SubpathwayMiner: a software package for flexible identification of pathways

Li, Chunquan; Li, Xia; Miao, Yingbo; Wang, Qianghu; Jiang, Wei; Xu, Chun; Li, Jing; Han, Junwei; Zhang, Fan; Gong, Binsheng; Xu, Liangde

doi:10.1093/nar/gkp667

Cited by 175 publications

(206 citation statements)

References 39 publications

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“…The 'pathway' database, which contains approximately 300 biological pathways, records the networks of molecular interactions in cells as well as their variants specific to particular organisms. SubpathwayMiner (Li et al, 2009) was used to convert metabolic pathways to enzyme-enzyme (KEGG Orthology, KO-KO) pathway graphs, with enzymes as nodes and compounds as edges. The K-Cliques method was used to identify sub-pathways based on pathway structure data provided by KEGG, with the K value setting as 3.…”

Section: Kegg Pathway-enrichment Analysismentioning

confidence: 99%

Gene expression profile and enrichment pathways in different stages of bladder cancer

Fang

Zang²,

Chen³

et al. 2013

Genet. Mol. Res.

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ABSTRACT. Bladder cancer is a highly heterogeneous neoplasm. We examined the gene expression profile in 3 bladder cancer stages (Ta, T1, T2) using expression microarray analysis of 40 bladder tumors. Differentially expressed genes were found by the t-test, with <0.005 as the significance threshold. KEGG pathway-enrichment analysis was used to study the signaling pathways of the genes. We found 36 genes that could be used as molecular markers for predicting the transition from Ta-T1 to T1-T2. Among these, 11 overlapped between Ta-T1 and T1-T2 stages. Six genes were downregulated at the Ta-T1 stage, but were up-regulated at the T1-T2 stage (ANXA5, ATP6V1B2, CTGF, GEM, IL13RA1, and LCP1); 5 genes were up-regulated at the Ta-T1 stage, but down-regulated at the T1-T2 stage (ACPP, GNL1, RIPK1, RAPGEF3, and ZER1). Another 25 genes changed relative expression levels at the T1-T2 stage. These genes (including COL1A1, COL1A2, FN1, ITGA5, LGALS1, SPP1, VIM, POSTN, and COL18A1) may be involved in bladder cancer progression by affecting extracellular matrix-receptor interaction and focal adhesion. The cytokine-cytokine receptor interaction, neuroactive ligandreceptor interaction, and calcium-signaling pathway were associated with bladder cancer progression at both the Ta-T1 and T1-T2 stages.

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Section: Kegg Pathway-enrichment Analysismentioning

confidence: 99%

Gene expression profile and enrichment pathways in different stages of bladder cancer

Fang

Zang²,

Chen³

et al. 2013

Genet. Mol. Res.

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“…org/src/contrib/Archive/SubpathwayMiner), which is a flexible subpathway identification software, was used to obtain subpathways associated with OS metastasis (12). DEGs between patients with OS who did or did not develop metastases were imported into Subpathway Miner, which identified significantly enriched subpathways using hypergeometric tests (12). This software converts pathway structure data from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database (www.genome.jp/ kegg) into undirected R graph objects.…”

Section: Identification Of Subpathways Associated With Os Metastasismentioning

confidence: 99%

Identification of candidate drugs for the treatment of metastatic osteosarcoma through a subpathway analysis method

Yan

2017

Oncology Letters

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Abstract. Osteosarcoma (OS) is the third most frequent type of cancer in adolescents and represents >56% of all bone tumors. In addition, metastatic OS frequently demonstrates resistance to conventional chemotherapy; thus, the development of novel therapeutic agents for the treatment of patients with metastatic OS is warranted. In the present study, the metabolic mechanisms underlying OS metastasis were investigated using a subpathway analysis method and lead to the identification of candidate drugs for the treatment of metastatic OS. Using the GSE14827 microarray dataset from the Gene Expression Omnibus database, 546 differentially expressed genes were identified between samples from patients with OS who did or did not develop metastatic OS. Furthermore, nine significantly enriched metabolic subpathways were identified, which may be involved in OS metastasis. Finally, using an integrated analysis of metastatic OS-associated subpathways and drug-affected subpathways, 98 small molecule drug candidates capable of targeting the metastatic OS-associated subpathways were identified. This method identified existing anti-cancer drugs, including semustine, in addition to predicting potential drugs, such as lansoprazole, for the treatment of metastatic OS. Transwell and wound healing assays demonstrated that lansoprazole reduced the invasiveness and migration of U2OS cells. These small molecule drug candidates identified through a bioinformatics approach may provide insights into novel therapy options for the treatment of patients with metastatic OS.

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“…Except traditional entire KEGG pathway, SubpathwayMiner detects the local structure of an entire pathway (subpathway), which limited to local area of pathway and help to understand the detail information of interested genes (Li et al, 2009). For a given KEGG pathway, the subpathways were obtained by searching all possible paths between start-points and end-points in the adjacency matrix generated by node relationships.…”

Section: Analysis Of Kegg Pathway and Subpathwaymentioning

confidence: 99%

Comprehensive Bioinformation Analysis of the MRNA Profile of Fascin Knockdown in Esophageal Squamous Cell Carcinoma

Wu¹,

Luo²,

Li³

et al. 2013

Asian Pacific Journal of Cancer Prevention

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Background: Fascin, an actin-bundling protein forming actin bundles including filopodia and stress fibers, is overexpressed in multiple human epithelial cancers including esophageal squamous cell carcinoma (ESCC). Previously we conducted a microarray experiment to analyze fascin knockdown by RNAi in ESCC. Method: In this study, the differentially expressed genes from mRNA expression profilomg of fascin knockdown were analyzed by multiple bioinformatics methods for a comprehensive understanding of the role of fascin. Results: Gene Ontology enrichment found terms associated with cytoskeleton organization, including cell adhesion, actin filament binding and actin cytoskeleton, which might be related to fascin function. Except GO categories, the differentially expressed genes were annotated by 45 functional categories from the Functional Annotation Chart of DAVID. Subpathway analysis showed thirty-nine pathways were disturbed by the differentially expressed genes, providing more detailed information than traditional pathway enrichment analysis. Two subpathways derivated from regulation of the actin cytoskeleton were shown. Promoter analysis results indicated distinguishing sequence patterns and transcription factors in response to the co-expression of downregulated or upregulated differentially expressed genes. MNB1A, c-ETS, GATA2 and Prrx2 potentially regulate the transcription of the downregulated gene set, while Arnt-Ahr, ZNF42, Ubx and TCF11-MafG might co-regulate the upregulated genes. Conclusions: This multiple bioinformatic analysis helps provide a comprehensive understanding of the roles of fascin after its knockdown in ESCC.

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SubpathwayMiner: a software package for flexible identification of pathways

Cited by 175 publications

References 39 publications

Gene expression profile and enrichment pathways in different stages of bladder cancer

Gene expression profile and enrichment pathways in different stages of bladder cancer

Identification of candidate drugs for the treatment of metastatic osteosarcoma through a subpathway analysis method

Comprehensive Bioinformation Analysis of the MRNA Profile of Fascin Knockdown in Esophageal Squamous Cell Carcinoma

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