circmimi 0.15.0

A toolset for investigating the interactions between circRNA - miRNA - mRNA.

CircMiMi

A toolset for investigating the interactions between circRNA - miRNA - mRNA.

Table of Contents

• Requirements
• Installation
• Quick Start
• Usage
  • Generate the references
    • Parameters
    • Available species and sources
  • Run the main pipeline
    • Parameters
    • Input file
    • Output files
      • summary_list.tsv
      • all_interactions.tsv
  • Create the network file for Cytoscape
    • Parameters

Requirements

• Python (3.6 or above)
• External tools
  • bedtools (2.29.0) (https://github.com/arq5x/bedtools2)
  • miranda (aug2010, 3.3a) (http://www.microrna.org/microrna/getDownloads.do)
  • blat (https://genome.ucsc.edu/FAQ/FAQblat.html)

Installation

The recommended way is via conda, a package and environment management system. (https://docs.conda.io/en/latest/)

You may install circmimi by the following steps:

$ conda create -n circmimi python3
$ conda activate circmimi
$ pip install circmimi

For the external tools, they can also be installed via conda with the bioconda(https://bioconda.github.io/) channel:

$ conda install -c bioconda bedtools miranda blat

Now, you can try the following command to test the installation,

$ circmimi_tools --help

it should print out with the help messages.

Quick Start

1. Generate the references

$ circmimi_tools genref --species hsa --source ensembl --version 98 ./refs

2. Run the main pipeline of CircMiMi

$ circmimi_tools run -r ./refs -i circRNAs.tsv -o ./out/ -p 5 --checkAA --miranda-sc 175

3. Create the network file for Cytoscape

$ circmimi_tools network create ./out/out.tsv ./out/out.xgmml

Usage

Generate the references

circmimi_tools genref --species SPECIES --source SOURCE [--version RELEASE_VER] REF_DIR

Parameters

Parameter	Description
--species SPECIES	Assign the species for references. Use the species code for SPECIES. [required]
--source SOURCE	Available values for SOURCE: "ensembl", "ensembl_plants", "ensembl_metazoa", "gencode". [required]
--version RELEASE_VER	The release version of the SOURCE. For examples, "98" for ("hsa", "ensembl"), "M24" for ("mmu", "gencode"). If the version is not assigned, the latest one will be used.

Available species and sources

Code	Name	E	G	EP	EM	MB	MTB	MDB
ath	Arabidopsis thaliana			V		V	V
bmo	Bombyx mori				V	V	V
bta	Bos taurus	V				V	V
cel	Caenorhabditis elegans	V			V	V	V
cfa	Canis familiaris	V				V	V	V
dre	Danio rerio	V				V	V
dme	Drosophila melanogaster	V				V	V
gga	Gallus gallus	V				V	V	V
hsa	Homo sapiens	V	V			V	V	V
mmu	Mus musculus	V	V			V	V	V
osa	Oryza sativa			V		V	V
ola	Oryzias latipes	V				V	V
oar	Ovis aries	V				V	V
rno	Rattus norvegicus	V				V	V	V
ssc	Sus scrofa	V				V	V
tgu	Taeniopygia guttata	V				V	V
xtr	Xenopus tropicalis	V				V	V

Gene annotation

• E: Ensembl (https://www.ensembl.org/index.html)
• G: Gencode (https://www.gencodegenes.org/)
• EP: Ensembl Plants (https://plants.ensembl.org/index.html)
• EM: Ensembl Metazoa (https://metazoa.ensembl.org/index.html)

Database for miRNAs

• MB: miRBase (v22) (http://www.mirbase.org/)

Databases for miRNA-mRNA interactions

• MTB: miRTarBase (v7.0) (http://mirtarbase.mbc.nctu.edu.tw/php/index.php)
• MDB: miRDB (v6.0) (http://mirdb.org/)

Run the main pipeline

circmimi_tools run -r REF_DIR -i CIRC_FILE [-o OUT_PREFIX] [-p NUM_PROC] [--checkAA] \
[--miranda-sc SCORE] [--miranda-en ENERGY] [--miranda-scale SCALE] [--miranda-strict] [--miranda-go X] [--miranda-ge Y]

Parameters

Parameter	Description
-r, --ref REF_DIR	The directory of the pre-genereated reference files. [required]
-i, --circ CIRC_FILE	The file of circRNAs. [required]
-o, --out-prefix OUT_PREFIX	Assign the prefix for the output filenames. (default: "./out/")
-p, --num_proc NUM_PROC	Assign the number of processes.
--checkAA	Check the circRNAs if there are ambiguous alignments.

The miRanda parameters are also available (see the manual of miRanda).

Parameters	Description
--miranda-sc SCORE	Set the alignment score threshold to SCORE. Only alignments with scores >= SCORE will be used for further analysis. (default: 140.0)
--miranda-en ENERGY	Set the energy threshold to ENERGY. Only alignments with energies <= ENERGY will be used for further analysis. A negative value is required for filtering to occur. (default: 1.0)
--miranda-scale SCALE	Set the scaling parameter to SCALE. This scaling is applied to match / mismatch scores in the critical 7bp region near the 5' end of the microRNA. Many known examples of miRNA:Target duplexes are highly complementary in this region. This parameter can be thought of as a contrast function to more effectively detect alignments of this type. (default: 4.0)
--miranda-strict	Require strict alignment in the seed region (offset positions 2-8). This option prevents the detection of target sites which contain gaps or non-cannonical base pairing in this region.
--miranda-go X	Set the gap-opening penalty to X for alignments. This value must be negative. (default: -4.0)
--miranda-ge Y	Set the gap-extend penalty to Y for alignments. This value must be negative. (default: -9.0)

Input file

The input file(CIRC_FILE) is a TAB-separated file with the following columns:

#	Column	Description
1	chr	Chromosome name
2	pos1	One of the position of the circRNA junction site
3	pos2	Another position of the circRNA junction site
4	strand	+ / -

Note.

• The chromosome name must be the same as the name in the SOURCE.
  • For example, "1" for "ensembl", and "chr1" for "gencode".

Output files

The main pipeline of CircMiMi outputs two main files: "summary_list.tsv" and "all_interactions.tsv".

summary_list.tsv

The summary list contains the counts of interactions and some checking results of the circRNAs.

#	Column	Description
1	chr	Chromosome name
2	pos1	One of the position of the circRNA junction site
3	pos2	Another position of the circRNA junction site
4	strand	+ / -
5	pass	'yes' for the circRNA passing all of the checking items (column 9 to 13). Otherwise 'no'.
6	#circRNA_miRNA	Count for the circRNA-miRNA interactions.
7	#circRNA_mRNA	Count for the circRNA-mRNA interactions.
8	#circRNA_miRNA_mRNA	Count for the circRNA-miRNA-mRNA interactions.
9	donor site not at the annotated boundary	'1' if the donor site of the circRNA is NOT at the annotated exon boundary. Otherwise '0'.
10	acceptor site not at the annotated boundary	'1' if the acceptor site of the circRNA is NOT at the annotated exon boundary. Otherwise '0'.
11	donor/acceptor sites not at the same transcript isoform	'1' if the donor and acceptor are not at the same annotated transcript isoform. Otherwise '0'.
12	ambiguity with an co-linear explanation	'1' if the merged flanking sequence of the circRNA junction sites has an co-linear explanation. Otherwise '0'.
13	ambiguity with multiple hits	'1' if the merged flanking sequence of the circRNA junction sites is with multiple hits. Otherwise '0'.

all_interactions.tsv

#	Column	Description
1	chr	Chromosome name
2	pos1	One of the position of the circRNA junction site
3	pos2	Another position of the circRNA junction site
4	strand	+ / -
5	host_gene	Host gene of the circRNA
6	mirna	The miRNA which may bind on the circRNA
7	max_score	The maximum binding score reported by miRanda
8	count	The number of the miRNA-binding sites on the circRNA
9	cross_boundary	If there is a binding site across the junction of the circRNA
10	target_gene	The miRNA-targeted gene
11	miRTarBase	Is the miRNA-mRNA interaction reported from miRTarBase
12	miRDB	Is the miRNA-mRNA interaction reported from miRDB
13	miRTarBase__ref_count	The number of references reporting the interaction
14	miRDB__targeting_score	The predicted target score from miRDB

Create the network file for Cytoscape

circmimi_tools network create IN_FILE OUT_FILE

Parameters

Parameter	Description
IN_FILE	Input the file "all_interactions.tsv" produced from the CircMiMi main pipeline.
OUT_FILE	The output filename. The file extension should be ".xgmml" or ".xml", so that the Cytoscape would recognize this file as an XGMML network file.

This command can generate a Cytoscape-executable file (.xgmml) for visualization of the input circRNA-miRNA-mRNA regulatory axes in Cytoscape.