Data mining of the cancer-related lncRNAs GO terms and KEGG pathways by using mRMR method.

LncRNAs plays an important role in the regulation of gene expression. Identification of cancer-related lncRNAs GO terms and KEGG pathways is great helpful for revealing cancer-related functional biological processes. Therefore, in this study, we proposed a computational method to identify novel cancer-related lncRNAs GO terms and KEGG pathways. By using existing lncRNA database and Max-relevance Min-redundancy (mRMR) method, GO terms and KEGG pathways were evaluated based on their importance on distinguishing cancer-related and non-cancer-related lncRNAs. Finally, GO terms and KEGG pathways with high importance were presented and analyzed. Our literature reviewing showed that the top 10 ranked GO terms and pathways were really related to interpretable tumorigenesis according to recent publications.

[1]  Xiaoyong Pan,et al.  Discriminating cirRNAs from other lncRNAs using a hierarchical extreme learning machine (H-ELM) algorithm with feature selection , 2017, Zeitschrift für Induktive Abstammungs- und Vererbungslehre.

[2]  Tingting Zhang,et al.  Long Non Coding RNA MALAT1 Promotes Tumor Growth and Metastasis by inducing Epithelial-Mesenchymal Transition in Oral Squamous Cell Carcinoma , 2015, Scientific Reports.

[3]  T. Xia,et al.  Long noncoding RNA associated-competing endogenous RNAs in gastric cancer , 2014, Scientific Reports.

[4]  M. Gribaa,et al.  Partial KCNQ1OT1 hypomethylation: A disguised familial Beckwith–Wiedemann syndrome as a sporadic adrenocortical tumor , 2014, Applied & translational genomics.

[5]  O. Reina,et al.  Inosine modifications in human tRNAs are incorporated at the precursor tRNA level , 2015, Nucleic acids research.

[6]  H. Lodish,et al.  Long noncoding RNAs during normal and malignant hematopoiesis , 2014, International Journal of Hematology.

[7]  P. Kapranov,et al.  The Landscape of long noncoding RNA classification. , 2015, Trends in genetics : TIG.

[8]  Jing Bai,et al.  Identification of cancer-related lncRNAs through integrating genome, regulome and transcriptome features. , 2015, Molecular bioSystems.

[9]  R. Sidman,et al.  PRUNE2 is a human prostate cancer suppressor regulated by the intronic long noncoding RNA PCA3 , 2015, Proceedings of the National Academy of Sciences.

[10]  M. Titmus,et al.  Transport of Neuronal BC1 RNA in Mauthner Axons , 2002, The Journal of Neuroscience.

[11]  S. Efroni,et al.  A novel mitosis-associated lncRNA, MA-linc1, is required for cell cycle progression and sensitizes cancer cells to Paclitaxel , 2015, Oncotarget.

[12]  A. Hochberg,et al.  Oncofetal H19 RNA promotes tumor metastasis. , 2014, Biochimica et biophysica acta.

[13]  Li Liu,et al.  Regulation of lncRNA expression , 2014, Cellular & Molecular Biology Letters.

[14]  Zhiqiang Chen,et al.  Osteogenic growth peptide promotes osteogenic differentiation of mesenchymal stem cells mediated by LncRNA AK141205-induced upregulation of CXCL13. , 2015, Biochemical and biophysical research communications.

[15]  Eugenia G. Giannopoulou,et al.  The oestrogen receptor alpha-regulated lncRNA NEAT1 is a critical modulator of prostate cancer , 2014, Nature Communications.

[16]  Y. Bossé,et al.  Altered DNA Methylation of Long Noncoding RNA H19 in Calcific Aortic Valve Disease Promotes Mineralization by Silencing NOTCH1 , 2016, Circulation.

[17]  J. Mcneil,et al.  XIST RNA paints the inactive X chromosome at interphase: evidence for a novel RNA involved in nuclear/chromosome structure , 1996, The Journal of cell biology.

[18]  H. Nagase,et al.  Pyrrole-imidazole polyamide-mediated silencing of KCNQ1OT1 expression induces cell death in Wilms' tumor cells. , 2015, International journal of oncology.

[19]  Tao Huang,et al.  Analysis of cancer-related lncRNAs using gene ontology and KEGG pathways , 2017, Artif. Intell. Medicine.

[20]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

[21]  Lisong Shen,et al.  Activation of TLR4 signaling promotes gastric cancer progression by inducing mitochondrial ROS production , 2013, Cell Death and Disease.

[22]  S. Fedewa,et al.  Cancer screening in the United States, 2015: A review of current American Cancer Society guidelines and current issues in cancer screening , 2015, CA: a cancer journal for clinicians.

[23]  Yu-Dong Cai,et al.  Analysis and Prediction of Nitrated Tyrosine Sites with the mRMR Method and Support Vector Machine Algorithm , 2016 .

[24]  Juan Li,et al.  The long noncoding RNA SPRY4-IT1 increases the proliferation of human breast cancer cells by upregulating ZNF703 expression , 2015, Molecular Cancer.

[25]  Y. Jiao,et al.  Warburg meets non-coding RNAs: the emerging role of ncRNA in regulating the glucose metabolism of cancer cells , 2014, Tumor Biology.

[26]  E. Kopczynska.  The potential therapeutic applications and prognostic significance of metastasis-associated in colon cancer-1 (MACC1) in cancers , 2016, Contemporary oncology.

[27]  K. Książek,et al.  The double-edged sword of long non-coding RNA: The role of human brain-specific BC200 RNA in translational control, neurodegenerative diseases, and cancer. , 2015, Mutation research. Reviews in mutation research.

[28]  Yulun Huang,et al.  Tumor-suppressive function of long noncoding RNA MALAT1 in glioma cells by downregulation of MMP2 and inactivation of ERK/MAPK signaling , 2016, Cell Death and Disease.

[29]  A. Sadanandam,et al.  Molecular or Metabolic Reprograming: What Triggers Tumor Subtypes? , 2016, Cancer research.

[30]  P. Porporato,et al.  (+)-Catechin in a 1:2 Complex with Lysine Inhibits Cancer Cell Migration and Metastatic Take in Mice , 2017, Frontiers in Pharmacology.

[31]  Jian Zhang,et al.  Whole exome sequencing identifies lncRNA GAS8-AS1 and LPAR4 as novel papillary thyroid carcinoma driver alternations. , 2016, Human molecular genetics.

[32]  J. Lawrence,et al.  Stable C0T-1 Repeat RNA Is Abundant and Is Associated with Euchromatic Interphase Chromosomes , 2014, Cell.

[33]  Simon W. Jones,et al.  Transcriptional profiling identifies differential expression of long non-coding RNAs in Jo-1 associated and inclusion body myositis , 2017, Scientific Reports.

[34]  N. Brockdorff.  SAT in silence. , 2009, Developmental cell.

[35]  Lu Xie,et al.  SySAP: a system-level predictor of deleterious single amino acid polymorphisms , 2011, Protein & Cell.

[36]  David R. Kelley,et al.  Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks , 2012, Nature Protocols.

[37]  Jiandie D. Lin,et al.  Conserved function of the long noncoding RNA Blnc1 in brown adipocyte differentiation , 2016, Molecular Metabolism.

[38]  Young-Jin Choi,et al.  Proteogenomic Study beyond Chromosome 9: New Insight into Expressed Variant Proteome and Transcriptome in Human Lung Adenocarcinoma Tissues. , 2015, Journal of proteome research.

[39]  Yu-Dong Cai,et al.  The Use of Gene Ontology Term and KEGG Pathway Enrichment for Analysis of Drug Half-Life , 2016, PloS one.

[40]  Lysine methyltransferase SMYD2 promotes triple negative breast cancer progression , 2018, Cell Death & Disease.

[41]  Wei Zhang,et al.  miR675 upregulates long noncoding RNA H19 through activating EGR1 in human liver cancer , 2015, Oncotarget.

[42]  T. Dittmar,et al.  Lipopolysaccharide (LPS) Promotes Apoptosis in Human Breast Epithelial × Breast Cancer Hybrids, but Not in Parental Cells , 2016, PloS one.

[43]  Xue-Qing Zhang,et al.  Long noncoding RNA lnc-RI is a new regulator of mitosis via targeting miRNA-210-3p to release PLK1 mRNA activity , 2016, Scientific Reports.

[44]  Guodong Yang,et al.  LncRNA: a link between RNA and cancer. , 2014, Biochimica et biophysica acta.

[45]  Lai Wei,et al.  Prediction of Nitrated Tyrosine Residues in Protein Sequences by Extreme Learning Machine and Feature Selection Methods. , 2018, Combinatorial chemistry & high throughput screening.

[46]  Chen Chu,et al.  Gene Ontology and KEGG Pathway Enrichment Analysis of a Drug Target-Based Classification System , 2015, PloS one.

[47]  R. Tamimi,et al.  Established breast cancer risk factors and risk of intrinsic tumor subtypes. , 2015, Biochimica et biophysica acta.

[48]  Yu-Dong Cai,et al.  Prediction of protein-peptide interaction with nearest neighbor algorithm , 1969 .

[49]  Lei Chen,et al.  Analysis of Tumor Suppressor Genes Based on Gene Ontology and the KEGG Pathway , 2014, PloS one.

[50]  Jing Lu,et al.  Analysis and Identification of Aptamer-Compound Interactions with a Maximum Relevance Minimum Redundancy and Nearest Neighbor Algorithm , 2016, BioMed research international.

[51]  Yu Zhang,et al.  c-Myc-activated long non-coding RNA H19 downregulates miR-107 and promotes cell cycle progression of non-small cell lung cancer. , 2015, International journal of clinical and experimental pathology.

[52]  Jian-zhong Wu,et al.  Long noncoding RNA SPRY4-IT1 predicts poor patient prognosis and promotes tumorigenesis in gastric cancer , 2015, Tumor Biology.

[53]  A. Rebollo,et al.  Deregulation of Aiolos expression in chronic lymphocytic leukemia is associated with epigenetic modifications. , 2011, Blood.

[54]  Guoxiong Xu,et al.  Clinical value of lncRNA MALAT1 as a prognostic marker in human cancer: systematic review and meta-analysis , 2015, BMJ Open.

[55]  Mei Xue,et al.  Long non-coding RNA UCA1 promotes glycolysis by upregulating hexokinase 2 through the mTOR–STAT3/microRNA143 pathway , 2014, Cancer science.

[56]  L. Bi,et al.  Quantitative Proteomics Analysis Reveals Novel Insights into Mechanisms of Action of Long Noncoding RNA Hox Transcript Antisense Intergenic RNA (HOTAIR) in HeLa Cells* , 2015, Molecular & Cellular Proteomics.

[57]  Wenbo Li,et al.  Down-regulation of LncRNA TUG1 enhances radiosensitivity in bladder cancer via suppressing HMGB1 expression , 2017, Radiation Oncology.

[58]  Morgan C. Giddings,et al.  High-Throughput SHAPE Analysis Reveals Structures in HIV-1 Genomic RNA Strongly Conserved across Distinct Biological States , 2008, PLoS biology.

[59]  Yuquan Wei,et al.  Long Noncoding RNA LINC00092 Acts in Cancer-Associated Fibroblasts to Drive Glycolysis and Progression of Ovarian Cancer. , 2017, Cancer research.

[60]  F. Major,et al.  Noncoding regions of C. elegans mRNA undergo selective adenosine to inosine deamination and contain a small number of editing sites per transcript , 2015, RNA biology.

[61]  Xiaoyong Pan,et al.  Gene expression differences among different MSI statuses in colorectal cancer , 2018, International journal of cancer.

[62]  Susumu Goto,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 2000, Nucleic Acids Res..

[63]  Chen Chu,et al.  Predicting the types of metabolic pathway of compounds using molecular fragments and sequential minimal optimization. , 2016, Combinatorial chemistry & high throughput screening.

[64]  Zhi-ping Chen,et al.  RP5-833A20.1/miR-382-5p/NFIA–Dependent Signal Transduction Pathway Contributes to the Regulation of Cholesterol Homeostasis and Inflammatory Reaction , 2015, Arteriosclerosis, thrombosis, and vascular biology.

[65]  Wei Hao,et al.  Long non‐coding RNA MALAT1 functions as a mediator in cardioprotective effects of fentanyl in myocardial ischemia‐reperfusion injury , 2017, Cell biology international.

[66]  Peilong Li,et al.  Role of TGFBIp in Wound Healing and Mucin Expression in Corneal Epithelial Cells , 2017, Yonsei medical journal.

[67]  Majid Mohammad Beigi,et al.  Prediction of allergenic proteins by means of the concept of Chou's pseudo amino acid composition and a machine learning approach. , 2012 .

[68]  Minoru Kanehisa,et al.  KEGG as a reference resource for gene and protein annotation , 2015, Nucleic Acids Res..

[69]  Juancarlos Chan,et al.  Gene Ontology Consortium: going forward , 2014, Nucleic Acids Res..

[70]  B. Stewart,et al.  World cancer report 2014. , 2014 .

[71]  W. Gu,et al.  Downregulation of a long noncoding RNA-ncRuPAR contributes to tumor inhibition in colorectal cancer , 2014, Tumor Biology.

[72]  Tao Huang,et al.  Identification of the core regulators of the HLA I-peptide binding process , 2017, Scientific Reports.

[73]  Lai Wei,et al.  Analysis and prediction of drug–drug interaction by minimum redundancy maximum relevance and incremental feature selection , 2017, Journal of biomolecular structure & dynamics.

[74]  Wentian Li.  Mutual information functions versus correlation functions , 1990 .

[75]  Jun Shen,et al.  Expression and regulation of long noncoding RNAs in TLR4 signaling in mouse macrophages , 2015, BMC Genomics.

[76]  Y. Nie,et al.  Long non-coding RNA RP5-833A20.1 inhibits proliferation, metastasis and cell cycle progression by suppressing the expression of NFIA in U251 cells. , 2016, Molecular medicine reports.

[77]  Yongqing Xu,et al.  Silencing of Long Non-Coding RNA NONHSAT009968 Ameliorates the Staphylococcal Protein A-Inhibited Osteogenic Differentiation in Human Bone Mesenchymal Stem Cells , 2016, Cellular Physiology and Biochemistry.

[78]  Jennifer B Dennison,et al.  Long Noncoding RNA Ceruloplasmin Promotes Cancer Growth by Altering Glycolysis. , 2015, Cell reports.

[79]  Tao Huang,et al.  Identification of compound–protein interactions through the analysis of gene ontology, KEGG enrichment for proteins and molecular fragments of compounds , 2016, Molecular Genetics and Genomics.

[80]  D. Karolchik,et al.  The UCSC Genome Browser database: 2016 update , 2015, bioRxiv.

[81]  Antoine H. F. M. Peters,et al.  Polycomb group proteins Ezh2 and Rnf2 direct genomic contraction and imprinted repression in early mouse embryos. , 2008, Developmental cell.

[82]  Li Zhang,et al.  The lncRNA H19 promotes epithelial to mesenchymal transition by functioning as miRNA sponges in colorectal cancer , 2015, Oncotarget.

[83]  B. Long,et al.  CARL lncRNA inhibits anoxia-induced mitochondrial fission and apoptosis in cardiomyocytes by impairing miR-539-dependent PHB2 downregulation , 2014, Nature Communications.

[84]  Junfeng Geng,et al.  Combined identification of long non-coding RNA XIST and HIF1A-AS1 in serum as an effective screening for non-small cell lung cancer. , 2015, International journal of clinical and experimental pathology.

[85]  Lei Chen,et al.  A Feature and Algorithm Selection Method for Improving the Prediction of Protein Structural Class. , 2017, Combinatorial chemistry & high throughput screening.

[86]  Xuan Zhou,et al.  Classification of G-protein coupled receptors based on support vector machine with maximum relevance minimum redundancy and genetic algorithm , 2010, BMC Bioinformatics.

[87]  Wei Zhao,et al.  The Functional Characterization of Long Noncoding RNA SPRY4-IT1 in Human Melanoma Cells , 2014, Oncotarget.

[88]  S. Tsuji,et al.  Molecular Cloning and Expression of a Fifth Type of α2,8-Sialyltransferase (ST8Sia V) , 1996, The Journal of Biological Chemistry.

[89]  Hongzhe Li,et al.  A functional genomic approach identifies FAL1 as an oncogenic long noncoding RNA that associates with BMI1 and represses p21 expression in cancer. , 2014, Cancer cell.

[90]  Lei Chen,et al.  Analysis and Prediction of Myristoylation Sites Using the mRMR Method, the IFS Method and an Extreme Learning Machine Algorithm. , 2017, Combinatorial chemistry & high throughput screening.

[91]  Jialiang Yang,et al.  Identify Key Sequence Features to Improve CRISPR sgRNA Efficacy , 2017, IEEE Access.

[92]  Minati Singh.  Dysregulated A to I RNA editing and non-coding RNAs in neurodegeneration , 2013, Front. Gene..

[93]  Fuhui Long,et al.  Feature selection based on mutual information criteria of max-dependency, max-relevance, and min-redundancy , 2003, IEEE Transactions on Pattern Analysis and Machine Intelligence.

[94]  H. Aburatani,et al.  Novel lnc RNA regulated by HIF‐1 inhibits apoptotic cell death in the renal tubular epithelial cells under hypoxia , 2017, Physiological reports.

[95]  Lingling Wu,et al.  Identification of the long noncoding RNA NEAT1 as a novel inflammatory regulator acting through MAPK pathway in human lupus. , 2016, Journal of autoimmunity.

[96]  Zhenggang Zhu,et al.  Overexpression of lncRNA H19 enhances carcinogenesis and metastasis of gastric cancer , 2014, Oncotarget.

[97]  Lei Chen,et al.  Gene expression profiling gut microbiota in different races of humans , 2016, Scientific Reports.

[98]  Yongfeng Jin,et al.  ADAR-mediated RNA editing in non-coding RNA sequences , 2013, Science China Life Sciences.

[99]  David Haussler,et al.  Current status and new features of the Consensus Coding Sequence database , 2013, Nucleic Acids Res..

[100]  Lennart Martens,et al.  LNCipedia: a database for annotated human lncRNA transcript sequences and structures , 2012, Nucleic Acids Res..

[101]  Xing Chen,et al.  LncRNADisease: a database for long-non-coding RNA-associated diseases , 2012, Nucleic Acids Res..

[102]  Mark A. Hall,et al.  Myc suppression of Nfkb2 accelerates lymphomagenesis , 2010, BMC Cancer.

[103]  G. Mills,et al.  Comprehensive Genomic Characterization of Long Non-coding RNAs across Human Cancers. , 2015, Cancer cell.

[104]  Zhuo Xi,et al.  Knockdown of long non-coding RNA XIST exerts tumor-suppressive functions in human glioblastoma stem cells by up-regulating miR-152. , 2015, Cancer letters.

[105]  C. Deal,et al.  H19 sense and antisense transgenes modify insulin-like growth factor-II mRNA levels. , 2000, European journal of biochemistry.