Expression and gene regulation network of TYMS and BCL2L1 in colorectal cancer based on data mining

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RT @PeerJLife: Jie et al. @sma_lv analyzed the expression and gene regulation network of TYMS and BCL2L1 in colorectal cancer based on data…
RT @PeerJLife: Jie et al. @sma_lv analyzed the expression and gene regulation network of TYMS and BCL2L1 in colorectal cancer based on data…
Jie et al. @sma_lv analyzed the expression and gene regulation network of TYMS and BCL2L1 in colorectal cancer based on data mining Read the full @PeerJLife article https://t.co/8COZlqLeaR #Bioinformatics #Genetics #Oncology #DataMining https://t.co/t2Rsd7SMZg
Bioinformatics and Genomics

Main article text

 

Introduction

Materials and Methods

Open targets analysis

Expression of TYMS and BCL2L1 in colorectal cancer

C-BioPortal analysis

Survival analysis

Immunohistochemistry analysis

GeneMANIA analysis

Functional annotation of genes interacted with TYMS and BCL2L1

LinkedOmics analysis

qRT-PCR verification

Results

The correlation between TYMS and BCL2L1 and gastrointestinal diseases

Expression of TYMS and BCL2L1 in colorectal cancer

Genomic alterations of TYMS and BCL2L1 in colorectal cancer

Survival analysis of TYMS and BCL2L1 in colorectal cancer

Immunohistochemistry analysis of TYMS and BCL2L1 in colorectal cancer

PPI network and functional annotation of genes interacted with TYMS and BCL2L1

Co-expression genes correlated with TYMS and BCL2L1

qRT-PCR verification

Discussion

Conclusions

Supplemental Information

Co-expression genes with BCL2L1

DOI: 10.7717/peerj.11368/supp-2

Co-expression genes with TYMS

DOI: 10.7717/peerj.11368/supp-3

Additional Information and Declarations

Competing Interests

The authors declare there are no competing interests.

Author Contributions

Yanghua Jie conceived and designed the experiments, analyzed the data, prepared figures and/or tables, and approved the final draft.

Xiaobei Yang performed the experiments, analyzed the data, authored or reviewed drafts of the paper, and approved the final draft.

Weidong Chen conceived and designed the experiments, authored or reviewed drafts of the paper, and approved the final draft.

Human Ethics

The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):

This study was approved by the ethical committee of Affiliated Hospital of traditional Chinese medicine, Xinjiang Medical University.

Ethics

The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):

This study was approved by the ethical committee of Affiliated Hospital of traditional Chinese medicine, Xinjiang Medical University (2019XE0207).

Data Availability

The following information was supplied regarding data availability:

The datasets analyzed for this work are available from public databases: The Cancer Genome Atlas (TCGA) from UCSC Xena (GDC TCGA Colon Cancer (COAD)), The Open Targets Platform (20 diseases associated with BCL2L1, 97 diseases associated with TYMS), The cBio Cancer Genomics Portal (Colorectal Adenocarcinoma (TCGA, PanCancer Atlas)), The Human Protein Atlas (THPA) (ENSG00000176890-TYMS; ENSG00000171552-BCL2L1), GeneMANIA (https://genemania.org/search/homo-sapiens/TYMS/BCL2L1/), the LinkedOmics database and the Gene Expression Omnibus (GEO) (GSE12945 and GSE89076).

- GDC TCGA Colon Cancer (COAD)

https://xenabrowser.net/datapages/?dataset=TCGA-COAD.htseq_counts.tsv&host=https

- 20 diseases associated with BCL2L1

https://www.targetvalidation.org/target/ENSG00000176890/associations?fcts=therapeutic_area:EFO_0010282&view=t:bubbles

- 97 diseases associated with TYMS

https://www.targetvalidation.org/target/ENSG00000171552/associations?fcts=therapeutic_area:EFO_0010282&view=t:bubbles

- Colorectal Adenocarcinoma (TCGA, PanCancer Atlas)

http://www.cbioportal.org/results/oncoprint?genetic_profile_ids_PROFILE_MUTATION_EXTENDED=coadread_tcga_pan_can_atlas_2018_mutations&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=coadread_tcga_pan_can_atlas_2018_gistic&genetic_profile_ids_PROFILE_MRNA_EXPRESSION=coadread_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_Zscores&cancer_study_list=coadread_tcga_pan_can_atlas_2018&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&data_priority=0&profileFilter=0&case_set_id=coadread_tcga_pan_can_atlas_2018_3way_complete&gene_list=TYMS

- ENSG00000176890-TYMS

https://www.proteinatlas.org/ENSG00000176890-TYMS/pathology/colorectal+cancer#img

- ENSG00000171552-BCL2L1

https://www.proteinatlas.org/ENSG00000171552-BCL2L1/pathology/colorectal+cancer#img

- TYMS/BCL2L1

https://genemania.org/search/homo-sapiens/TYMS/BCL2L1/

- LinkedOmics database. Data from this database can be found in the Supplemental Information

http://www.linkedomics.org/login.php

Funding

This work was supported by the Youth Foundation of Natural Science Foundation of Xinjiang Uygur Autonomous Region (2017D01C173). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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