TY - JOUR AU - Yang, Xinan Holly AU - Li, Meiyi AU - Wang, Bin AU - Zhu, Wanqi AU - Desgardin, Aurelie AU - Onel, Kenan AU - de Jong, Jill AU - Chen, Jianjun AU - Chen, Luonan AU - Cunningham, John M. PY - 2015 DA - 2015/03/24 TI - Systematic computation with functional gene-sets among leukemic and hematopoietic stem cells reveals a favorable prognostic signature for acute myeloid leukemia JO - BMC Bioinformatics SP - 97 VL - 16 IS - 1 AB - Genes that regulate stem cell function are suspected to exert adverse effects on prognosis in malignancy. However, diverse cancer stem cell signatures are difficult for physicians to interpret and apply clinically. To connect the transcriptome and stem cell biology, with potential clinical applications, we propose a novel computational “gene-to-function, snapshot-to-dynamics, and biology-to-clinic” framework to uncover core functional gene-sets signatures. This framework incorporates three function-centric gene-set analysis strategies: a meta-analysis of both microarray and RNA-seq data, novel dynamic network mechanism (DNM) identification, and a personalized prognostic indicator analysis. This work uses complex disease acute myeloid leukemia (AML) as a research platform. SN - 1471-2105 UR - https://doi.org/10.1186/s12859-015-0510-7 DO - 10.1186/s12859-015-0510-7 ID - Yang2015 ER -