recent whole transcriptome studies have revealed that about three quarters of the human genome is capable of being transcribed , while protein - coding regions account for just 2% of the genome ( 13 ) .
therefore , the vast majority of transcribed sequences do not encode proteins , and are called non - coding rna ( ncrna ) .
accumulating evidence shows that non - coding rnas play key roles in various biological processes , such as imprinting control , the circuitry controlling pluripotency and differentiation , immune responses , and chromosome dynamics ( 4 ) .
ncrnas are as important as protein - coding genes to cellular functions ( 5,6 ) .
notably , a growing number of long ncrnas ( lncrnas ) , which are considered to be > 200 nt in length and are often multiexonic ( 7 ) , have been implicated in disease etiology ( 810 ) .
it is therefore of great importance to collect lncrna information and store this information in a one - stop knowledge gateway for lncrnas , the noncode database .
the development of high - throughput sequencing methodologies has reduced the cost of rna sequencing , and as a result there has been an explosive rise in the number of newly identified lncrnas .
established a consensus set of 384 066 predicted transcripts from 7256 rna - seq libraries , which were designated as the mitranscriptome assembly ( 11 ) . since then the revolutionary advancement of sequencing methods , such as single - molecule long - read techniques , leads us closer to the real lncrna transcriptome . given sufficient material , amplification - free sequencing of full - length cdna molecules
noncode has collected data from literature published since the last update and includes the latest versions of several public databases ( ensembl ( 13 ) , refseq(14 ) , lncrnadb ( 15 ) and gencode ( 16 ) ) .
after the removal of false and redundant lncrnas , noncode contains a total of 527,336 transcripts .
in addition to the identification of new lncrnas , data on the genetics and biochemical properties of lncrnas has accumulated rapidly . of the papers retrieved from pubmed for lncrnas
, we found that the vast majority studied lncrna function , especially the relationship between lncrnas and disease ( 810 ) .
in large - scale searches for single - base differences between diseased and healthy individuals , about 40% of the disease - related differences show up in genomic regions outside of protein - coding genes .
this implicates non - coding regions as vital for genetic risk factors of disease ( 2 ) . in order to enable a systematic compilation and integration of this information
the sources for these annotations were derived from literature mining , differential lncrna analysis utilizing public rna - seq data and microarray data and mutation analysis from public genome - wide association study ( gwas ) data . along with the ever increasing number of lncrnas and the amount and functional study data , genome - wide conservation information is required for biologists to study the mechanisms of lncrna actions . in order to explore the conservation information of lncrnas , noncode collected six new mammalian species ( chimpanzee , gorilla , orangutan , rhesus macaque , opossum and platypus ) ( 17 ) .
users can browse the conserved counterparts of any human lncrna gene in other species through a phylogenetic tree layout .
similar to the former iterations of noncode ( 1821 ) , the source of noncode 2016 includes the previous versions of noncode , the collated literature and other public databases .
noncoding ,  non - coding ,  no code ,  non - code ,  lncrna and  lincrna , and found 6532 new articles since 1 june 2013 ( the last collection date for noncode ) .
we retrieved the newly identified lncrnas and their annotations from the supplementary material or web site of these articles .
together with the newest data from ensembl , refseq , lncrnadb , gencode and the old versions of noncode data , literature data were processed through a standard pipeline for each species .
all of the input data were processed into bed or gtf formats based on one assembly version , for example , hg38 for human and mm10 for mouse.combination .
all of the normalized data files were combined together using the cuffcompare program in the cufinks suite ( 22 ) . after eliminating redundancy , every new transcript i d and the accompanying resources were extracted.filtering protein - coding rna .
firstly , the rna was compared with the coding rna in refseq and ensembl , and the  =  and  c transcripts were excluded . secondly , the rna was filtered through the coding - non - coding index ( cnci ) ( 23 ) program and only the rnas considered non - coding by cnci were kept.information retrieval .
we assigned each transcript a name according to the criterion of noncode v4 and extracted basic information such as location ( 24 ) , exons , length , assembly sequence , source , etc.advanced annotation .
advanced annotations included expression profiles , predicted functions , conservation , disease information , etc .
human expression profiles were collected from 16 tissues of the human bodymap 2.0 data ( ena archive : erp000546 ) and eight cell lines ( geo accession no .
gse30554 ) , while mouse data was collected from six different tissues ( ena archive : erp000591 ) .
functions for the lncrna genes were predicted by lnc - gfp ( 25 ) , a coding  non - coding co - expression network ( 26,27 ) based global function predictor.web presence .
more annotation information has been added and a more user - friendly interface has been introduced .
all of the input data were processed into bed or gtf formats based on one assembly version , for example , hg38 for human and mm10 for mouse .
all of the normalized data files were combined together using the cuffcompare program in the cufinks suite ( 22 ) . after eliminating redundancy ,
firstly , the rna was compared with the coding rna in refseq and ensembl , and the  =  and  c transcripts were excluded .
secondly , the rna was filtered through the coding - non - coding index ( cnci ) ( 23 ) program and only the rnas considered non - coding by cnci were kept .
we assigned each transcript a name according to the criterion of noncode v4 and extracted basic information such as location ( 24 ) , exons , length , assembly sequence , source , etc .
advanced annotations included expression profiles , predicted functions , conservation , disease information , etc .
human expression profiles were collected from 16 tissues of the human bodymap 2.0 data ( ena archive : erp000546 ) and eight cell lines ( geo accession no .
gse30554 ) , while mouse data was collected from six different tissues ( ena archive : erp000591 ) .
functions for the lncrna genes were predicted by lnc - gfp ( 25 ) , a coding  non - coding co - expression network ( 26,27 ) based global function predictor .
more annotation information has been added and a more user - friendly interface has been introduced .
noncode contains 527,336 lncrna transcripts from 16 species ( human , mouse , cow , rat , chimpanzee , gorilla , orangutan , rhesus macaque , opossum , platypus , chicken , zebrafish , fruitfly , caenorhabditiselegans , yeast and arabidopsis , ) . according to the definition of lncrna genes ( 18 ) ,
a total of 101,700 and 86,935 genes were generated from 167,150 and 130,558 lncrnas from human and mouse ( shown in table 1 ) , respectively .
following the nomenclature of noncode v4 ( 18 ) , both lncrna transcripts and genes were designated systematically : non+ three characters ( representing a species ) + t ( transcript ) or g ( gene ) + six sequential numbers .
noncode has annotated expression profiles from all the human and mouse transcripts and genes , and a large number of these genes were annotated with predicted functions .
definitive evidence has proven that transcription of the non - coding genome has produced functional rnas ( 1 ) . in particular , lncrnas have been implicated in biological , developmental , and pathological processes , and acted through mechanisms such as chromatin reprogramming , cis regulation at enhancers , and post - transcriptional regulation of mrna processing ( 28 ) .
lncrnas are therefore considered to be important regulators of tissue physiology and disease processes including cancer ( 11 ) .
although we have collected functional interactions between ncrnas and biomolecules in npinter ( 2931 ) , we think it is also necessary to include disease information into noncode .
recent published papers have been explored , and the proven associations between noncode transcripts and diseases has been integrated into the latest version .
the noncode assembly also assessed the overlaps of transcripts with the unique disease - associated single - nucleotide polymorphisms ( snps ) from a catalog of gwass ( 32 ) and the snp database ( dbsnp ) ( 33 ) .
there were also a lot of relational data between lncrnas and diseases which were analyzed from rna - seq and microarray data .
after collecting the basic data , we compared it with the lncrnas in noncode and retained data that overlapped with noncode lncrnas .
noncode 2016 contains 1110 lncrnas which were related to 284 diseases . among these associations ,
disease related data acquisition pipeline in the lncrna gene description pages , users can retrieve the related diseases of the entry , and also get the source of the information , such as the pmid(s ) of the reference paper(s ) .
there is also mutational information retrieved from the literature , gwass and the dbsnp database .
compared to protein - coding genes and small rnas ( e.g. mirnas and snornas ) , several reports have suggested that lncrnas are modestly conserved ( 11 ) .
most lncrnas are less conserved in sequence ( 34 ) , but there are still many lncrnas that are conserved in their genomic loci , exonic sequences and promoter regions ( 35 ) .
these are preserved across multiple species , attesting to their important functional potentials ( 36 ) .
benefiting from next - generation sequencing technologies , ncrnas are now more easily identied via transcript sequencing .
noncode has added six new species , mainly from multi - species rna - seq data ( 37,38 ) .
an evolutionary tree from 12 commonly studied species ( human , mouse , cow , rat , chicken , zebrafish , chimpanzee , gorilla , orangutan , rhesus macaque , opossum and platypus ) was constructed using methods introduced in phylononcode ( 39 ) .
each human lncrna gene counterpart from the other listed species can be retrieved through browsing the evolutionary tree ( shown in figure 2 ) .
the counterpart of each lncrna was computed using the ucsc liftover tool ( 40 ) . in brief , liftover utilized blastz ( 41 ) , an independent implementation of the gapped blast algorithm specifically designed for aligning two long genomic sequences , as a core algorithm to detect homologous regions in other genomes . after mapping to the second species ,
however , a proper method of in silico transcript reconstruction is an ongoing challenge . according to an assessment by the paul bertone group , < 40% of known transcripts
the complexity of higher eukaryotic genomes imposes severe limitations on transcript recall and splice product discrimination that are likely to remain limiting factors for the analysis of current - generation rna - seq data ( 42 ) .
furthermore , multiple amplification steps during library preparation complicate the quantification of expression levels . to some extent
given sufficient material , amplification - free and fragmentation - free sequencing of full - length cdna molecules provides a more direct view of rna molecules ( 12 ) .
noncode contacted the authors of the third - generation single - molecule long - read survey of the human transcriptome paper ( 12 ) .
after our analysis , the single - molecule lncrna transcripts were included into noncode . to meet the quality demands of researchers
users can choose the subset which is considered high quality . the quality controls include the source of the data , literature support , other database support and long - read sequencing method support .
the controls also include selection of exon numbers , the lengths of the transcripts and prediction tools support .
the web interface will return the subset according to the conditions users chose and allow users to download the data .
noncode 2016 contains 527,336 lncrnas from 16 different species , this compares favorably with other lncrna databases .
for example , lncipedia ( human only ) contains 111 685 transcripts ( 43 ) , lncrnator ( human , mouse , fly , zebrafish , worm and yeast ) contains 34 605 transcripts ( 44 ) , while the lncrnawiki ( human only ) contains 105 255 transcripts ( 45 ) . as mentioned above , technical limitations imposed by short - read sequencing lead to a number of computational challenges in transcript reconstruction and quantification . for many transcripts ,
automated methods failed to identify all of the constituent exons , and in cases in which all exons were reported , the protocols tested often failed to assemble the exons into complete isoforms ( 42 ) .
for example , although we have obtained all the data from mitranscriptome ( 11 ) , which contains 384 066 human lncrnas from 7256 rna - seq libraries , the detection of precise refseq splicing patterns from mitranscriptome was only 31% , and the fraction of annotated genes within the entire mitranscriptome was only 46% .
although it is reasonable to assume that unannotated transcription is unique to specific lineages , the low refseq detection rate was unusual .
we therefore made a decision that noncode would not include mitranscriptome data in the current version . in the future
, we will attempt to make clear the real reason(s ) . perhaps a more comprehensive construction tool is required to answer this question .
national high technology research and development program (  863 program ) of china [ 2014aa021103 , 2014aa021502 ] ; training program of the major research plan of the national natural science foundation of china ; national natural science foundation of china [ 31371320 , 31401119 ] ; chinese academy of science strategic project of leading science and technology [ xda01020402 ] .
funding for open access charge : national high technology research and development program (  863 program ) of china [ 2014aa021103 ] .
 noncode ( http://www.bioinfo.org/noncode/ ) is an interactive database that aims to present the most complete collection and annotation of non - coding rnas , especially long non - coding rnas ( lncrnas ) . 
 the recently reduced cost of rna sequencing has produced an explosion of newly identified data . 
 revolutionary third - generation sequencing methods have also contributed to more accurate annotations . 
 accumulative experimental data also provides more comprehensive knowledge of lncrna functions . in this update 
 , noncode has added six new species , bringing the total to 16 species altogether . 
 the lncrnas in noncode have increased from 210 831 to 527,336 . for human and mouse , 
 the lncrna numbers are 167,150 and 130,558 , respectively . 
 noncode 2016 has also introduced three important new features : ( i ) conservation annotation ; ( ii ) the relationships between lncrnas and diseases ; and ( iii ) an interface to choose high - quality datasets through predicted scores , literature support and long - read sequencing method support . 
 noncode is also accessible through http://www.noncode.org/. 
INTRODUCTION
DATA COLLECTION AND PROCESSING
STATISTICS OF NONCODE
LNCRNAS AND DISEASES
lNCRNA CONSERVATION
QUALITY OF LNCRNAS
DISCUSSION
FUNDING