With abundant mammalians lncRNAs identified recently, a comprehensive annotation resource for these novel lncRNAs is in urgent need. Since its first release in November 2016, AnnoLnc is the only online server for comprehensively annotating novel human lncRNAs on-the-fly. Here, with significant updates to multiple annotation modules, backend datasets as well as the code base, AnnoLnc2 now continues its effort to provide scientific community a one-stop online portal for systematically annotating novel human and mouse lncRNAs with a comprehensive functional spectrum covering from sequences, structure, expression, regulation, to genetic association and evolution. In response to numerous requests from multiple users, a standalone package is also provided for large-scale offline analysis. We believe that updated AnnoLnc2 will help both computational and bench biologists for curating lncRNA function and investigating underling mechanisms.
Click here to see more details about the methods in AnnoLnc2.
|Linux||Ubuntu 18.04 LTS||not tested||n/a||n/a|
|Module||AnnoLnc2||AnnoLnc (only support Human)|
|Expression||Human: 52 RNA-seq samples for 26 tissues, 39 CCLE cancer cell lines, and 4 RNA-seq samples for H1 and GM12878 from ENCODE;
Mouse: 56 RNA-seq samples for 28 tissues and 13 RNA-seq samples for 7 cell lines from ENCODE.
|32 RNA-seq samples for 16 tissues, 30 CCLE cancer cell lines, 2 RNA-seq samples for H1 cell line.|
|Transcriptional regulation||Human: 13,515 ChIP-seq samples for 1,339 TFs;
Mouse: 10,728 ChIP-seq samples for 738 TFs.
|498 ChIP-seq samples for 159 TFs.|
|Subcellular localization||Human: 40 RNA-seq samples covering 10 ENCODE cell lines||NA|
|miRNA regulation||Human: 170 AGO CLIP-seq samples in various human tissues (e.g. brain cortex) and cell lines (e.g. H1, HK-2, and osteoblast);
Mouse: 153 AGO CLIP-seq in various mouse tissues (e.g. cortex, liver) and cell lines (e.g. mESC, CD4+ T cell, and keratinocytes).
|61 AGO CLIP-seq samples.|
|Protein interaction||Human: 385 CLIP-seq samples for 188 RBPs in various human tissues (e.g. brain, adrenal gland, hippocampus) and cell lines (e.g. HEK293T, HeLa, K562);
Mouse: 238 CLIP-seq samples for 62 RBPs in various mouse tissues (e.g. brain, testis, cortex) and cell lines (e.g. B cell, mESC, 220-8 cell, N2A cell).
|112 CLIP-seq samples for 51 RBPs.|
|Genetic association||Human: 96,455 trait-associated SNPs from GWAS catalog, 298,590 SNPs which are in linkage disequilibrium with GWAS SNPs from dbSNP, and 4,365,369 eQTLs from GTEx;
Mouse: 4,013 phenotypic alleles and 997 QTL alleles from MGI.
|298,590 SNPs which are in linkage disequilibrium with GWAS SNPs from dbSNP.|
|Evolution||Human: phyloP and phastCons scores for Primate, Mammal, and Vertebrate clades were computed by a local implemented UCSC MultiZ-Phast pipeline based on 100-way multiple alignments from UCSC Genome Browser; Derived allele frequency (DAF) is based on 1000 Genomes Project;
Mouse: phyloP and phastCons scores for Glire, Euarchontoglire, Placental, and Vertebrate clade were based on 60-way multiple alignments from UCSC Genome Browser.
|phyloP scores and conserved elements for Primate, Mammal, and Vertebrate clades were based on 46-way multiple alignments from UCSC Genome Browser; DAF score is based on 1000 Genomes Project.|
Click here for more details about the AnnoLnc2 update.
Click here for more details about the comparision between AnnoLnc2 and other tools.