IGDB.NSCLC: integrated genomic database of non-small cell lung cancer

Kao, Sen Yeong; Shiau, Cheng-Kai; Gu, De-Leung; Ho, Chun-Ming; Su, Wen; Chen, Chian-Feng; Lin, Chi‐Hung; Jou, Yuh–Shan

doi:10.1093/nar/gkr1183

Cited by 25 publications

(17 citation statements)

References 44 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Down-regulated miR-27a might can also reverse multidrug resistance of esophageal squamous cell carcinoma [46]. Although the expression of miR-27a has been reported to be significantly reduced in both tissue and serum samples of NSCLC patients [26], [47], a relatively higher level of miR-27a expression was observed with the rs895819 G allele compared to the A allele [22]. These evidence may partly support our findings.…”

Section: Discussionsupporting

confidence: 84%

See 1 more Smart Citation

A Genetic Polymorphism in pre-miR-27a Confers Clinical Outcome of Non-Small Cell Lung Cancer in a Chinese Population

Yin

Shen

et al. 2013

PLoS ONE

View full text Add to dashboard Cite

BackgroundRecent evidence indicates that microRNAs (miRNAs) can function as tumor suppressors and oncogenes. Single nucleotide polymorphisms (SNPs) at miRNA genes can influence the maturation of miRNAs or miRNA-mediated transcriptional regulation. Our objective was to investigate the association of SNPs in deregulated miRNAs with clinical outcome in patients with non-small cell lung cancer (NSCLC) in a Chinese population.MethodsDeregulated miRNAs in NSCLC and their SNPs were identified through public databases. A single SNP, rs895819 in pre-miR-27a, was found suitable for selection. TaqMan assays were performed for genotyping and to assess the effect on the overall survival (OS) and chemotherapy response in 576 NSCLC patients.ResultsLog-rank test and Cox regression analysis indicated that the G allele of rs895819 was associated with shorter survival and increased risk of death in NSCLC [dominant model: 22.0 vs. 46.0 months, P<0.001; adjusted hazard ratio (HR) = 1.71, 95% confidential interval (CI): 1.12–2.26]. Further stepwise regression analysis suggested that this SNP was an independently unfavorable factor for the prognosis of NSCLC and the effect remained significant in subgroup analysis stratified by clinical parameters and treatment status. Moreover, multivariate logistic regression analysis showed that the subjects with AG/GG genotypes of rs895819 had significantly decreased response rate to platinum-based chemotherapy compared to those with the AA genotype.ConclusionOur results suggest that the pre-miR-27a rs895819 polymorphism may influence NSCLC patients’ clinical outcome. Further large sample studies should be used to validate our findings.

show abstract

Section: Discussionsupporting

confidence: 84%

“…The IGDB.NSCLC database (http://igdb.nsclc.ibms.sinica.edu.tw) [26] was used to identify deregulated miRNAs in NSCLC. A total of 28 up-regulated miRNAs in amplified regions and 28 down-regulated miRNAs in deleted regions were found.…”

Section: Resultsmentioning

confidence: 99%

A Genetic Polymorphism in pre-miR-27a Confers Clinical Outcome of Non-Small Cell Lung Cancer in a Chinese Population

Yin

Shen

et al. 2013

PLoS ONE

View full text Add to dashboard Cite

show abstract

“…We found that there were five common FFLs altered in both subtypes of NSCLC, involving E2F1_hsa-miR-195-5p_CCNE1, E2F1_hsa-let-7a-5p_AURKB, E2F1_hsa-miR-92a-3p_BCL2L11, EGR1_hsa-miR-30a-5p_GNAQ and SPI1_hsa-miR-146a-5p_TLR4. Most of the genes and miRNAs in these five FFLs had been examined and are aberrantly expressed in NSCLC [53]. …”

Section: Resultsmentioning

confidence: 99%

Systematic dissection of dysregulated transcription factor–miRNA feed-forward loops across tumor types

Jiang¹,

Mitra²,

Chen³

et al. 2015

Briefings in Bioinformatics

View full text Add to dashboard Cite

Transcription factor and microRNA (miRNA) can mutually regulate each other and jointly regulate their shared target genes to form feed-forward loops (FFLs). While there are many studies of dysregulated FFLs in a specific cancer, a systematic investigation of dysregulated FFLs across multiple tumor types (pan-cancer FFLs) has not been performed yet. In this study, using The Cancer Genome Atlas data, we identified 26 pan-cancer FFLs, which were dysregulated in at least five tumor types. These pan-cancer FFLs could communicate with each other and form functionally consistent subnetworks, such as epithelial to mesenchymal transition-related subnetwork. Many proteins and miRNAs in each subnetwork belong to the same protein and miRNA family, respectively. Importantly, cancer-associated genes and drug targets were enriched in these pan-cancer FFLs, in which the genes and miRNAs also tended to be hubs and bottlenecks. Finally, we identified potential anticancer indications for existing drugs with novel mechanism of action. Collectively, this study highlights the potential of pan-cancer FFLs as a novel paradigm in elucidating pathogenesis of cancer and developing anticancer drugs.

show abstract

“…Being influenced by tumor subtype, gender, ethnicity and exposure to carcinogens (e.g. smoking, radon gas, asbestos and cooking oil fumes), built up genomic alterations apply different tumorigenic mechanisms bringing about triggering of oncogenic signaling pathways and unrestrained tumor growth and metastasis [7].…”

Section: Introductionmentioning

confidence: 99%

Reconstruction of an Integrated Genome-Scale Co-Expression Network Reveals Key Modules Involved in Lung Adenocarcinoma

et al. 2013

View full text Add to dashboard Cite

Our goal of this study was to reconstruct a “genome-scale co-expression network” and find important modules in lung adenocarcinoma so that we could identify the genes involved in lung adenocarcinoma. We integrated gene mutation, GWAS, CGH, array-CGH and SNP array data in order to identify important genes and loci in genome-scale. Afterwards, on the basis of the identified genes a co-expression network was reconstructed from the co-expression data. The reconstructed network was named “genome-scale co-expression network”. As the next step, 23 key modules were disclosed through clustering. In this study a number of genes have been identified for the first time to be implicated in lung adenocarcinoma by analyzing the modules. The genes EGFR, PIK3CA, TAF15, XIAP, VAPB, Appl1, Rab5a, ARF4, CLPTM1L, SP4, ZNF124, LPP, FOXP1, SOX18, MSX2, NFE2L2, SMARCC1, TRA2B, CBX3, PRPF6, ATP6V1C1, MYBBP1A, MACF1, GRM2, TBXA2R, PRKAR2A, PTK2, PGF and MYO10 are among the genes that belong to modules 1 and 22. All these genes, being implicated in at least one of the phenomena, namely cell survival, proliferation and metastasis, have an over-expression pattern similar to that of EGFR. In few modules, the genes such as CCNA2 (Cyclin A2), CCNB2 (Cyclin B2), CDK1, CDK5, CDC27, CDCA5, CDCA8, ASPM, BUB1, KIF15, KIF2C, NEK2, NUSAP1, PRC1, SMC4, SYCE2, TFDP1, CDC42 and ARHGEF9 are present that play a crucial role in cell cycle progression. In addition to the mentioned genes, there are some other genes (i.e. DLGAP5, BIRC5, PSMD2, Src, TTK, SENP2, PSMD2, DOK2, FUS and etc.) in the modules.

show abstract

IGDB.NSCLC: integrated genomic database of non-small cell lung cancer

Cited by 25 publications

References 44 publications

A Genetic Polymorphism in pre-miR-27a Confers Clinical Outcome of Non-Small Cell Lung Cancer in a Chinese Population

A Genetic Polymorphism in pre-miR-27a Confers Clinical Outcome of Non-Small Cell Lung Cancer in a Chinese Population

Systematic dissection of dysregulated transcription factor–miRNA feed-forward loops across tumor types

Reconstruction of an Integrated Genome-Scale Co-Expression Network Reveals Key Modules Involved in Lung Adenocarcinoma

Contact Info

Product

Resources

About