pre-miRNA Information | |
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pre-miRNA | hsa-mir-3123 |
Genomic Coordinates | chr1: 241132272 - 241132346 |
Description | Homo sapiens miR-3123 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | |||||||||||||||
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Mature miRNA | hsa-miR-3123 | ||||||||||||||
Sequence | 49| CAGAGAAUUGUUUAAUC |65 | ||||||||||||||
Evidence | Experimental | ||||||||||||||
Experiments | Illumina | ||||||||||||||
Editing Events in miRNAs |
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SNPs in miRNA |
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Putative Targets |
miRNA Expression profile | |
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miRNAs in Extracellular Vesicles |
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Circulating MicroRNA Expression Profiling |
Gene Information | |||||||||||||||||||||
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Gene Symbol | MRPS21 | ||||||||||||||||||||
Synonyms | MDS016, MRP-S21, RPMS21 | ||||||||||||||||||||
Description | mitochondrial ribosomal protein S21 | ||||||||||||||||||||
Transcript | NM_018997 | ||||||||||||||||||||
Other Transcripts | NM_031901 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on MRPS21 | |||||||||||||||||||||
3'UTR of MRPS21 (miRNA target sites are highlighted) |
>MRPS21|NM_018997|3'UTR 1 GGCCTGTGGGTGGGACACCCAGTGCGAAACCCTCATCCAGTTTTCTCTCCATCTCTTTTCTTTGTACAATCCCATTTCCT 81 ATTACCATTCTCTGCAATAAACTCAAATCACATGTCTGCAAGAAGGCCTCCAAATATAGAAACAATCCCATTAGTCAGCA 161 GTGGACCCTGTCTTTTATTAAGTGAAAGAAGAAACTGAGTCTGAAAGTACTCTAGGAGTAGAATGGTATTTGCCAGGGAC 241 TGGAGGAGGGGGCAGTGAGGAGTTATTGTTTAATGGGTACAGAGTTTCAGTTTGGGCAGATGAAAAAGTTCAGGAGACGA 321 TGGCCTGGCATGGTGGCTCACGCCTGTTATCCCAACACTTTGGGAGGCTGAGGCGGGCGGCTCACTTGAGGCCAGGAGTT 401 TGAGACCAGCTTGGCCAATGTGGTGAAACCCCATCTCTACTAAAAATACAAAAAAAAATTGGCCGGGCGTGGTGGTGCAC 481 GCCTGTAATCCCAGATACTTGGGTGGCTGAGGCAGGAGAATTGCTTGAACTGGGGAGGAAGAGGTTGCAGTGAGCCAAGA 561 TCATGCCACTGCACTCCAACCTGGGCGACAGAGTGAGACTCCATCTCAAAACAAAAAAACGGAGATGGATGATGAATGGT 641 GATGGCGGTTGCTCAAAAAGTTGAATGTACTTAATGCCACTGAACTATACCCTTAAATGGTCACGATGGTAAATTTTGTG 721 TTTTACTACAATAAAAACTTTTTTGAAAGTCAAAAAAAAAAAAAAAAAAAAAAAAAA Target sites
Provided by authors
Predicted by miRanda
DRVs
SNPs
DRVs & SNPs
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miRNA-target interactions (Predicted by miRanda) |
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DRVs in gene 3'UTRs | |||||||||||||||||||||
SNPs in gene 3'UTRs |
Experimental Support 1 for Functional miRNA-Target Interaction | |
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miRNA:Target | ---- |
Validation Method |
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Conditions | TZM-bl |
Location of target site | 3'UTR |
Tools used in this research | TargetScan , miRTarCLIP , Piranha |
Original Description (Extracted from the article) |
...
PAR-CLIP data was present in GSM1462574. RNA binding protein: AGO2. Condition:TZM-bl ami BaL
... - Whisnant AW; Bogerd HP; Flores O; Ho P; et al., 2013, mBio. |
Article |
- Whisnant AW; Bogerd HP; Flores O; Ho P; et al. - mBio, 2013
UNLABELLED: The question of how HIV-1 interfaces with cellular microRNA (miRNA) biogenesis and effector mechanisms has been highly controversial. Here, we first used deep sequencing of small RNAs present in two different infected cell lines (TZM-bl and C8166) and two types of primary human cells (CD4(+) peripheral blood mononuclear cells [PBMCs] and macrophages) to unequivocally demonstrate that HIV-1 does not encode any viral miRNAs. Perhaps surprisingly, we also observed that infection of T cells by HIV-1 has only a modest effect on the expression of cellular miRNAs at early times after infection. Comprehensive analysis of miRNA binding to the HIV-1 genome using the photoactivatable ribonucleoside-induced cross-linking and immunoprecipitation (PAR-CLIP) technique revealed several binding sites for cellular miRNAs, a subset of which were shown to be capable of mediating miRNA-mediated repression of gene expression. However, the main finding from this analysis is that HIV-1 transcripts are largely refractory to miRNA binding, most probably due to extensive viral RNA secondary structure. Together, these data demonstrate that HIV-1 neither encodes viral miRNAs nor strongly influences cellular miRNA expression, at least early after infection, and imply that HIV-1 transcripts have evolved to avoid inhibition by preexisting cellular miRNAs by adopting extensive RNA secondary structures that occlude most potential miRNA binding sites. IMPORTANCE: MicroRNAs (miRNAs) are a ubiquitous class of small regulatory RNAs that serve as posttranscriptional regulators of gene expression. Previous work has suggested that HIV-1 might subvert the function of the cellular miRNA machinery by expressing viral miRNAs or by dramatically altering the level of cellular miRNA expression. Using very sensitive approaches, we now demonstrate that neither of these ideas is in fact correct. Moreover, HIV-1 transcripts appear to largely avoid regulation by cellular miRNAs by adopting an extensive RNA secondary structure that occludes the ability of cellular miRNAs to interact with viral mRNAs. Together, these data suggest that HIV-1, rather than seeking to control miRNA function in infected cells, has instead evolved a mechanism to become largely invisible to cellular miRNA effector mechanisms.
LinkOut: [PMID: 23592263]
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Experimental Support 2 for Functional miRNA-Target Interaction | |
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miRNA:Target | ---- |
Validation Method |
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Conditions | Prostate Tissue |
Location of target site | 3'UTR |
Tools used in this research | TargetScan , miRTarCLIP , Piranha |
Original Description (Extracted from the article) |
...
PAR-CLIP data was present in SRX1760632. RNA binding protein: AGO2. Condition:AGO-CLIP-22RV1_C
... - Hamilton MP; Rajapakshe KI; Bader DA; Cerne et al., 2016, Neoplasia (New York, N.Y.). |
Article |
- Hamilton MP; Rajapakshe KI; Bader DA; Cerne et al. - Neoplasia (New York, N.Y.), 2016
MicroRNA (miRNA) deregulation in prostate cancer (PCa) contributes to PCa initiation and metastatic progression. To comprehensively define the cancer-associated changes in miRNA targeting and function in commonly studied models of PCa, we performed photoactivatable ribonucleoside-enhanced cross-linking immunoprecipitation of the Argonaute protein in a panel of PCa cell lines modeling different stages of PCa progression. Using this comprehensive catalogue of miRNA targets, we analyzed miRNA targeting on known drivers of PCa and examined tissue-specific and stage-specific pathway targeting by miRNAs. We found that androgen receptor is the most frequently targeted PCa oncogene and that miR-148a targets the largest number of known PCa drivers. Globally, tissue-specific and stage-specific changes in miRNA targeting are driven by homeostatic response to active oncogenic pathways. Our findings indicate that, even in advanced PCa, the miRNA pool adapts to regulate continuing alterations in the cancer genome to balance oncogenic molecular changes. These findings are important because they are the first to globally characterize miRNA changes in PCa and demonstrate how the miRNA target spectrum responds to staged tumorigenesis.
LinkOut: [PMID: 27292025]
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CLIP-seq Support 1 for dataset GSM4903833 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / CTL_TD_21_a |
Location of target site | NM_031901 | 3UTR | UCUCUCCAUCUCUUUUCUUUGUACAAUCCCAUUUCCUAUUACCAUUCUCUGCAAUAAACUCAAAUCAC |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 2 for dataset GSM4903834 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / CTL_TD_21_b |
Location of target site | NM_031901 | 3UTR | CCCAUUUCCUAUUACCAUUCUCUGCAAUAAACUCAAAUCAC |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 3 for dataset GSM1462574 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | TZM-bl / TZM-bl ami BaL |
Location of target site | ENST00000309092.7 | 3UTR | UACAAUCCCAUUUCCUAUUACCAUUCUCUGCAAUAAACUCAAAUCACAUGUCUG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23592263 / GSE59944 |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | |||||||
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MiRNA-Target Expression Profile (TCGA) | |||||||
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113 hsa-miR-3123 Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT058369 | TBCEL | tubulin folding cofactor E like | ![]() |
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2 | 4 | ||||||
MIRT059816 | EFNA1 | ephrin A1 | ![]() |
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2 | 2 | ||||||
MIRT066850 | TMEM19 | transmembrane protein 19 | ![]() |
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2 | 2 | ||||||
MIRT071503 | CALM1 | calmodulin 1 | ![]() |
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2 | 6 | ||||||
MIRT073758 | NUBP1 | nucleotide binding protein 1 | ![]() |
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2 | 2 | ||||||
MIRT074324 | TNRC6A | trinucleotide repeat containing 6A | ![]() |
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2 | 10 | ||||||
MIRT094805 | LMNB1 | lamin B1 | ![]() |
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2 | 2 | ||||||
MIRT099173 | MAP3K4 | mitogen-activated protein kinase kinase kinase 4 | ![]() |
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2 | 2 | ||||||
MIRT099545 | ID4 | inhibitor of DNA binding 4, HLH protein | ![]() |
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2 | 2 | ||||||
MIRT122643 | E2F3 | E2F transcription factor 3 | ![]() |
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2 | 2 | ||||||
MIRT180918 | RPRD2 | regulation of nuclear pre-mRNA domain containing 2 | ![]() |
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2 | 8 | ||||||
MIRT192844 | BLOC1S6 | biogenesis of lysosomal organelles complex 1 subunit 6 | ![]() |
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2 | 2 | ||||||
MIRT224984 | BAG4 | BCL2 associated athanogene 4 | ![]() |
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2 | 2 | ||||||
MIRT246065 | NRAS | NRAS proto-oncogene, GTPase | ![]() |
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2 | 2 | ||||||
MIRT357085 | PRRC1 | proline rich coiled-coil 1 | ![]() |
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2 | 2 | ||||||
MIRT378170 | C5ORF51 | chromosome 5 open reading frame 51 | ![]() |
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2 | 2 | ||||||
MIRT441636 | KDM5A | lysine demethylase 5A | ![]() |
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2 | 2 | ||||||
MIRT441802 | BCAS1 | breast carcinoma amplified sequence 1 | ![]() |
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2 | 2 | ||||||
MIRT443019 | C21orf91 | chromosome 21 open reading frame 91 | ![]() |
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2 | 2 | ||||||
MIRT443445 | SERPINB4 | serpin family B member 4 | ![]() |
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2 | 2 | ||||||
MIRT443661 | SERPINB3 | serpin family B member 3 | ![]() |
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2 | 2 | ||||||
MIRT443776 | STS | steroid sulfatase | ![]() |
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2 | 2 | ||||||
MIRT444663 | TSPAN14 | tetraspanin 14 | ![]() |
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2 | 2 | ||||||
MIRT444924 | KIAA1522 | KIAA1522 | ![]() |
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2 | 2 | ||||||
MIRT445378 | FOXO1 | forkhead box O1 | ![]() |
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2 | 2 | ||||||
MIRT447920 | PAIP2B | poly(A) binding protein interacting protein 2B | ![]() |
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2 | 2 | ||||||
MIRT449202 | PTPLAD2 | 3-hydroxyacyl-CoA dehydratase 4 | ![]() |
1 | 1 | |||||||
MIRT449713 | TSPYL1 | TSPY like 1 | ![]() |
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2 | 2 | ||||||
MIRT450403 | TMEM47 | transmembrane protein 47 | ![]() |
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2 | 2 | ||||||
MIRT450787 | PAPOLG | poly(A) polymerase gamma | ![]() |
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2 | 2 | ||||||
MIRT451381 | C19orf43 | telomerase RNA component interacting RNase | ![]() |
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2 | 2 | ||||||
MIRT452507 | WDR1 | WD repeat domain 1 | ![]() |
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2 | 2 | ||||||
MIRT453264 | PARP11 | poly(ADP-ribose) polymerase family member 11 | ![]() |
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2 | 2 | ||||||
MIRT454642 | FAM83H | family with sequence similarity 83 member H | ![]() |
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2 | 2 | ||||||
MIRT455513 | C6orf106 | chromosome 6 open reading frame 106 | ![]() |
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2 | 2 | ||||||
MIRT456709 | LDB1 | LIM domain binding 1 | ![]() |
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2 | 2 | ||||||
MIRT457231 | AP3D1 | adaptor related protein complex 3 delta 1 subunit | ![]() |
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2 | 2 | ||||||
MIRT459235 | MRPS21 | mitochondrial ribosomal protein S21 | ![]() |
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2 | 2 | ||||||
MIRT460553 | IFNAR1 | interferon alpha and beta receptor subunit 1 | ![]() |
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2 | 4 | ||||||
MIRT461424 | CTSL2 | cathepsin V | ![]() |
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2 | 3 | ||||||
MIRT462869 | CYP51A1 | cytochrome P450 family 51 subfamily A member 1 | ![]() |
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2 | 2 | ||||||
MIRT467178 | SPTY2D1 | SPT2 chromatin protein domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT469233 | RHOBTB3 | Rho related BTB domain containing 3 | ![]() |
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2 | 2 | ||||||
MIRT474125 | LIPC | lipase C, hepatic type | ![]() |
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2 | 2 | ||||||
MIRT475509 | HSP90B1 | heat shock protein 90 beta family member 1 | ![]() |
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2 | 4 | ||||||
MIRT478134 | DHX36 | DEAH-box helicase 36 | ![]() |
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2 | 2 | ||||||
MIRT481326 | ATP5A1 | ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle | ![]() |
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2 | 2 | ||||||
MIRT482003 | AMOTL2 | angiomotin like 2 | ![]() |
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2 | 2 | ||||||
MIRT482230 | AHCYL2 | adenosylhomocysteinase like 2 | ![]() |
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2 | 2 | ||||||
MIRT483436 | RHOXF2B | Rhox homeobox family member 2B | ![]() |
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2 | 2 | ||||||
MIRT483824 | ZC3H12B | zinc finger CCCH-type containing 12B | ![]() |
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2 | 2 | ||||||
MIRT492051 | TNFSF9 | TNF superfamily member 9 | ![]() |
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2 | 2 | ||||||
MIRT494114 | DLX6 | distal-less homeobox 6 | ![]() |
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2 | 2 | ||||||
MIRT498882 | ZNF12 | zinc finger protein 12 | ![]() |
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2 | 10 | ||||||
MIRT499674 | NPHP3 | nephrocystin 3 | ![]() |
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2 | 2 | ||||||
MIRT506932 | IGDCC4 | immunoglobulin superfamily DCC subclass member 4 | ![]() |
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2 | 6 | ||||||
MIRT509461 | ZNF587 | zinc finger protein 587 | ![]() |
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2 | 6 | ||||||
MIRT510048 | AKR1B10 | aldo-keto reductase family 1 member B10 | ![]() |
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2 | 4 | ||||||
MIRT514807 | NWD1 | NACHT and WD repeat domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT515217 | CRCP | CGRP receptor component | ![]() |
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2 | 2 | ||||||
MIRT515486 | INCENP | inner centromere protein | ![]() |
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2 | 4 | ||||||
MIRT517765 | ZNF366 | zinc finger protein 366 | ![]() |
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2 | 4 | ||||||
MIRT518216 | TRMT10B | tRNA methyltransferase 10B | ![]() |
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2 | 2 | ||||||
MIRT519602 | ZNF805 | zinc finger protein 805 | ![]() |
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2 | 2 | ||||||
MIRT523570 | GGCX | gamma-glutamyl carboxylase | ![]() |
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2 | 4 | ||||||
MIRT525795 | SOD2 | superoxide dismutase 2 | ![]() |
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2 | 2 | ||||||
MIRT533055 | ZBTB37 | zinc finger and BTB domain containing 37 | ![]() |
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2 | 2 | ||||||
MIRT534218 | SLC37A3 | solute carrier family 37 member 3 | ![]() |
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2 | 4 | ||||||
MIRT535633 | NR2E1 | nuclear receptor subfamily 2 group E member 1 | ![]() |
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2 | 2 | ||||||
MIRT535863 | MRPL17 | mitochondrial ribosomal protein L17 | ![]() |
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2 | 2 | ||||||
MIRT536344 | LEFTY1 | left-right determination factor 1 | ![]() |
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2 | 2 | ||||||
MIRT537923 | DSTYK | dual serine/threonine and tyrosine protein kinase | ![]() |
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2 | 2 | ||||||
MIRT543114 | SKA2 | spindle and kinetochore associated complex subunit 2 | ![]() |
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2 | 2 | ||||||
MIRT544717 | ZNF529 | zinc finger protein 529 | ![]() |
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2 | 2 | ||||||
MIRT544847 | BASP1 | brain abundant membrane attached signal protein 1 | ![]() |
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2 | 4 | ||||||
MIRT545536 | ARF3 | ADP ribosylation factor 3 | ![]() |
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2 | 2 | ||||||
MIRT547124 | PHLPP2 | PH domain and leucine rich repeat protein phosphatase 2 | ![]() |
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2 | 2 | ||||||
MIRT548070 | GIGYF1 | GRB10 interacting GYF protein 1 | ![]() |
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2 | 2 | ||||||
MIRT548446 | EIF1AX | eukaryotic translation initiation factor 1A, X-linked | ![]() |
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2 | 2 | ||||||
MIRT548626 | DAZAP1 | DAZ associated protein 1 | ![]() |
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2 | 4 | ||||||
MIRT550259 | FAM120AOS | family with sequence similarity 120A opposite strand | ![]() |
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2 | 2 | ||||||
MIRT551940 | AKAP8 | A-kinase anchoring protein 8 | ![]() |
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2 | 4 | ||||||
MIRT552511 | ZIK1 | zinc finger protein interacting with K protein 1 | ![]() |
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2 | 4 | ||||||
MIRT554015 | SPIRE1 | spire type actin nucleation factor 1 | ![]() |
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2 | 2 | ||||||
MIRT556647 | KPNA2 | karyopherin subunit alpha 2 | ![]() |
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2 | 4 | ||||||
MIRT559744 | ACOX1 | acyl-CoA oxidase 1 | ![]() |
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2 | 2 | ||||||
MIRT560393 | TMEM254 | transmembrane protein 254 | ![]() |
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2 | 2 | ||||||
MIRT562234 | HMGB2 | high mobility group box 2 | ![]() |
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2 | 2 | ||||||
MIRT563325 | ORC4 | origin recognition complex subunit 4 | ![]() |
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2 | 2 | ||||||
MIRT563697 | RPS26 | ribosomal protein S26 | ![]() |
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2 | 2 | ||||||
MIRT565066 | USP25 | ubiquitin specific peptidase 25 | ![]() |
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2 | 2 | ||||||
MIRT565349 | TMED2 | transmembrane p24 trafficking protein 2 | ![]() |
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2 | 2 | ||||||
MIRT565624 | SLC31A1 | solute carrier family 31 member 1 | ![]() |
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2 | 2 | ||||||
MIRT566379 | PNISR | PNN interacting serine and arginine rich protein | ![]() |
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2 | 2 | ||||||
MIRT567575 | FEM1C | fem-1 homolog C | ![]() |
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2 | 2 | ||||||
MIRT569383 | DDX20 | DEAD-box helicase 20 | ![]() |
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2 | 2 | ||||||
MIRT570037 | FAM228A | family with sequence similarity 228 member A | ![]() |
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2 | 2 | ||||||
MIRT573269 | DCAF10 | DDB1 and CUL4 associated factor 10 | ![]() |
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2 | 2 | ||||||
MIRT573912 | PARP1 | poly(ADP-ribose) polymerase 1 | ![]() |
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2 | 2 | ||||||
MIRT620034 | ST6GALNAC3 | ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 3 | ![]() |
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2 | 2 | ||||||
MIRT635606 | ZWILCH | zwilch kinetochore protein | ![]() |
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2 | 2 | ||||||
MIRT644413 | FRMD6 | FERM domain containing 6 | ![]() |
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2 | 2 | ||||||
MIRT652528 | TM9SF4 | transmembrane 9 superfamily member 4 | ![]() |
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2 | 2 | ||||||
MIRT656238 | MFSD6 | major facilitator superfamily domain containing 6 | ![]() |
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2 | 2 | ||||||
MIRT661373 | DYRK4 | dual specificity tyrosine phosphorylation regulated kinase 4 | ![]() |
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2 | 2 | ||||||
MIRT662530 | PNPLA4 | patatin like phospholipase domain containing 4 | ![]() |
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2 | 2 | ||||||
MIRT675551 | MALL | mal, T-cell differentiation protein like | ![]() |
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2 | 2 | ||||||
MIRT693650 | ACBD7 | acyl-CoA binding domain containing 7 | ![]() |
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2 | 2 | ||||||
MIRT696348 | SLC35D2 | solute carrier family 35 member D2 | ![]() |
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2 | 2 | ||||||
MIRT705815 | AKNA | AT-hook transcription factor | ![]() |
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2 | 2 | ||||||
MIRT707632 | TARDBP | TAR DNA binding protein | ![]() |
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2 | 2 | ||||||
MIRT717902 | COPS8 | COP9 signalosome subunit 8 | ![]() |
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2 | 2 | ||||||
MIRT723626 | SOBP | sine oculis binding protein homolog | ![]() |
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2 | 2 |
miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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