m6A-Atlas v2.0

Descriptions

The m⁶A-Atlas API set was designed to provide seamless programmatic access to all the data stored within our m⁶A-Atlas server. Our APIs aim to simplify and optimize your interaction with our extensive m⁶A epitranscriptome database.

By utilizing our APIs, users can efficiently fetch, analyze, and manipulate data in their preferred programming environments, including but not limited to Shell, Python, and Perl. This approach offers a more streamlined and personalized experience, eliminating the need for manual data exploration and extraction.
Our APIs can be accessed using a variety of tools, for instance, the command-line tool curl. This provides an efficient method of communication and data transfer between your applications and our database, facilitating faster research and analysis processes.
The m⁶A-Atlas APIs open up avenues for downloading both High Resolution Data and MeRIP-Seq Data, according to the specific queries of interest. Whether you're conducting academic research, developing a data-driven application, or performing complex bioinformatic analyses, our APIs serve as your conduit to a treasure trove of m⁶A regulatory data.
Each API endpoint offers a unique set of data – High Resolution Data includes comprehensive details such as gene names, strand orientation, gene type, genomic region, and more. MeRIP-Seq Data, on the other hand, provides rich sequence-based information. This includes, but is not limited to, sequence names, modification sites, peak width, gene identifiers, and more.
Embrace the power of programmatic access to advance your research and fuel your analyses with the m⁶A-Atlas API set.

Get MeRIP-Seq data
Description	Retrieve data of the m6A modification peaks from MeRIP-Seq
Query Format	species=[scientific name]: e.g., HomoSapiens, MusMusculus, DanioRerio. essential parameter. gene=[gene name]: e.g., PGBD2, Cr1l, Eif3a (default = All). essential for HomoSapiens and MusMusculus due to its large volume. genomicRegion=[genomic region]: 3' UTR, 5' UTR, Exon, Intron, Intergenic (default = All) callPeakMethod=[peak calling method]: MACS2, TRESS, exomePeak2 (default = All) supportMethodNum=[integer]: minimum number of supported peak calling methods (<=3, default = 0)
Response Format
Example	Get all MeRIP-Seq m6A peaks for human on exons, on gene PGBD2, and derived from exomePeak2 `curl 'http://www.rnamd.org/m6a/apiLowResolution.php?species=HomoSapiens&gene=PGBD2&genomicRegion=Exon&callPeakMethod=exomePeak2' > m6A-Atlas2_LowRes_HomoSapiens.txt` Get all MeRIP-Seq m6A peaks for bee on intron derived from at least 2 peak calling methods `curl 'http://www.rnamd.org/m6a/apiLowResolution.php?species=ApisMellifera&genomicRegion=Intron&supportMethodNum=2' > m6A-Atlas2_LowRes_ApisMellifera.txt`

Get MeRIP-Seq data

Description

Retrieve data of the m6A modification peaks from MeRIP-Seq

Query Format

species=[scientific name]: e.g., HomoSapiens, MusMusculus, DanioRerio. *essential parameter.
gene=[gene name]: e.g., PGBD2, Cr1l, Eif3a (default = All). *essential for HomoSapiens and MusMusculus due to its large volume.
genomicRegion=[genomic region]: 3' UTR, 5' UTR, Exon, Intron, Intergenic (default = All)
callPeakMethod=[peak calling method]: MACS2, TRESS, exomePeak2 (default = All)
supportMethodNum=[integer]: minimum number of supported peak calling methods (<=3, default = 0)

Response Format

Example

Get all MeRIP-Seq m6A peaks for human on exons, on gene PGBD2, and derived from exomePeak2

curl 
                            'http://www.rnamd.org/m6a/apiLowResolution.php?species=HomoSapiens&gene=PGBD2&genomicRegion=Exon&callPeakMethod=exomePeak2' > m6A-Atlas2_LowRes_HomoSapiens.txt

Get all MeRIP-Seq m6A peaks for bee on intron derived from at least 2 peak calling methods

curl 
                            'http://www.rnamd.org/m6a/apiLowResolution.php?species=ApisMellifera&genomicRegion=Intron&supportMethodNum=2' > m6A-Atlas2_LowRes_ApisMellifera.txt

Get high resolution data
Description	Retrieve data of the high resolution m6A modification sites
Query Format	species=[scientific name]: e.g., HomoSapiens, MusMusculus, DanioRerio. essential parameter. gene=[gene name]: e.g., PGBD2, Cr1l, Eif3a (default = All) genomicRegion=[genomic region]: 3' UTR, 5' UTR, Exon, Intron, Intergenic (default = All) techniqueNum=[integer]: minimum number of supported mapping techniques (<=12, default = 0) cellLineNum=[integer]: minimum number of supported cell lines (default = 0) conditionNum=[integer]*: minimum number of supported experiment conditions (default = 0)
Response Format
Example	Get all high resolution m6A sites for rat on exon as supported by at least 2 cell lines `curl 'http://www.rnamd.org/m6a/apiHighResolution.php?species=RattusNorvegicus&genomicRegion=Exon&cellLineNum=2' > m6A-Atlas2_HighRes_RattusNorvegicus.txt` Get all high resolution m6A sites for mouse on 3'UTR as supported by at least 2 experiment conditions `curl 'http://www.rnamd.org/m6a/apiHighResolution.php?species=MusMusculus&genomicRegion=3'UTR&conditionNum=2' > m6A-Atlas2_HighRes_MusMusculus.txt`

Get high resolution data

Description

Retrieve data of the high resolution m6A modification sites

Query Format

species=[scientific name]: e.g., HomoSapiens, MusMusculus, DanioRerio. *essential parameter.
gene=[gene name]: e.g., PGBD2, Cr1l, Eif3a (default = All)
genomicRegion=[genomic region]: 3' UTR, 5' UTR, Exon, Intron, Intergenic (default = All)
techniqueNum=[integer]: minimum number of supported mapping techniques (<=12, default = 0)
cellLineNum=[integer]: minimum number of supported cell lines (default = 0)
conditionNum=[integer]: minimum number of supported experiment conditions (default = 0)

Response Format

Example

Get all high resolution m6A sites for rat on exon as supported by at least 2 cell lines

curl 
                            'http://www.rnamd.org/m6a/apiHighResolution.php?species=RattusNorvegicus&genomicRegion=Exon&cellLineNum=2' > m6A-Atlas2_HighRes_RattusNorvegicus.txt

Get all high resolution m6A sites for mouse on 3'UTR as supported by at least 2 experiment conditions

curl 
                            'http://www.rnamd.org/m6a/apiHighResolution.php?species=MusMusculus&genomicRegion=3'UTR&conditionNum=2' > m6A-Atlas2_HighRes_MusMusculus.txt

Species	Genome version	Type	Download
Arabidopsis Thaliana	TAIR10	Basic sites Information	RDS TXT
Drosophila Melanogaster	BDGP6	Basic sites Information	RDS TXT
Homo Sapiens	hg38	Basic sites Information	RDS TXT
Mus Musculus	mm10	Basic sites Information	RDS TXT
Rattus Norvegicus	Rnor6	Basic sites Information	RDS TXT
Saccharomyces Cerevisiae	R64-1-1	Basic sites Information	RDS TXT
Danio Rerio	danRer10	Basic sites Information	RDS TXT

Species

Genome version

Type

Download

Arabidopsis Thaliana

TAIR10

Basic sites Information

RDS TXT

Drosophila Melanogaster

BDGP6

Basic sites Information

RDS TXT

Homo Sapiens

hg38

Basic sites Information

RDS TXT

Mus Musculus

mm10

Basic sites Information

RDS TXT

Rattus Norvegicus

Rnor6

Basic sites Information

RDS TXT

Saccharomyces Cerevisiae

R64-1-1

Basic sites Information

RDS TXT

Danio Rerio

danRer10

Basic sites Information

RDS TXT

Species	Type	Download
Species	Type
Arabidopsis Thaliana	RBP Information	RDS TXT
Arabidopsis Thaliana	SNP Information	RDS TXT
Arabidopsis Thaliana	Condition Information	RDS TXT
Arabidopsis Thaliana	Quantification Information	RDS TXT
Drosophila Melanogaster	RBP Information	RDS TXT
Drosophila Melanogaster	miRNA Information	RDS TXT
Drosophila Melanogaster	Splicing Site Information	RDS TXT
Drosophila Melanogaster	Condition Information	RDS TXT
Homo Sapiens	RBP Information	RDS TXT
Homo Sapiens	SNP Information	RDS TXT
Homo Sapiens	miRNA Information	RDS TXT
Homo Sapiens	Splicing Site Information	RDS TXT
Homo Sapiens	Condition Information	RDS TXT
Homo Sapiens	Quantification Information	RDS TXT
Homo Sapiens	Conservation Information	RDS TXT
Homo Sapiens	phastCons Information	RDS TXT
Homo Sapiens	subLocal Information	RDS TXT
Homo Sapiens	Other modification Information	RDS TXT
Mus Musculus	RBP Information	RDS TXT
Mus Musculus	SNP Information	RDS TXT
Mus Musculus	miRNA Information	RDS TXT
Mus Musculus	Splicing Site Information	RDS TXT
Mus Musculus	Condition Information	RDS TXT
Mus Musculus	Quantification Information	RDS TXT
Mus Musculus	Conservation Information	RDS TXT
Mus Musculus	Other modification Information	RDS TXT
Rattus Norvegicus	SNP Information	RDS TXT
Rattus Norvegicus	Condition Information	RDS TXT
Rattus Norvegicus	Quantification Information	RDS TXT
Rattus Norvegicus	Conservation Information	RDS TXT
Saccharomyces Cerevisiae	SNP Information	RDS TXT
Saccharomyces Cerevisiae	Condition Information	RDS TXT
Saccharomyces Cerevisiae	Quantification Information	RDS TXT
Danio Rerio	SNP Information	RDS TXT
Danio Rerio	Condition Information	RDS TXT
Danio Rerio	Quantification Information	RDS TXT
Danio Rerio	Conservation Information	RDS TXT

Species

Type

Download

Species

Type

Arabidopsis Thaliana

RBP Information

RDS TXT

Arabidopsis Thaliana

SNP Information

RDS TXT

Arabidopsis Thaliana

Condition Information

RDS TXT

Arabidopsis Thaliana

Quantification Information

RDS TXT

Drosophila Melanogaster

RBP Information

RDS TXT

Drosophila Melanogaster

miRNA Information

RDS TXT

Drosophila Melanogaster

Splicing Site Information

RDS TXT

Drosophila Melanogaster

Condition Information

RDS TXT

Homo Sapiens

RBP Information

RDS TXT

Homo Sapiens

SNP Information

RDS TXT

Homo Sapiens

miRNA Information

RDS TXT

Homo Sapiens

Splicing Site Information

RDS TXT

Homo Sapiens

Condition Information

RDS TXT

Homo Sapiens

Quantification Information

RDS TXT

Homo Sapiens

Conservation Information

RDS TXT

Homo Sapiens

phastCons Information

RDS TXT

Homo Sapiens

subLocal Information

RDS TXT

Homo Sapiens

Other modification Information

RDS TXT

Mus Musculus

RBP Information

RDS TXT

Mus Musculus

SNP Information

RDS TXT

Mus Musculus

miRNA Information

RDS TXT

Mus Musculus

Splicing Site Information

RDS TXT

Mus Musculus

Condition Information

RDS TXT

Mus Musculus

Quantification Information

RDS TXT

Mus Musculus

Conservation Information

RDS TXT

Mus Musculus

Other modification Information

RDS TXT

Rattus Norvegicus

SNP Information

RDS TXT

Rattus Norvegicus

Condition Information

RDS TXT

Rattus Norvegicus

Quantification Information

RDS TXT

Rattus Norvegicus

Conservation Information

RDS TXT

Saccharomyces Cerevisiae

SNP Information

RDS TXT

Saccharomyces Cerevisiae

Condition Information

RDS TXT

Saccharomyces Cerevisiae

Quantification Information

RDS TXT

Danio Rerio

SNP Information

RDS TXT

Danio Rerio

Condition Information

RDS TXT

Danio Rerio

Quantification Information

RDS TXT

Danio Rerio

Conservation Information

RDS TXT

ID	ID encoded in m⁶A-Atlas v2.0, e.g., m6A_mm10_27966
Seqname	Name of the sequence, e.g., chr1
Position	Position of modification site, e.g., 10000
Strand	The strand orientation, e.g., + or -
Condition	It contains GEO Accession Number; Technique; Cell Line/Tissue and Treatment, e.g., GSE116334;miCLIP;Arabidopsis_thaliana;leaf;Ctrl
ConditionNum	Number of supported conditions, e.g., 3
GeneName	Name of the gene, e.g., Cr1l
GeneBiotype	Type of gene, e.g., protein_coding
Region	The genomic region, e.g., exon
RBPNum	Number of RNA-binding proteins, e.g., 2
miRNANum	Number of targeted microRNAs, e.g., 3
SplicingSiteNum	Number of splicing sites, e.g., 4
SNPNum	Number of single nucleotide polymorphisms, e.g., 5
CellLine	The used cell line where m6A is detected, e.g., HeLa
CellLineNum	The number of used cell line where m6A is detected, e.g., 2
Technique	The used technique where m6A is detected, e.g., miCLIP
TechniqueNum	The number of used technique where m6A is detected, e.g., 2
Quantification	Is there a quantification? 0: No; 1:Yes

PeakID	Peak ID encoded in m⁶A-Atlas v2.0
Seqname	Name of the sequence, e.g., chr1
Start	Position of modification start site, e.g., 10000
End	Position of modification end site, e.g., 10050
Width	The width of the peak, e.g., 50
Strand	The strand orientation, e.g., + or -
GeneID	Identifier of the gene, e.g., ENSG00000123456
GeneName	Name of the gene, e.g., Cr1l
Log2FC	Log2 fold change, e.g., 1.5
PValue	P-value of the significance test, e.g., 0.05
GSE	GEO accession number, e.g., GSE12345
CellLine	The used cell line, e.g., HeLa
Treatment	The treatment applied, e.g., DrugA
TPM	Transcripts Per Kilobase Million, e.g., 1000
DRACH	DRACH motif presence (1: present, 0: absent)
Region	The genomic region, e.g., exon
SupportMethods	Supported peak calling methods, e.g., MACS2
CallPeakMethods	Peak calling method, e.g., exomePeak2