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ChIPBase specifications


Unique identifier OMICS_00527
Name ChIPBase
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 2.0
Maintained Yes


  • ChIP-Function
  • Co-Expression


  • person_outline Jian-Hua Yang
  • person_outline Liang-Hu Qu
  • person_outline Ke-Ren Zhou

Publications for ChIPBase

ChIPBase citations


LncRNA OIP5 AS1 is overexpressed in undifferentiated oral tumors and integrated analysis identifies as a downstream effector of stemness associated transcription factors

Sci Rep
PMCID: 5935738
PMID: 29728583
DOI: 10.1038/s41598-018-25451-3

[…] For gene expression comparison and identification of target genes from the list of predicted genes cancer datasets from TCGA database was analyzed and downloaded using cBioportal and ChIPBase v2. online tools. Predictions of miRNA targets were performed and retrieved from TargetScan, miRanda, miRcode, Starbase and DIANA online prediction tools. For prediction of RNA-RNA interactio […]


Bioinformatic analysis and prediction of the function and regulatory network of long non coding RNAs in hepatocellular carcinoma

PMCID: 5934726
PMID: 29740493
DOI: 10.3892/ol.2018.8271

[…] tween HOTAIR and MALAT1, 9 of which were HCC-associated miRNAs according to the HMDD database. hsa-miR-1 and hsa-miR20a-5p were identified to be downregulated in HCC and selected for further analysis.ChIPBase was used to predict the transcription factors for lncRNAs (MALAT1 and HOTAIR) and miRNAs (hsa-miR-1 and hsa-miR-20a-5p). The results demonstrated that 9 transcription factors for lncRNAs (STA […]


FOXA1 inhibits hepatocellular carcinoma progression by suppressing PIK3R1 expression in male patients

PMCID: 5718070
PMID: 29208003
DOI: 10.1186/s13046-017-0646-6

[…] Putative target genes controlled by FOXA1 were identified in silico analysis using the Cistrome Dataset Browser ( [] and ChIPBase v2.0 ( [] databases on ChIP-seq data from HepG2 cells. Genes that scored higher than 2.5 points or encoded proteins were selected for further analysis using t […]


DeepCpG: accurate prediction of single cell DNA methylation states using deep learning

Genome Biol
PMCID: 5387360
PMID: 28395661
DOI: 10.1186/s13059-017-1189-z

[…] eatures), iii) transcription factor binding sites (24 features), iv) histone modification marks (28 features) and v) DNaseI hypersensitivity sites (one feature). These features were obtained from the ChipBase database and UCSC Genome Browser for the GRCm37 mouse genome and mapped to the GRCm38 mouse genome using the liftOver tool from the UCSC Genome Browser.We trained a separate random forest mod […]


LncRNAs: From Basic Research to Medical Application

PMCID: 5370437
PMID: 28367094
DOI: 10.7150/ijbs.16968

[…] adisease) provides full comments of reported disease-related lncRNAs. NRED ( provides the lncRNA expression information of human and mouse based on chip data . ChIPBase ( provides the map of lncRNA, comprehensive identification, and annotation of the transcription regulation . It also integrated lncRNAs identified by hig […]


The rs1550117 A>G variant in DNMT3A gene promoter significantly increases non small cell lung cancer susceptibility in a Han Chinese population

PMCID: 5410319
PMID: 28423585
DOI: 10.18632/oncotarget.15625

[…] d to predicted that the rs1550117 A>G variant creates the transcription factor (TF) binding sites for SP1 and GR (Figure ). However, the chromatin immunoprecipitation (ChIP) sequencing results in the ChIPBase v2.0 database ( and previous investigation results collectively suggested that SP1 but not GR could bind to the DNMT3A promoter region [, ]. In this study, th […]

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ChIPBase institution(s)
Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, China
ChIPBase funding source(s)
This work was supported by Ministry of Science and Technology of China; National Basic Research Program [2011CB811300]; National Natural Science Foundation of China [31230042, 31370791, 31401975, 31471223, 91440110, 31671349]; Guangdong Province Funds [S2012010010510, S2013010012457]; The project of Science and Technology New Star in ZhuJiang Guangzhou city [2012J2200025]; Fundamental Research Funds for the Central Universities [2011330003161070, 14lgjc18]; China Postdoctoral Science Foundation [200902348]; Guangdong Province Key Laboratory of Computational Science; Guangdong Province Computational Science Innovative Research Team.

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