Background
Characterization of circRNAs
Biogenesis of circRNAs
Function mechanisms of circRNAs
Translation potential of circRNAs
CircRNA degradation
Principles and challenges for circRNA discovery and annotation
Software | Seq type | Language | Latest update | Download link | Characteristic | Refs. |
---|---|---|---|---|---|---|
MapSplice | II | C++ | 2016 | / | [74] | |
PcircRNA_finder | II | Python, Perl | 2016 | Predict circRNAs in plants with frequently used circRNA detect tools | [75] | |
PredcircRNATool | II | Python | 2016 | Identification of circular RNAs based on conformational and thermodynamic properties in the flanking introns | [108] | |
CircPro | II | Perl | 2017 | Identify the protein-coding potential circRNAs | [198] | |
CIRI | II | Perl | 2017 | De novo assemble novel circRNA with variable sequencing data | [82] | |
ACFS | II | Perl, Shell | 2017 | Discovery and annotate circRNA from single-end RNA-seq | [91] | |
find_circ | II | Python | 2017 | De novo assemble novel circRNA transcripts and widely used in circbase | [49] | |
circseq-cup | II | Python | 2017 | Identify full-length sequence of circRNAs | [207] | |
KNIFE | II | Python, Shell, Perl | 2017 | Detect and quantify circRNAs from junctional alignments | [208] | |
PredcircRNA | II | Python | 2017 | Distinguish circRNA from other lncRNAs using multiple kernel learning | [76] | |
CPSS | II | PHP, Perl, R | 2017 | For small RNA sequencing data analysis | [209] | |
miARma-seq | II | Perl, Python, R | 2018 | Integration of mRNA, miRNA and circRNA analysis | [210] | |
CIRI-AS | II | Perl | 2018 | Identify circRNA internal components and alternative splicing events de novo | [211] | |
hppRNA | II | Perl, R | 2018 | Analysis circRNA with different core-workflows from a large number of samples | [212] | |
segemehl | II | C + + | 2018 | Detect back-splice reads and gene fusion | [83] | |
STARChip | II | Perl, Shell | 2018 | Output the chimeric reads and discovery fusions circRNAs | [89] | |
UROBORUS | II | Perl | 2018 | Suggest detecting circRNAs with low expression levels in RNA-seq | [133] | |
WebCircRNA | II | Python | 2018 | Using machine-learning based method to predict stem cell specific circRNAs | [213] | |
circRNA_finder | II | Perl, Awk, Shell | 2019 | / | [81] | |
CircRNAFisher | II | Perl | 2019 | Identify circRNA de novo | [214] | |
PRAPI | III | Python | 2019 | One-stop solution of post-transcriptional regulation analysis for Iso-seq, suitable for third generation sequencing | [101] | |
CircRNAWrap | II | Shell, R | 2019 | Integrate multiple circRNA-detect tools to discovery confidence circRNAs | [85] | |
RAISE | II | Shell, Perl | 2019 | Integrating detection, quantification and prediction of internal structure | [84] | |
DeepCirCode | II | Python, R | 2019 | Using machine-learning model to predict back-splice sites of circRNA | [77] | |
ROP | II | Shell, Python | 2019 | Discover the source of all reads with Python2, but it is no longer maintained | [215] | |
ACValidator | II | Python, Shell | 2020 | Assemble circRNA from pseudo-reference file | [216] | |
CircDBG | II | C + + | 2020 | Detect circRNA by de Brujin graph | [217] | |
CircMarker | II | C + + . Java | 2020 | / | [218] | |
AutoCirc | II | Perl | 2020 | Identify back-splice junctions of potential circRNAs from RNA-seq de novo quickly | [24] | |
Pcirc | II | Python | 2020 | Identify plant circRNA with random forest methods | [110] | |
cirRNAPL | II | Java | 2020 | Identification of circRNAs based on extreme learning machine | [109] | |
circDeep | II | Python | 2020 | Identification of circRNAs with deep learning | [111] | |
CLEAR | II | Python | 2020 | Combine with ribo-seq & RNA-seq as input, and quantify the expression of circRNAs | [219] | |
NCLcomparator | II | Roff | 2020 | Detect circRNAs by combined several non-co-linear transcript | [220] | |
CIRCexplorer | II | Python | 2021 | De novo assemble novel circRNA with supporting many common aligners | [13] | |
CIRI-full | II | Perl | 2021 | Reconstruct and quantify full-length circular RNAs from RNA-seq data sets | [134] | |
CIRI-long | III | Perl | 2021 | Identify circRNA from long-reads sequencing data | [102] | |
CIRIquant | II | Perl | 2021 | Quantify circRNA expression from RNA-seq data | [221] | |
CirCompara2 | II | Python, R | 2021 | Integrate multiple circRNA-detect tools to discovery confidence circRNAs | [86] | |
circAST | II | Python | 2021 | Assemble full-length circRNAs and quantification using RNA-Seq data with the back-spliced events | [222] | |
DCC and CircTest | II | Python | 2022 | Detect and quantify circRNAs from chimeric reads | [78] | |
Ularcirc | II | R | 2022 | Analysis and visualize the canonical and back-splice junctions, annotate circRNA with overlapping gene information | [80] | |
NCLscan | II | C + + , Python | 2022 | Identify both intragenic and intergenic non-co-linear transcript | [205] | |
circall | II | C + + , R | 2022 | Discovery circRNAs from paired-end RNA-seq | [223] | |
CYCLeR | II | R | 2022 | Reconstruct and quantify circRNAs from RNA-seq datasets accurately | [224] | |
stackCirRNAPred | II | Python | 2022 | Identification of circRNAs based on stacking strategy | [107] | |
circtools | II | Python, R | 2023 | Integrate the cumbersome circRNA analysis process of analysis | [225] | |
circfull | III | Python | 2023 | Detect and quantify full-length circRNA isoforms from circFL-seq | [105] | |
isocirc | III | Python, R | 2023 | Integrated pipeline to characterize full-length circRNA isoforms using rolling circle amplification | [104] |
Canonical BSJ-based circRNA identification
Fusion circRNA identification
circRNA identification using long-read sequencing data
circRNA identification using machine learning
Database for circRNA annotation and functional study
New insight into strategies to determine circRNA functions
Strategies for circRNA detection
New insight into the knockdown/out of functional circRNAs
Overexpression of functional circRNAs
ceRNA prediction
circRNA-RBP prediction
circR-loops: circRNA:DNA hybrids
New insights into biomedical application of cancer-related circRNA
CircRNA is a promising biomarker in cancer
Cancer | Name | Up/down | Characteristic | Refs. |
---|---|---|---|---|
Hematologic malignancies | ||||
AML | Circ_0009910 | Up | Silencing Circ_0009910 can significantly inhibit proliferation, sphere formation and promote apoptosis | [226] |
AML | Circ-SFMBT2 | Up | Silencing Circ-SFMBT2 can inhibit the proliferation, migration, invasion and glycolysis of AML cells and induce apoptosis | [227] |
AML | circ_0040823 | Down | Overexpression of circ_0040823 inhibited the proliferation of AML cells and induced apoptosis and cell cycle arrest | [184] |
AML | hsa_circ_0079480 | Up | Associated with overall survival and relapse-free survival of AML | [228] |
AML | circ_0004277 | Down | Overexpression of circ 0004277 inhibited the migration and invasion of AML cells | [183] |
ALL | Circ_0000745 | Up | Knockdown of Circ_0000745 inhibits cell cycle progression and glycolysis, and induces apoptosis and iron death | [229] |
ALL | circ_0008012 | Up | related to proliferation and apoptosis of ALL cells | [230] |
CLL | circ-CBFB | Up | Knockdown of circ-CBFB inhibited the proliferation of CLL cells, stopped the cell cycle and induced apoptosis | [231] |
CLL | hsa_circ_0132266 | Down | Inhibition of CLL cell apoptosis and impaired proliferation | [232] |
CLL | Hsa_circ_0064574 | Up | highly expressed in the plasma of CLL patients | [233] |
CLL | circZNF91 | Up | Silencing circZNF91 can inhibit CLL cell proliferation, induce apoptosis and block cell cycle | [234] |
CML | Hsa_circ_0058493 | Up | Increase the resistance of CML cells to imatinib | [235] |
CML | circ_0080145 | Up | Increase the resistance of CML cells to imatinib | [236] |
CML | circ_0051886 | Up | Increase the resistance of CML cells to imatinib | [236] |
MM | Circ_0000190 | Down | Inhibiting the viability, proliferation and inducing apoptosis | [237] |
MM | hsa_circ_0007841 | Up | Associated with drug resistance and chromosome aberration | [38] |
MM | circITCH | Down | Related to the resistance of MM cells to bortezomib (BTZ) | [238] |
Digestive system malignancy | ||||
CRC | Hsa_circ_0082182 | Up | Associated with tumor proliferation and lymph node metastasis | [239] |
CRC | Hsa_circ_0000370 | Up | Associated with tumor proliferation and lymph node metastasis | [239] |
CRC | hsa_circ_0004585 | Up | Positively correlated with tumor size | [240] |
CRC | hsa_circ_0000567 | Down | Negatively correlated with tumor size, lymph node metastasis, remote metastasis, and TNM staging | [241] |
CRC | hsa_circ_0004771 | Up | Upregulated in tumor cell-derived plasma exosomes | [242] |
HCC | circIPO11 | Up | Drives self-renewal of liver cancer | [123] |
HCC | hsa_circ_0000798 | Up | High expression in liver cancer tissues was negatively correlated with the overall survival cycle of patients | [243] |
HCC | hsa_circ_0027089 | Up | Distinguishing cirrhosis | [244] |
HCC | hsa_circ_0058124 | Up | Associated with invasive characteristics, also regulates the resistance of liver cancer cells to sorafenib | [245] |
HCC | hsa_circSMARCA5 | Down | Related to proliferation, invasion and metastasis | [246] |
HCC | hsa_circ_0068669 | Down | Related to tumor microvascular invasion and TNM staging | [247] |
HCC | hsa_circ_0028502 | Down | associated with lymph node metastasis and TNM stage | [248] |
HCC | hsa_circ_0076251 | Down | Associated with Barcelona Clinic Liver Cancer (BCLC) stage | [248] |
HCC | circUBAP2 | Up | Negatively correlated with aggressive clinical characteristics | [249] |
HCC | circRNA-YBX1 | Down | Mediate phase separation suppresses the metastasis | |
GC | circNRIP1 | Inhibit the growth of gastric cancer | [179] | |
GC | hsa_circ_0003159 | Down | Negative correlation between tumor metastasis and TNM stage | [250] |
GC | hsa_circ_0000096 | Down | Affects the growth and migration of GC cells | [251] |
GC | hsa_circ_002059 | Down | Associated with distal metastasis of tumor cells and TNM staging | [252] |
GC | hsa_circ_0000190 | Down | Related to tumor diameter, lymphoid metastasis, distal metastasis and TNM stage | [253] |
GC | hsa_circ_0000181 | Down | Associated with tumor diameter, lymphoid metastasis | [254] |
GC | hsa_circ_0000467 | Up | Closely related to TNM staging | [255] |
GC | hsa_circ_0001895 | Down | Down-regulated in GC tissue and precancerous stage of GC | [256] |
GC | hsa_circ_0017728 | Up | Associated with short overall survival, poor pathological differentiation, higher TNM stage and lymph node metastasis | [257] |
GC | circPDIA4 | Up | Accelerate the invasion of cancer cells in vitro, promote the progression of GC and indicate poor prognosis | [258] |
BC | Hsa_circ_0001136 | Up | Associated with tumor grade, tumor stage, lymph node invasion and distal metastasis | [259] |
BC | hsa_circ_0137439 | Up | Related to tumor grade, tumor stage, lymph node invasion, also can distinguish between MIBC and NMIBC | [260] |
BC | hsa_circ_0001361 | Up | Promoted the invasion and metastasis of bladder cancer cells and was positively correlated with pathological grade | [261] |
BC | circSLC8A1 | Down | Overexpression inhibits the migration, invasion and proliferation of tumor cells | [262] |
PC | circANAPC7 | Down | Inhibits Tumor Growth and Muscle Wasting | [180] |
PC | Circ-MBOAT2 | Up | Regulates cell proliferation, migration, invasion and glutamine catabolism | [181] |
PC | circRNA IARS | Up | Positively correlated with hepatic metastasis, vascular infiltration and TNM stage of pancreatic ductal adenocarcinoma (PDAC), and negatively correlated with postoperative survival time | [263] |
PC | hsa_circRNA_001859 | Down | Inhibit the proliferation, invasion and EMT of pancreatic cancer | [264] |
OSCC | Hsa_circ_0001971 | Up | Related to TNM stage of tumor | [265] |
OSCC | Hsa_circ_0001874 | Up | Related to tumor grade and TNM stage | [265] |
OSCC | Hsa_circ_0003829 | Down | Negatively correlated with lymph node metastasis and TNM stage | [266] |
OSCC | Circ_0109291 | Up | Silencing circ_0109291 can improve tumor sensitivity to DDP | [267] |
ESCC | Hsa_circ_0003823 | Up | Promotes the Tumor Progression, Metastasis and Apatinib Resistance | [167] |
ESCC | circPUM1 | Up | Regulates oxidative phosphorylation | [168] |
ESCC | circCYP24A1 | Up | Facilitates esophageal squamous cell carcinoma progression | [169] |
ESCC | circCNOT6L | Up | Regulates cell development | [170] |
ESCC | circGSK3β | Up | Promotes metastasis | [171] |
EC | circ-VIM | Up | Silencing circ-VIM in vitro can inhibit immune escape and multiple carcinogenic activities of EC cells, as well as inhibit internal xenograft growth and lung metastasis | [182] |
Lung cancer | ||||
LC | Hsa_circ_0001715 | Up | Related to TNM stage and distant metastasis of lung adenocarcinoma, and inversely proportional to overall survival | [268] |
LC | Hsa_circ_0005962 | Up | Promote the proliferation of lung adenocarcinoma cells (LUAD) | [269] |
LC | Hsa_circ_0086414 | Down | Plasma hsa_circ_0086414 was related to EGFR mutations | [269] |
LC | Hsa_circ_002178 | Up | Promotes the expression of PDL1/PD1 in lung adenocarcinoma cells and is also present in exosomes | [270] |
LC | Hsa_circ_0037515 | Down | Significantly down-regulated in non-small cell lung cancer (NSCLC) | [271] |
LC | Hsa_circ_0037516 | Down | significantly down-regulated in non-small cell lung cancer | [271] |
LC | hsa_circ_0001073 | Down | Indicates the lung adenocarcinoma (LUAD) subtype in non-small cell lung cancer | [165] |
LC | hsa_circ_0001495 | Up | Indicates the squamous cell carcinoma (LUSC) subtype in non-small cell lung cancer | [165] |
Others | ||||
RC | circHIAT1 | Down | Overexpression inhibits the malignant progression of clear cell renal cell carcinoma | [272] |
RC | hsa_circ_001895 | Up | Promotes ccRCC cell proliferation, invasion and migration and is associated with poor prognosis | [273] |
GM | circRNA-104718 | Up | Indicates a poor prognosis and promotes invasion and migration of tumor cells | [274] |
GM | circ-GLIS3 | Up | Related to the resistance of temozolomide (TMZ) and promotes the proliferation, invasion and migration of glioma cells | [275] |
GM | Circ_0047688 | Up | Promote malignant behavior of glioma cells | [276] |
GM | Circ_0001982 | Up | Promote the proliferation, migration and invasion of glioma cells | [277] |
GM | has-circ-0072688 | Up | Promote the proliferation of glioblastoma and inhibit apoptosis | [278] |
GM | hsa_circ_0030018 | Up | Promote proliferation and inhibit apoptosis of glioma cells | [279] |
Breast cancer | hsa_circ_0008673 | Up | Related to tumor size and distal metastasis | [280] |
Breast cancer | Circ-LARP4 | Down | High expression indicates good prognosis and is negatively correlated with tumor size | [175] |
Breast cancer | circRNA-CREIT | Down | Increases drug resistance in triple negative breast cancer (TNBC) and is associated with poor prognosis | [40] |
OC | circBNC2 | Down | associated with advanced cancer and lymph node metastasis in epithelial ovarian cancer (EOC) | [281] |
TC | Hsa_circ_0137287 | Down | related to tumor size, lymph node metastasis and TNM stage | [282] |
CC | Circ_0000745 | Up | Knockdown Circ_0000745 inhibited proliferation, migration, invasion and glycolysis of cervical cancer cells | [283] |