pre-miRNA Information | |
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pre-miRNA | hsa-mir-921 |
Genomic Coordinates | chr1: 166154743 - 166154798 |
Synonyms | MIRN921, hsa-mir-921, MIR921 |
Description | Homo sapiens miR-921 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | |||||||||||||
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Mature miRNA | hsa-miR-921 | ||||||||||||
Sequence | 2| CUAGUGAGGGACAGAACCAGGAUUC |26 | ||||||||||||
Evidence | Experimental | ||||||||||||
Experiments | Cloned | DRVs in miRNA |
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SNPs in miRNA |
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Putative Targets |
miRNA Expression profile | |
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Human miRNA Tissue Atlas | |
Circulating MicroRNA Expression Profiling |
Gene Information | |||||||||||||||||||||
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Gene Symbol | KANSL1 | ||||||||||||||||||||
Synonyms | CENP-36, KDVS, KIAA1267, MSL1v1, NSL1, hMSL1v1 | ||||||||||||||||||||
Description | KAT8 regulatory NSL complex subunit 1 | ||||||||||||||||||||
Transcript | NM_015443 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on KANSL1 | |||||||||||||||||||||
3'UTR of KANSL1 (miRNA target sites are highlighted) |
>KANSL1|NM_015443|3'UTR 1 GCGGGAGACAGCCATCTAAACAGACTCACTAACTATTGGCATTAAAGCTTCAGAAATCTCTGCGTTTGATATTCAAACAT 81 CATATGCCGGAAATTTTCACAGTTTTTAGTGAACTTAAGGAATTTAGATCCTACTTTGGTATTTTTTTTTCTTGTTTTAA 161 TTTTTGTTTTGTTTTTGTTTCCATGTTTTCTTGTCACACACCTGAGCACTTCCTCCCGTTGGCAAACAGAAGTTCAGGAT 241 GAGACCCTGCTGGCCTGGTCCTGGCACATCCTCTGCACTGTTGAATCACTGGACTTACTGATCTTAGATGACCACCCCCT 321 CCCTCACACCTGTGGGCAGGGCAGAACAGCCTGGCGGGCTACAGTTTAGCATGGCCTTCTTGAGCTAGGGTGGAATGGGG 401 CAGGGTGCTCTGGACTCTTACCCCCTCCCCTCCCATCTGTGGCTTGGCTCTGCTGTGGCCCTCCTGGCTGGGTCCCCTTG 481 GTTTTTCGTGCTGGAACATCCCCACCAGAGCCTCTCTGCCATAACTGCCAGCTGCTCTCCCCGAGTGCTCAGCTGGCAGA 561 ACACCTTTCCTTTCTCACCCAGAACTTAAGAGACTGATTTTTTGTTTCATCTGCATTTGGTCTTCTCTGTTTTGACTCTT 641 TCACTGCAGTAACCTGGCTGTGGCTGCTCAGGTTCCCCTCCTCATGCCCCTTGGTACCCTTCCCTGTCTGCTCTCCCATG 721 CCATGTACACACCCACAACCCGTCCTTCCACTTGGAATATTTTTACCACCTATCCTGATCTTTGAAGGTAGGGTTAGGAC 801 TACTTAACCTCTATTCCCACTCCCCTGCAAACTGGGGGTTGTGGGAAGTGAGCAGCCATCTCCCTGTGTGATTTTTTTTT 881 TTTTTCCCTCTGATTCACTTTGCCATGTTTCCTTCACATCCAGATCCCTGTCGGTGTTAGTTCCACTCTTGGTCTTTCAC 961 GCTCCCCTTGCCTGTGGAACATTGTCTGGTCCTAGCTGTGGTTCCCATTGTTCCCCCTTCACCCTTCTCTGTTAACCTTG 1041 TGCCTGTCTCCTGTATGATCACATCACCAAAAAGGGGGAGGGGGGAGAAGACTCTTTTTTTTTGGCCATTTTGTAATCGT 1121 ATAAAAATAGTAGACAACTGCTTAATGGTTGGGGTTTTTTCACAATTTTCAACATTAGTGATTTTTTTTTCTGTTTGCAA 1201 GTTAAAGGGTTTGTCATTGTTTCTTTAAAAAAAAATACAATAATGCACCATATCCCTATGCATAAAGTGCTTCTTCTATT 1281 TATAAGGTTGAAAATTCTGAATAACCCTTTTAGCATTGAAAAAAAAAACAAAAACAAAAAATGGAAAAAAAAAACCTTGT 1361 ATTTTGTAAATATTTTCTTTTCCTGCTTTGGAGCTGTGTAATGGCAGCGAAACATGTAGCTGTCTTTGTTCTATAGAAAT 1441 GCTTTTCTTCAGAGAAGCTGATCTTTGTTAATGTCTTGATTCTGTTCGCAAAGCACAGACTAGTGCTTAAAAAAAAAAAA 1521 GAAGGAAAAATTGAAAAAAATAAAAAAAAAAGTTACAGAAAAAAAAAA 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 | HEK293 | ||||||
Disease | 284058.0 | ||||||
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 GSM714644. RNA binding protein: AGO2. Condition:completeT1
"PAR-CLIP data was present in GSM714645. RNA binding protein: AGO2. Condition:completeT1
... - Kishore S; Jaskiewicz L; Burger L; Hausser et al., 2011, Nature methods. |
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miRNA-target interactions (Provided by authors) |
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Article |
- Kishore S; Jaskiewicz L; Burger L; Hausser et al. - Nature methods, 2011
Cross-linking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins. We developed a method for CLIP data analysis, and applied it to compare CLIP with photoactivatable ribonucleoside-enhanced CLIP (PAR-CLIP) and to uncover how differences in cross-linking and ribonuclease digestion affect the identified sites. We found only small differences in accuracies of these methods in identifying binding sites of HuR, which binds low-complexity sequences, and Argonaute 2, which has a complex binding specificity. We found that cross-link-induced mutations led to single-nucleotide resolution for both PAR-CLIP and CLIP. Our results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect their binding sites sufficiently under the denaturing conditions used during the CLIP procedure, and we show that extensive digestion with sequence-specific RNases strongly biases the recovered binding sites. This bias can be substantially reduced by milder nuclease digestion conditions.
LinkOut: [PMID: 21572407]
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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 | C8166 |
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 GSM1462572. RNA binding protein: AGO2. Condition:C8166 NL4-3
... - 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 3 for Functional miRNA-Target Interaction | |
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miRNA:Target | ---- |
Validation Method |
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Conditions | MCF7 |
Location of target site | 3'UTR |
Tools used in this research | TargetScan , miRTarCLIP , Piranha |
Original Description (Extracted from the article) |
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PAR-CLIP data was present in SRR1045082. RNA binding protein: AGO2. Condition:Untreated
... - Farazi TA; Ten Hoeve JJ; Brown M; et al., 2014, Genome biology. |
Article |
- Farazi TA; Ten Hoeve JJ; Brown M; et al. - Genome biology, 2014
BACKGROUND: Various microRNAs (miRNAs) are up- or downregulated in tumors. However, the repression of cognate miRNA targets responsible for the phenotypic effects of this dysregulation in patients remains largely unexplored. To define miRNA targets and associated pathways, together with their relationship to outcome in breast cancer, we integrated patient-paired miRNA-mRNA expression data with a set of validated miRNA targets and pathway inference. RESULTS: To generate a biochemically-validated set of miRNA-binding sites, we performed argonaute-2 photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation (AGO2-PAR-CLIP) in MCF7 cells. We then defined putative miRNA-target interactions using a computational model, which ranked and selected additional TargetScan-predicted interactions based on features of our AGO2-PAR-CLIP binding-site data. We subselected modeled interactions according to the abundance of their constituent miRNA and mRNA transcripts in tumors, and we took advantage of the variability of miRNA expression within molecular subtypes to detect miRNA repression. Interestingly, our data suggest that miRNA families control subtype-specific pathways; for example, miR-17, miR-19a, miR-25, and miR-200b show high miRNA regulatory activity in the triple-negative, basal-like subtype, whereas miR-22 and miR-24 do so in the HER2 subtype. An independent dataset validated our findings for miR-17 and miR-25, and showed a correlation between the expression levels of miR-182 targets and overall patient survival. Pathway analysis associated miR-17, miR-19a, and miR-200b with leukocyte transendothelial migration. CONCLUSIONS: We combined PAR-CLIP data with patient expression data to predict regulatory miRNAs, revealing potential therapeutic targets and prognostic markers in breast cancer.
LinkOut: [PMID: 24398324]
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CLIP-seq Support 1 for dataset GSM714644 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | HEK293 / completeT1, repA |
Location of target site | ENST00000574590.1 | 3UTR | CCAUCUAAACAGACUCACUAACUAUUGGCAUUAAAGCUUCA |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 21572407 / GSE28865 |
CLIP-seq Viewer | Link |
CLIP-seq Support 2 for dataset GSM714645 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | HEK293 / completeT1, repB |
Location of target site | ENST00000574590.1 | 3UTR | CCAUCUAAACAGACUCACUAACUAUUGGCAUUAAAG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 21572407 / GSE28865 |
CLIP-seq Viewer | Link |
CLIP-seq Support 3 for dataset SRR1045082 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | MCF7 / Untreated |
Location of target site | ENST00000574590.1 | 3UTR | ACUCACUAACUAUUGGCAUUAAAG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 24398324 / SRX388831 |
CLIP-seq Viewer | Link |
CLIP-seq Support 4 for dataset GSM1462572 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | C8166 / C8166 NL4-3 |
Location of target site | ENST00000574590.1 | 3UTR | ACUCACUAACUAUUGGCAUUAAAG |
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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63 hsa-miR-921 Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT054764 | ANGPTL1 | angiopoietin like 1 | ![]() |
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3 | 1 | |||||
MIRT066171 | PIP4K2C | phosphatidylinositol-5-phosphate 4-kinase type 2 gamma | ![]() |
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2 | 2 | ||||||
MIRT069409 | ZFYVE21 | zinc finger FYVE-type containing 21 | ![]() |
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2 | 8 | ||||||
MIRT102284 | DNAJB9 | DnaJ heat shock protein family (Hsp40) member B9 | ![]() |
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2 | 4 | ||||||
MIRT107595 | DNAJA1 | DnaJ heat shock protein family (Hsp40) member A1 | ![]() |
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2 | 6 | ||||||
MIRT178618 | HIAT1 | major facilitator superfamily domain containing 14A | ![]() |
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2 | 2 | ||||||
MIRT182407 | TIPRL | TOR signaling pathway regulator | ![]() |
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2 | 4 | ||||||
MIRT186552 | ZBTB18 | zinc finger and BTB domain containing 18 | ![]() |
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2 | 2 | ||||||
MIRT273662 | HOXC8 | homeobox C8 | ![]() |
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2 | 2 | ||||||
MIRT283191 | C16ORF52 | chromosome 16 open reading frame 52 | ![]() |
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2 | 2 | ||||||
MIRT284890 | NFAT5 | nuclear factor of activated T-cells 5 | ![]() |
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2 | 2 | ||||||
MIRT347670 | LSM14A | LSM14A, mRNA processing body assembly factor | ![]() |
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2 | 2 | ||||||
MIRT400222 | SLC35F6 | solute carrier family 35 member F6 | ![]() |
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2 | 2 | ||||||
MIRT403517 | ASPH | aspartate beta-hydroxylase | ![]() |
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2 | 2 | ||||||
MIRT442251 | DCTN5 | dynactin subunit 5 | ![]() |
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2 | 2 | ||||||
MIRT443023 | SDR39U1 | short chain dehydrogenase/reductase family 39U member 1 | ![]() |
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2 | 2 | ||||||
MIRT443097 | RNF20 | ring finger protein 20 | ![]() |
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2 | 2 | ||||||
MIRT444560 | TRA2B | transformer 2 beta homolog | ![]() |
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2 | 2 | ||||||
MIRT445696 | PRKG1 | protein kinase, cGMP-dependent, type I | ![]() |
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2 | 2 | ||||||
MIRT454084 | TMEM209 | transmembrane protein 209 | ![]() |
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2 | 2 | ||||||
MIRT455463 | LYPLA2 | lysophospholipase II | ![]() |
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2 | 2 | ||||||
MIRT456653 | TIFA | TRAF interacting protein with forkhead associated domain | ![]() |
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2 | 2 | ||||||
MIRT458147 | LYRM4 | LYR motif containing 4 | ![]() |
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2 | 6 | ||||||
MIRT467073 | SRRD | SRR1 domain containing | ![]() |
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2 | 4 | ||||||
MIRT467245 | SPPL2A | signal peptide peptidase like 2A | ![]() |
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2 | 2 | ||||||
MIRT468246 | SFXN4 | sideroflexin 4 | ![]() |
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2 | 2 | ||||||
MIRT471589 | PAQR5 | progestin and adipoQ receptor family member 5 | ![]() |
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2 | 19 | ||||||
MIRT476639 | G2E3 | G2/M-phase specific E3 ubiquitin protein ligase | ![]() |
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2 | 2 | ||||||
MIRT482433 | ADM | adrenomedullin | ![]() |
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2 | 10 | ||||||
MIRT486848 | PERP | PERP, TP53 apoptosis effector | ![]() |
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2 | 6 | ||||||
MIRT489656 | SHMT1 | serine hydroxymethyltransferase 1 | ![]() |
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2 | 2 | ||||||
MIRT493441 | KANSL1 | KAT8 regulatory NSL complex subunit 1 | ![]() |
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2 | 6 | ||||||
MIRT493841 | FOXN3 | forkhead box N3 | ![]() |
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2 | 4 | ||||||
MIRT501378 | RBFOX2 | RNA binding protein, fox-1 homolog 2 | ![]() |
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2 | 10 | ||||||
MIRT509679 | ATAD5 | ATPase family, AAA domain containing 5 | ![]() |
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2 | 4 | ||||||
MIRT510280 | MED28 | mediator complex subunit 28 | ![]() |
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2 | 2 | ||||||
MIRT512221 | ATXN3 | ataxin 3 | ![]() |
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2 | 6 | ||||||
MIRT514030 | BNIP2 | BCL2 interacting protein 2 | ![]() |
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2 | 2 | ||||||
MIRT521375 | RDX | radixin | ![]() |
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2 | 4 | ||||||
MIRT521444 | RAD51 | RAD51 recombinase | ![]() |
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2 | 2 | ||||||
MIRT526055 | CBR1 | carbonyl reductase 1 | ![]() |
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2 | 2 | ||||||
MIRT528658 | FUNDC2 | FUN14 domain containing 2 | ![]() |
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2 | 2 | ||||||
MIRT529975 | TNFAIP8L1 | TNF alpha induced protein 8 like 1 | ![]() |
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2 | 2 | ||||||
MIRT544098 | IPMK | inositol polyphosphate multikinase | ![]() |
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2 | 2 | ||||||
MIRT545579 | SNRPA1 | small nuclear ribonucleoprotein polypeptide A' | ![]() |
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2 | 2 | ||||||
MIRT547424 | MED4 | mediator complex subunit 4 | ![]() |
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2 | 2 | ||||||
MIRT548955 | CD2AP | CD2 associated protein | ![]() |
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2 | 2 | ||||||
MIRT549537 | NDUFA6 | NADH:ubiquinone oxidoreductase subunit A6 | ![]() |
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2 | 4 | ||||||
MIRT552550 | ZFP36L2 | ZFP36 ring finger protein like 2 | ![]() |
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2 | 4 | ||||||
MIRT554640 | ROBO1 | roundabout guidance receptor 1 | ![]() |
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2 | 2 | ||||||
MIRT564904 | YTHDF1 | YTH N6-methyladenosine RNA binding protein 1 | ![]() |
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2 | 2 | ||||||
MIRT565578 | SLC6A8 | solute carrier family 6 member 8 | ![]() |
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2 | 2 | ||||||
MIRT568312 | BAG4 | BCL2 associated athanogene 4 | ![]() |
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2 | 2 | ||||||
MIRT617891 | PTCHD3 | patched domain containing 3 | ![]() |
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2 | 2 | ||||||
MIRT621892 | TAF13 | TATA-box binding protein associated factor 13 | ![]() |
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2 | 2 | ||||||
MIRT642850 | RNF135 | ring finger protein 135 | ![]() |
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2 | 2 | ||||||
MIRT665395 | WEE1 | WEE1 G2 checkpoint kinase | ![]() |
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2 | 2 | ||||||
MIRT697879 | UBE2B | ubiquitin conjugating enzyme E2 B | ![]() |
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2 | 2 | ||||||
MIRT698492 | THOC2 | THO complex 2 | ![]() |
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2 | 2 | ||||||
MIRT701227 | OCRL | OCRL, inositol polyphosphate-5-phosphatase | ![]() |
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2 | 2 | ||||||
MIRT701872 | MPLKIP | M-phase specific PLK1 interacting protein | ![]() |
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2 | 2 | ||||||
MIRT707045 | TRPV2 | transient receptor potential cation channel subfamily V member 2 | ![]() |
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2 | 2 | ||||||
MIRT715216 | NPVF | neuropeptide VF precursor | ![]() |
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2 | 2 |
miRNA-Drug Associations | |||||||||||||||||||||||||||
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miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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