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In BMC medical informatics and decision making ; h5-index 38.0

BACKGROUND : Gastrointestinal (GI) cancer including colorectal cancer, gastric cancer, pancreatic cancer, etc., are among the most frequent malignancies diagnosed annually and represent a major public health problem worldwide.

METHODS : This paper reports an aided curation pipeline to identify potential influential genes for gastrointestinal cancer. The curation pipeline integrates biomedical literature to identify named entities by Bi-LSTM-CNN-CRF methods. The entities and their associations can be used to construct a graph, and from which we can compute the sets of co-occurring genes that are the most influential based on an influence maximization algorithm.

RESULTS : The sets of co-occurring genes that are the most influential that we discover include RARA - CRBP1, CASP3 - BCL2, BCL2 - CASP3 - CRBP1, RARA - CASP3 - CRBP1, FOXJ1 - RASSF3 - ESR1, FOXJ1 - RASSF1A - ESR1, FOXJ1 - RASSF1A - TNFAIP8 - ESR1. With TCGA and functional and pathway enrichment analysis, we prove the proposed approach works well in the context of gastrointestinal cancer.

CONCLUSIONS : Our pipeline that uses text mining to identify objects and relationships to construct a graph and uses graph-based influence maximization to discover the most influential co-occurring genes presents a viable direction to assist knowledge discovery for clinical applications.

Wang Charles C N, Jin Jennifer, Chang Jan-Gowth, Hayakawa Masahiro, Kitazawa Atsushi, Tsai Jeffrey J P, Sheu Phillip C-Y


Bi-LSTM-CNN-CRF, Co-occurrence network, Gastrointestinal cancer, Influence maximization, Text mining