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CGAP specifications


Unique identifier OMICS_20656
Alternative name Chloroplast genome analysis platform
Interface Web user interface
Restrictions to use Academic or non-commercial use
Computer skills Basic
Stability No
Maintained No


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Publication for Chloroplast genome analysis platform

CGAP citations


NFkB hyperactivation causes invasion of esophageal squamous cell carcinoma with EGFR overexpression and p120 catenin down regulation

PMCID: 5834278
PMID: 29541406
DOI: 10.18632/oncotarget.24358

[…] he 50th percentile, and EGFR-low otherwise. Unsupervised hierarchical cluster was performed on p120ctn-high/EGFR-low and p120ctn-low/EGFR-high cases [], using an NFkB gene list from Biocarta ( […]


Chloroplast Genome Sequence Annotation of <i>Dendrobium nobile</i> (Asparagales: Orchidaceae), an Endangered Medicinal Orchid from Northeast India

PLoS Curr
PMCID: 5501700
PMID: 28736679
DOI: 10.1371/currents.tol.cf1709613759c2223eb582c0fa694cc7
call_split See protocol

[…] / Genome annotation Protein-coding and ribosomal RNA genes were annotated using the Basic Local Alignment Search Tool (BLAST; BLASTN, PHI-BLAST and BLASTX), CGAP and DOGMA. The boundaries of each annotated gene were manually determined by comparison with orthologous genes from other orchid cp genomes. The tRNA genes were predicted using ARAGORN. The circu […]


Integrative clustering reveals a novel split in the luminal A subtype of breast cancer with impact on outcome

PMCID: 5372339
PMID: 28356166
DOI: 10.1186/s13058-017-0812-y

[…] (here, mRNA expression and copy number) in a patient sample [, ]. The pathway concepts (genes, complexes and abstract processes) are derived from the Pathway Interaction Database [], BioCarta (, and Reactome databases []. Copy number is estimated from AROMA CRMA v2 followed by circular binary segmentation (non-paired CBS) to gene level measurement […]


A Combined Pathway and Regional Heritability Analysis Indicates NETRIN1 Pathway Is Associated With Major Depressive Disorder

Biol Psychiatry
PMCID: 5262437
PMID: 27422368
DOI: 10.1016/j.biopsych.2016.04.017
call_split See protocol

[…] For both samples, SNPs were annotated to 1035 pathways (640 from Reactome [], 216 from BioCarta [], and 179 from Kyoto Encyclopedia of Genes and Genomes []) (). For the GS:SFHS genotype data set (nSNP = 592,690; nsample = 6455), […]


GWAS of self reported mosquito bite size, itch intensity and attractiveness to mosquitoes implicates immune related predisposition loci

Hum Mol Genet
PMCID: 5390679
PMID: 28199695
DOI: 10.1093/hmg/ddx036

[…] org/; UCSC Genome Browser,; HaploReg,; Immunobase,; BIOCARTA, […]


Recurrent fusion transcripts in squamous cell carcinomas of the vulva

PMCID: 5370005
PMID: 28186972
DOI: 10.18632/oncotarget.15167

[…] etected has increased exponentially after the introduction of next generation sequencing (NGS) methodology. To date, the Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer ( reports 10.277 fusion transcripts (update February 2016) found in different types of tumors, of which 1.430 were identified in SCC of different locations. To our […]


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CGAP institution(s)
Department of Computational Biology and Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China; Nanjing Forestry University, Nanjing, China
CGAP funding source(s)
Supported by National Natural Science Foundation of China (81102746, 81100077, 31201768), Beijing Natural Science Foundation (5113033, 6133033), Special Foundation of China Postdoctoral Science (2012T50067), China Postdoctoral Science Foundation funded project (2011M500014, 2012M510011), Scientific Research Foundation of the State Human Resource Ministry and the Education Ministry for Returned Chinese Scholars, PUMC Youth Fund, the Fundamental Research Funds for the Central Universities, the Research Fund for the Doctoral Program of Higher Education (20111106120028), “Major Drug Discovery” major science and technology research “12nd Five-Year Plan” (2012ZX09301-002-001-025), Basic Scientific Research Operation Cost of State-Leveled Public Welfare Scientific Research Courtyard (YZ-12-15), China Medical Board of New York (A2009001), Program for New Century Excellent Talents in University (NCET-12-0074).

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