Identification of Potential Long Non-Coding RNA Candidates that Contribute to Triple-Negative Breast Cancer in Humans through Computational Approach
Abstract
:1. Introduction
2. Results
2.1. Identification of lncRNA Transcripts
2.2. Expression Profiles of lncRNAs and mRNAs
2.3. Differential Expression Analysis of lncRNAs and mRNAs
2.4. Analysis of lncRNA-miRNA-Gene Interaction
2.5. GO Term and KEGG Pathway Enrichment Analysis
3. Discussion
4. Materials and Methods
4.1. Data Collection
4.2. Quality Control, Mapping, and Transcript Assembly
4.3. Transcripts Filtration
4.4. Assessment of the Coding Potential
4.5. Differential Expression Analysis
4.6. GO and KEGG Enrichment Analysis
4.7. LncRNA–miRNA-Gene Interaction Network Analysis
5. Conclusions
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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mRNA ID | Location | No. of Exons | Length | Base Mean | LFC | p-Value | Gene |
---|---|---|---|---|---|---|---|
TCONS_00027847 | chr16:72054592-72061056 | 7 | 1448 | 3419.94 | Inf | 0.00041 | HP |
TCONS_00062848 | chr5:150401637-150412936 | 9 | 1681 | 2201.54 | Inf | 0.00058 | CD74 |
TCONS_00027845 | chr16:72054592-72061056 | 5 | 1271 | 2210.50 | Inf | 0.00058 | HP |
TCONS_00062849 | chr5:150401637-150412936 | 8 | 1489 | 2166.03 | Inf | 0.00058 | CD74 |
TCONS_00037794 | chr19:6677835-6720682 | 41 | 5132 | 2131.98 | Inf | 0.00059 | C3 |
TCONS_00027846 | chr16:72054592-72061056 | 5 | 1271 | 2125.11 | Inf | 0.00060 | HP |
TCONS_00030302 | chr17:34255277-34257201 | 3 | 747 | 1907.13 | Inf | 0.00067 | CCL2 |
TCONS_00008098 | chr10:58513144-58831437 | 21 | 5471 | 1317.61 | Inf | 0.00087 | BICC1 |
TCONS_00062847 | chr5:150401637-150412936 | 6 | 1305 | 1274.15 | Inf | 0.00089 | CD74 |
TCONS_00005374 | chr1:89052304-89065360 | 11 | 3050 | 1164.10 | Inf | 0.00096 | GBP1 |
TCONS_00065563 | chr6:27866792-27867581 | 1 | 790 | 301.37 | −12.6 | 8.98 × 10−06 | HIST1H1B |
TCONS_00028779 | chr16:30104810-30113557 | 10 | 1098 | 105.09 | −Inf | 1.25 × 10−05 | GDPD3 |
TCONS_00010969 | chr10:128096661-128126204 | 14 | 11,415 | 114.64 | −Inf | 1.44 × 10−05 | MKI67 |
TCONS_00010970 | chr10:128096661-128126204 | 15 | 12,495 | 119.33 | −Inf | 1.45 × 10−05 | MKI67 |
TCONS_00012090 | chr11:62270155-62273157 | 3 | 506 | 117.08 | −Inf | 1.80 × 10−05 | SCGB2A2 |
TCONS_00031424 | chr17:79778178-79787650 | 5 | 4265 | 42.19 | −Inf | 1.84 × 10−05 | CBX2 |
TCONS_00082965 | chrX:154651972-154653579 | 3 | 764 | 24.78 | −Inf | 1.85 × 10−05 | CTAG2 |
TCONS_00054384 | chr3:170037947-170085395 | 4 | 2013 | 18.08 | −Inf | 2.11 × 10−05 | GPR160 |
TCONS_00082964 | chrX:154651972-154653579 | 2 | 993 | 20.37 | −Inf | 2.50 × 10−05 | CTAG2 |
TCONS_00018204 | chr12:52806543-52814116 | 9 | 2147 | 45.76 | −14.4 | 2.61 × 10−05 | KRT4 |
lncRNA ID | Location | No. of Exons | Length | Base Mean | LFC | p-Value | Gene |
---|---|---|---|---|---|---|---|
TCONS_00057817 | chr4:78645994-78684501 | 4 | 4214 | 362.9557 | Inf | 0.00254 | LINC01094 |
TCONS_00057819 | chr4:78645994-78684501 | 3 | 4120 | 352.7188 | Inf | 0.00260 | LINC01094 |
TCONS_00057820 | chr4:78645994-78684501 | 3 | 4105 | 345.6054 | Inf | 0.00263 | LINC01094 |
TCONS_00057818 | chr4:78645994-78684501 | 4 | 4192 | 339.0413 | Inf | 0.00266 | LINC01094 |
TCONS_00057821 | chr4:78645994-78684501 | 3 | 4066 | 338.1632 | Inf | 0.00268 | LINC01094 |
TCONS_00057816 | chr4:78645994-78684501 | 5 | 4286 | 331.5815 | Inf | 0.00270 | LINC01094 |
TCONS_00006590 | chr1:169690665-169708856 | 7 | 2206 | 176.9738 | Inf | 0.00426 | SELL |
TCONS_00062278 | chr5:91368632-91383373 | 8 | 4332 | 208.4584 | Inf | 0.00443 | ARRDC3 |
TCONS_00062275 | chr5:91368632-91380297 | 8 | 4621 | 200.0444 | Inf | 0.00463 | ARRDC3 |
TCONS_00009315 | chr10:17214239-17229985 | 3 | 1875 | 121.2627 | Inf | 0.00557 | VIM-AS1 |
TCONS_00082872 | chrX:152708261-152714549 | 5 | 825 | 2.665319 | −Inf | 0.00012 | CSAG3 |
TCONS_00081533 | chrX:152753921-152760222 | 5 | 825 | 2.704539 | −Inf | 0.00018 | CSAG3 |
TCONS_00035347 | chr19:751113-764319 | 4 | 1048 | 12.04587 | −Inf | 0.00025 | MISP |
TCONS_00017579 | chr12:6848808-6851930 | 5 | 1615 | 5.361052 | −Inf | 0.00076 | CDCA3 |
TCONS_00017578 | chr12:6848808-6851930 | 6 | 1792 | 5.745075 | −Inf | 0.00085 | CDCA3 |
TCONS_00012837 | chr11:111912736-111926871 | 5 | 1527 | 30.57432 | −Inf | 0.00105 | HSPB2-C11orf52 |
TCONS_00024012 | chr15:43593834-43599406 | 9 | 2842 | 10.85619 | −11.3 | 0.00140 | CKMT1B |
TCONS_00081534 | chrX:152753921-152760222 | 5 | 789 | 0.786254 | −Inf | 0.00198 | CSAG3 |
TCONS_00082873 | chrX:152708261-152714549 | 5 | 789 | 0.968629 | −Inf | 0.00266 | CSAG3 |
TCONS_00082981 | chrX:155061625-155071272 | 6 | 2755 | 2.456605 | −Inf | 0.00322 | MTCP1 |
lncRNA ID | Location | No. of Exons | Length | Base Mean | LFC | p-Value | Gene |
---|---|---|---|---|---|---|---|
TCONS_00076394 | chr8:102648777-102655902 | 4 | 2309 | 36.34 | Inf | 0.0146 | KLF10 |
TCONS_00002947 | chr1:182789449-182830384 | 11 | 2728 | 32.38 | Inf | 0.0391 | NPL |
TCONS_00051377 | chr22:17734140-17774665 | 5 | 1901 | 9.47 | Inf | 0.0434 | BID |
TCONS_00082872 | chrX:152708261-152714549 | 5 | 825 | 2.67 | −Inf | 0.0001 | CSAG3 |
TCONS_00081533 | chrX:152753921-152760222 | 5 | 825 | 2.70 | −Inf | 0.0002 | CSAG3 |
TCONS_00082981 | chrX:155061625-155071272 | 6 | 2755 | 2.46 | −Inf | 0.0032 | MTCP1 |
TCONS_00026822 | chr16:4788397-4796491 | 6 | 883 | 22.91 | −7.6 | 0.0033 | SMIM22 |
TCONS_00049160 | chr20:47298126-47356889 | 5 | 1346 | 2.07 | −3.5 | 0.0076 | ZMYND8 |
TCONS_00054549 | chr3:184361714-184368595 | 5 | 1723 | 4.02 | −6.8 | 0.0220 | POLR2H |
TCONS_00054548 | chr3:184361714-184368595 | 6 | 1871 | 4.60 | −5.9 | 0.0233 | POLR2H |
GO/Pathway ID | GO/Pathway Name | No. of Genes | p-Value |
---|---|---|---|
Biological Process | |||
GO:0051781 | Positive regulation of cell division | 3 | 0.0036 |
GO:0030593 | Neutrophil chemotaxis | 3 | 0.0070 |
GO:0006600 | Creatine metabolic process | 2 | 0.0208 |
GO:0001934 | Positive regulation of protein phosphorylation | 3 | 0.0243 |
GO:0042832 | Defense response to protozoan | 2 | 0.0356 |
GO:0008285 | Negative regulation of cell proliferation | 4 | 0.0390 |
Cellular Component | |||
GO:0005743 | Mitochondrial inner membrane | 4 | 0.0449 |
Molecular Function | |||
GO:0016772 | Transferase activity, transferring phosphorus-containing groups | 2 | 0.0094 |
GO:0016301 | Kinase activity | 4 | 0.0105 |
GO:0004111 | Creatine kinase activity | 2 | 0.0113 |
GO:0008083 | Growth factor activity | 3 | 0.0376 |
KEGG pathway | |||
hsa05215 | Prostate cancer | 3 | 0.0265 |
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Rahman, M.M.; Hossain, M.T.; Reza, M.S.; Peng, Y.; Feng, S.; Wei, Y. Identification of Potential Long Non-Coding RNA Candidates that Contribute to Triple-Negative Breast Cancer in Humans through Computational Approach. Int. J. Mol. Sci. 2021, 22, 12359. https://doi.org/10.3390/ijms222212359
Rahman MM, Hossain MT, Reza MS, Peng Y, Feng S, Wei Y. Identification of Potential Long Non-Coding RNA Candidates that Contribute to Triple-Negative Breast Cancer in Humans through Computational Approach. International Journal of Molecular Sciences. 2021; 22(22):12359. https://doi.org/10.3390/ijms222212359
Chicago/Turabian StyleRahman, Md. Motiar, Md. Tofazzal Hossain, Md. Selim Reza, Yin Peng, Shengzhong Feng, and Yanjie Wei. 2021. "Identification of Potential Long Non-Coding RNA Candidates that Contribute to Triple-Negative Breast Cancer in Humans through Computational Approach" International Journal of Molecular Sciences 22, no. 22: 12359. https://doi.org/10.3390/ijms222212359