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Protocols

ncFANs specifications

Information


Unique identifier OMICS_13566
Name ncFANs
Alternative name non-coding RNA Function ANnotation server
Interface Web user interface
Restrictions to use None
Input data Affymetrix array raw data (CEL files), the label file
Input format ZIP
Output data A results web page, including the pre-processed gene expression profile and the functional annotation results (according to the ‘Functional Annotation’ or the ‘Functional Enrichment’ strategy)
Computer skills Basic
Version 2.0
Stability No
Maintained No

Taxon


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus

Documentation


Maintainer


This tool is not available anymore.

Publication for non-coding RNA Function ANnotation server

ncFANs citations

 (11)
library_books

FSPP: A Tool for Genome Wide Prediction of smORF Encoded Peptides and Their Functions

2018
Front Genet
PMCID: 5896265
PMID: 29675032
DOI: 10.3389/fgene.2018.00096

[…] e targets. Network-based function prediction has been proposed for predicting protein function in early 2001 when Hishigaki annotated the protein with protein-protein interaction network (). Besides, ncFANs is the first web server that relies on calculating coding and non-coding gene expression networks to predict lncRNA functions (). Lnc-GFP was developed to predict non-coding RNA functions based […]

library_books

Microarray data re annotation reveals specific lncRNAs and their potential functions in non small cell lung cancer subtypes

2017
PMCID: 5647101
PMID: 28849055
DOI: 10.3892/mmr.2017.7244

[…] Following functional annotation using ncFANs and calculating fold change value, mRNA and lncRNA profiles were obtained. As a result of the bidirectional hierarchical cluster of lncRNA profiles, it was observed that the samples were cluste […]

library_books

The long non coding RNA NONHSAG026900 predicts prognosis as a favorable biomarker in patients with diffuse large B cell lymphoma

2017
Oncotarget
PMCID: 5470975
PMID: 28423735
DOI: 10.18632/oncotarget.16163

[…] We quantified the expression levels of messenger RNAs and long non-coding RNAs by the re-annotation of Affymetrix microarray probes using the Non-coding RNA Function Annotation Server (ncFANs) []. We submitted 7 microarray datasets with a CEL format to ncFANs and acquired lncRNA and protein-coding gene expression values (log2-transformed) u […]

library_books

LncRNAs: From Basic Research to Medical Application

2017
PMCID: 5370437
PMID: 28367094
DOI: 10.7150/ijbs.16968

[…] NAdb 2.0 . Another well-known ncRNA research database NONCODE (http://www.noncode.org) also provides full comments on lncRNAs, including expression and functions predicted by their computer software (ncFANs) . Now the version has been updated to NONCODE v4 . LNCipedia (http://www.lncipedia.org) provides the sequence and full comments on structures of human lncRNAs-. LncRNA disease (http://cmbi.bjm […]

call_split

Transcriptome analysis of coding and long non coding RNAs highlights the regulatory network of cascade initiation of permanent molars in miniature pigs

2017
BMC Genomics
PMCID: 5303240
PMID: 28187707
DOI: 10.1186/s12864-017-3546-4
call_split See protocol

[…] ates from E50, E60 and E70 were merged using Cuffmerge, and aligned the short reads to WZSP, mouse, human (NONCODEv4 database hg19) and cow genome respectively for quantification and annotation using ncFANs to identify the putative lincRNAs. Raw data were transformed in FPKM (fragments per kilobase of exon per million fragments mapped) and quantiles normalized before statistical analysis. For deta […]

library_books

Dynamic co expression network analysis of lncRNAs and mRNAs associated with venous congestion

2016
PMCID: 4991739
PMID: 27431002
DOI: 10.3892/mmr.2016.5480

[…] To re-annotate micro-array data, a non-coding RNA function annotation server (ncFANs) was used to re-annotate the probes of the HG-U133 Plus 2.0 array as described on the ncFANs website (). Then each probe was converted into gene Ensem […]

Citations

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ncFANs institution(s)
Bioinformatics Research Group, Key Laboratory of Intelligent Information Processing, Advanced Computing Research Laboratory, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China; Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China; Key Laboratory for Tropical Diseases Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China; Graduate School of the Chinese Academy of Sciences, Beijing, China; Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, CAMS & PUMC, Beijing, China; Bioinformatics Laboratory and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
ncFANs funding source(s)
Knowledge Innovation Program of the Chinese Academy of Sciences (KSCX2-EW-R-01); 2010 Innovation Program of Beijing Institutes of Life Science, the Chinese Academy of Sciences; National Natural Science Foundation of China (No. 31071137, 31000586, 30970623); International Science and Technology Cooperation Projects (2010DFA31840, 2010DFB33720)

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