lncRNAs has not been comprehensively surveyed in ADC at a genome-wide scale. Herein we examined landscapes of the lncRNAs and their potential target genes in an integrative fashion in ADC. The differences expression level of lncRNAs and mRNA were determined by microarray. qRT-PCR was performed to validate the lncRNAs expression level in a cohort of 42 tumor tissues and adjacent normal lung tissues. R and Bioconductor were used for data analysis. TF-lncRNAs-gene networks were generated by Cytoscape software. A total of 3045 lncRNAs were differentially expressed between tumor and normal tissues (1048 up and 1997 down). The qRT-PCR of 9 lncRNAs results showed that the expression patterns of these lncRNAs were consistent with the microarray data. Meanwhile, we find NONHSAT077036 expression was associated with N classification and clinical stage. Further, we analyzed the potential co-regulatory relationship between the lncRNAs and target genes using the ‘cis’ and ‘trans’ model. In the 25 related transcription factors (TFs), our analysis in TCGA database found that patients with lower expression of POU2F2 and higher expression of TRIM28 had a shorter overall survival time, suggesting that POU2F2 and TRIM28 could be biomarkers for poor prognosis of ADC. Hence, “POU2F2-lncRNAs” “TRIM28-lncRNAs” two element networks and “POU2F2-lncRNAs-mRNAs” “TRIM28-lncRNAs-mRNAs” there element relationship tables were generated.

2017-02-01 | GSE85716 | GEO

Expression data of LncRNA from Human rectal cancer tissues and adjacent non-cancerous tissues

Project description:Rectal carcinoma(RC) is one of the most common malignant tumor of the digestive tract in humans.Long non-coding RNA (lncRNA) plays a vital role in tumor regulation.Nevertheless, the exact expression features and functions of lncRNAs are still obscure.To investigate aberrantly expressed lncRNAs and mRNAs in RC, we screened the crucial differentially expressed lncRNA and mRNA in RC tissues and paire-matched adjacent non-cancerous tissues.These differentially expressed lncrnas are likely to play a key role in the tumorigenesis and development of RC, and may be used as a novel tumor biomarker for the diagnosis or prognosis of RC. We used Affymetrix human GeneChip to screen the candidate differentially expressed lncRNAs and mRNAs in RC tissues and paire-matched adjacent non-cancerous tissues.Subsequently, the candidate differentially expressed lncRNAs and mRNAs were verified by qRT-PCR.

2019-11-02 | GSE139814 | GEO

Human rectal adenoma (8 cases) vs. rectal carcinoma (8 cases)

Project description:Genomic profiling of human rectal adenoma and carcinoma by array-based comparative genomic hybridization Two group experiment, rectal adenoma vs. rectal carcinoma. Biological replicates: 8 adenomas vs. 8 carcinomas

2011-12-20 | E-GEOD-34472 | biostudies-arrayexpress

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Early-onset sporadic rectal cancer : Wnt- vs. Wnt+ rectal tumor [GE]

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Project description:Copy number profiling of early-onset sporadic rectal adenocarcinoma, comparing Wnt- and Wnt+ rectal tumor. Goal was to determine differentially altered genes between them based on global copy no.

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Construction and analysis of lncRNA-lncRNA synergistic networks to reveal clinically relevant lncRNAs in cancer.

Project description: Not available

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Project description:TCGA Analysis of DNA Methylation for rectal adenocarcinoma (READ) Using Illumina Infinium Human DNA Methylation 27 platform EXP-550 Assay Type: Methylation Provider: Illumina Array Designs: jhu-usc.edu_OV.HumanMethylation27.v2 Organism: home sapiens (ncbitax) Tissue Sites: rectal Material Types: Primary solid_tumor, Control Cell Line, organism_part, Solid normal_tissue Disease States: Rectal Adenocarcinoma, NOT SPECIFIED, [Not Available], Rectal Mucinous Adenocarcinoma

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