BCIP: a gene-centered platform for identifying potential regulatory genes in breast cancer.
Breast cancer is a disease with high heterogeneity. Many issues on tumorigenesis and progression are still elusive. It is critical to identify genes that play important roles in the progression of tumors, especially for tumors with poor prognosis such as basal-like breast cancer and tumors in very young women. To facilitate the identification of potential regulatory or driver genes, we present the Breast Cancer Integrative Platform (BCIP, http://omics.bmi.ac.cn/bcancer/). BCIP maintains multi-omics data selected with strict quality control and processed with uniform normalization methods, including gene expression profiles from 9,005 tumor and 376 normal tissue samples, copy number variation information from 3,035 tumor samples, microRNA-target interactions, co-expressed genes, KEGG pathways, and mammary tissue-specific gene functional networks. This platform provides a user-friendly interface integrating comprehensive and flexible analysis tools on differential gene expression, copy number variation, and survival analysis. The prominent characteristic of BCIP is that users can perform analysis by customizing subgroups with single or combined clinical features, including subtypes, histological grades, pathologic stages, metastasis status, lymph node status, ER/PR/HER2 status, TP53 mutation status, menopause status, age, tumor size, therapy responses, and prognosis. BCIP will help to identify regulatory or driver genes and candidate biomarkers for further research in breast cancer.
Beijing Institute of Basic Medical Sciences, Beijing 100850, China.
Jiaqi
J
Wu
Beijing Institute of Basic Medical Sciences, Beijing 100850, China.
Shuofeng
S
Hu
Beijing Institute of Basic Medical Sciences, Beijing 100850, China.|Department of Obstetrics and Gynecology, Fuzhou General Hospital of Nanjing Military Command, Fuzhou, Fujian 350025, China.
Yaowen
Y
Chen
Beijing Institute of Basic Medical Sciences, Beijing 100850, China.|Translational Medicine Center of Stem Cells, 307-Ivy Translational Medicine Center, Laboratory of Oncology, Affiliated Hospital, Academy of Military Medical Sciences, Beijing 100071, China.
Zongcheng
Z
Li
Beijing Institute of Basic Medical Sciences, Beijing 100850, China.
Jian
J
Zhang
Beijing Institute of Basic Medical Sciences, Beijing 100850, China.
Hanyu
H
Yuan
Beijing Institute of Basic Medical Sciences, Beijing 100850, China.
Qiang
Q
Shi
Beijing Institute of Basic Medical Sciences, Beijing 100850, China.
Ningsheng
N
Shao
Beijing Institute of Basic Medical Sciences, Beijing 100850, China.
Xiaomin
X
Ying
D001943:Breast Neoplasms / Q000453:epidemiology / Q000235:genetics* / Q000473:pathology; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D006801:Humans; D009362:Neoplasm Metastasis; D018719:Erb-b2 Receptor Tyrosine Kinases / Q000235:genetics; D012984:Software; D016159:Tumor Suppressor Protein p53 / Q000235:genetics
D018719:Erb-b2 Receptor Tyrosine Kinases; D016159:Tumor Suppressor Protein p53; C495901:TP53 protein, human; C508053:ERBB2 protein, human