Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR8798084_1.fastq.gz	Fastqsanger.gz
	SRR8798084_2.fastq.gz	Fastqsanger.gz
	SRR8798085_1.fastq.gz	Fastqsanger.gz
	SRR8798085_2.fastq.gz	Fastqsanger.gz
	SRR8798086_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

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.

Project description:BackgroundRectal adenocarcinoma (READ) is one of the deadliest malignancies, and the molecular mechanisms underlying the initiation and development of READ remain largely unknown. In this study, we aimed to find key long noncoding RNAs (lncRNAs) and mRNAs in READ by RNA sequencing.MethodsRNA sequencing was performed to identify differentially expressed mRNAs (DEmRNAs) and lncRNAs (DElncRNAs) between READ and normal tissue. READ-specific protein-protein interaction (PPI), DElncRNA-DEmRNA coexpression, and DElncRNA-nearby DEmRNA interaction networks were constructed. DEmRNAs and DEmRNAs coexpressed with DElncRNAs were functionally annotated.ResultsA total of 2113 DEmRNAs and 150 DElncRNAs between READ and normal tissue were identified. The PPI network identified several hub proteins, including CDK1, AURKB, CDC6, FOXQ1, NUF2, and TOP2A. The DElncRNA-DEmRNA coexpression and DElncRNA-nearby DEmRNA interaction networks identified some hub lncRNAs, including CCAT1, LOC105374879, GAS5, and B3GALT5-AS1. The colorectal cancer pathway, the intestinal immune network for IgA production and the p53 signaling pathway were three pathways significantly enriched in DEmRNAs and DEmRNAs coexpressed with DElncRNAs. MSH6 coexpressed with two DElncRNAs (LOC105374879 and CASC15) and BCL2 coexpressed with B3GALT5-AS1 were significantly enriched in the colorectal cancer signaling pathway. TNFRSF17 coexpressed with B3GALT5-AS1 was enriched in the intestinal immune network for IgA production. CCNB2 coexpressed with LOC105374879 was enriched in the p53 signaling pathway.ConclusionA total of four DEmRNAs (MSH6, BCL2, TNFRSF17, and CCNB2) and three DElncRNAs (LOC105374879, CASC15, and B3GALT5-AS1) may be involved in the pathogenesis of READ; this data may contribute to understanding the mechanisms of READ and the development of therapeutic strategies for READ.

| S-EPMC6639256 | biostudies-literature

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

Analysis of lncRNAs for the characterization of the response to neoadjuvant chemoradiotherapy

Project description:We investigated the role of lncRNAs to predict the response to preoperative tretament in locally advanced rectal adenocarcinoma

2018-09-01 | GSE116742 | GEO

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

Project description:Transcriptional profiling of early-onset sporadic rectal adenocarcinoma, comparing Wnt- and Wnt+ rectal tumor. Goal was to determine differentially expressed genes between them based on global gene expression.

2017-10-30 | GSE78250 | GEO

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

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.

2017-10-30 | GSE79328 | GEO

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

Project description:Long non-coding RNAs (lncRNAs) play key roles in diverse biological processes. Moreover, the development and progression of cancer often involves the combined actions of several lncRNAs. Here we propose a multi-step method for constructing lncRNA-lncRNA functional synergistic networks (LFSNs) through co-regulation of functional modules having three features: common coexpressed genes of lncRNA pairs, enrichment in the same functional category and close proximity within protein interaction networks. Applied to three cancers, we constructed cancer-specific LFSNs and found that they exhibit a scale free and modular architecture. In addition, cancer-associated lncRNAs tend to be hubs and are enriched within modules. Although there is little synergistic pairing of lncRNAs across cancers, lncRNA pairs involved in the same cancer hallmarks by regulating same or different biological processes. Finally, we identify prognostic biomarkers within cancer lncRNA expression datasets using modules derived from LFSNs. In summary, this proof-of-principle study indicates synergistic lncRNA pairs can be identified through integrative analysis of genome-wide expression data sets and functional information.

| S-EPMC4694810 | biostudies-literature

caArray_EXP-550: TCGA (READ): Analysis of DNA Methylation for rectal adenocarcinoma (READ) Using Illumina Infinium Human DNA Methylation 27 platform (HumanMethylation27)(jhu-usc)

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

2015-05-12 | E-GEOD-68751 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data