pre-miRNA Information | |
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pre-miRNA | hsa-mir-4491 |
Genomic Coordinates | chr11: 111347757 - 111347824 |
Description | Homo sapiens miR-4491 stem-loop |
Comment | None |
RNA Secondary Structure |
Mature miRNA Information | |||||||||||||||||||||||||
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Mature miRNA | hsa-miR-4491 | ||||||||||||||||||||||||
Sequence | 46| AAUGUGGACUGGUGUGACCAAA |67 | ||||||||||||||||||||||||
Evidence | Experimental | ||||||||||||||||||||||||
Experiments | Illumina | ||||||||||||||||||||||||
SNPs in miRNA |
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Putative Targets |
Gene Information | |||||||||||||||||||||
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Gene Symbol | HSPB8 | ||||||||||||||||||||
Synonyms | CMT2L, DHMN2, E2IG1, H11, HMN2, HMN2A, HSP22 | ||||||||||||||||||||
Description | heat shock protein family B (small) member 8 | ||||||||||||||||||||
Transcript | NM_014365 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on HSPB8 | |||||||||||||||||||||
3'UTR of HSPB8 (miRNA target sites are highlighted) |
>HSPB8|NM_014365|3'UTR 1 GATGCCAGTACTGGCCCATCCTTGTTTTGTCCCCAACCCTAGGGCTTCTCTGATTCCAGGATACATTACTTTAGCTGAAC 81 TCAGATTTAGTGCAAGTAAAATGTTAGAGGGTGCGGGGGTGAGGACTGACCACAGATTCCCTGGATAGTGTAGTGGTAGA 161 TTTCTCCACAGGATAGCGCAATTGGCAAATCATGCTTGGTTGTGTTAGGCCAAAATACTAGTTTTGCTTTCTTTACCTTT 241 TCTATCTTGATGAAAATGTTGCACATTCTATAGTTGCAAAACACATAAAAGGGGACTTAACATTTCACGTTGTATCTTAC 321 TTGCAGTGAATGCAAGGGTTACTTTTCTCTGGGGACCTCCCCCATCACCCAGGTTCCTACTCTGGGCTCCCGATTCCCAT 401 GGCTCCCAAACCATGCCGCATGGTTTGGTTAATGAAACCCAGTAGCTAACCCCACTGTGCTTCCACATGCCTGGCCTAAA 481 ATGGGTGATATACAGGTCTTATATCCCCATATGGAATTTATCCATCAACCACATAAAAACAAACAGTGCCTTCTGCCCTC 561 TGCCCAGATGTGTCCAGCACGTTCTCAAAGTTTCCACATTAGCACTCCCTAAGGACGCTGGGAGCCTGTCAGTTTATGAT 641 CTGACCTAGGTCCCCCCTTTCTTCTGTCCCCTGTGTTTAAGTCGGGATTTTTACAGAGGGAGCTGTCTCCAGACAGCTCC 721 ATCAGGAACCAAGCAAAGGCCAGATAGCCTGACAGATAGGCTAGTGGTATTGTGTATATGGGCGGGACGTGTGTGTCATT 801 ATTATTTGAGTTATGCTGTTGTTTAGGGGTAAATAACAGTAAATAATTAATAATAATAATAATAATAATAAAGGAGCTGA 881 CGTTCTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 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 | MCF7 | ||||||
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 SRR1045082. RNA binding protein: AGO2. Condition:Untreated
... - Farazi TA; Ten Hoeve JJ; Brown M; et al., 2014, Genome biology. |
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miRNA-target interactions (Provided by authors) |
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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 GSM4903825 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / PID14_NS |
Location of target site | NM_014365 | 3UTR | AAAGUUUCCACAUUAGCACUCCCUAAGGACGCUGGGAGC |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161237 |
CLIP-seq Viewer | Link |
CLIP-seq Support 2 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_014365 | 3UTR | AUAUCCCCAUAUGGAAUUUAUCCAUCAACCACAUAAAAACAAACAGUGCCUUCUGCCCUCUGCCCAGAUGUGUCCAGCACGUUCUCAAAGUUUCCACAUUAGCACUCCCUAAGGACGCUGGGAGC |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 3 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_014365 | 3UTR | AACAAACAGUGCCUUCUGCCCUCUGCCCAGAUGUGUCCAGCACGUUCUCAAAGUUUCCACAUUAGCACUCCCUAAGGACGCUGGGAGC |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 4 for dataset GSM4903835 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / CTL_TD_21_c |
Location of target site | NM_014365 | 3UTR | CCACAUAAAAACAAACAGUGCCUUCUGCCCUCUGCCCAGAUGUGUCCAGCACGUUCUCAAAGUUUCCACAUUAGCACUCCCUAAGGACGCUGGGAGC |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 5 for dataset GSM4903836 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / 124_TD_21_a |
Location of target site | NM_014365 | 3UTR | UGCCUUCUGCCCUCUGCCCAGAUGUGUCCAGCACGUUCUCAAAGUUUCCACAUUAGCACUCCCUAAGGACGCUGGGAGC |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 6 for dataset GSM4903837 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / 124_TD_21_b |
Location of target site | NM_014365 | 3UTR | CAACCACAUAAAAACAAACAGUGCCUUCUGCCCUCUGCCCAGAUGUGUCCAGCACGUUCUCAAAGUUUCCACAUUAGCACUCCCUAAGGACGCUGGGAGC |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 7 for dataset GSM4903838 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / 124_TD_21_c |
Location of target site | NM_014365 | 3UTR | AGUGCCUUCUGCCCUCUGCCCAGAUGUGUCCAGCACGUUCUCAAAGUUUCCACAUUAGCACUCCCUAAGGACGCUGGGAGC |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 8 for dataset SRR1045082 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | MCF7 / Untreated |
Location of target site | ENST00000281938.2 | 3UTR | CUAACCCCACUGUGCUUCCACAUG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 24398324 / SRX388831 |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | |||||||
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MiRNA-Target Expression Profile (TCGA) | |||||||
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67 hsa-miR-4491 Target Genes:
Functional analysis:
ID | Target | Description | Validation methods | |||||||||
Strong evidence | Less strong evidence | |||||||||||
MIRT056779 | ARID5B | AT-rich interaction domain 5B | 2 | 2 | ||||||||
MIRT061577 | BTG2 | BTG anti-proliferation factor 2 | 2 | 2 | ||||||||
MIRT063828 | SRP9 | signal recognition particle 9 | 2 | 4 | ||||||||
MIRT102306 | DNAJB9 | DnaJ heat shock protein family (Hsp40) member B9 | 2 | 10 | ||||||||
MIRT186634 | COX20 | COX20, cytochrome c oxidase assembly factor | 2 | 8 | ||||||||
MIRT191243 | STYX | serine/threonine/tyrosine interacting protein | 2 | 2 | ||||||||
MIRT195908 | SRSF11 | serine and arginine rich splicing factor 11 | 2 | 4 | ||||||||
MIRT240343 | UBXN2B | UBX domain protein 2B | 2 | 2 | ||||||||
MIRT271178 | PTPN14 | protein tyrosine phosphatase, non-receptor type 14 | 2 | 2 | ||||||||
MIRT286219 | TMEM97 | transmembrane protein 97 | 2 | 4 | ||||||||
MIRT314182 | OCLN | occludin | 2 | 4 | ||||||||
MIRT323938 | AKAP2 | A-kinase anchoring protein 2 | 2 | 4 | ||||||||
MIRT323940 | PALM2-AKAP2 | PALM2-AKAP2 readthrough | 2 | 4 | ||||||||
MIRT340113 | TXLNA | taxilin alpha | 2 | 2 | ||||||||
MIRT450333 | LRWD1 | leucine rich repeats and WD repeat domain containing 1 | 2 | 2 | ||||||||
MIRT451283 | ZNF101 | zinc finger protein 101 | 2 | 2 | ||||||||
MIRT451879 | SOD2 | superoxide dismutase 2 | 2 | 8 | ||||||||
MIRT453577 | CRCP | CGRP receptor component | 2 | 2 | ||||||||
MIRT454366 | ASAH2 | N-acylsphingosine amidohydrolase 2 | 2 | 2 | ||||||||
MIRT454797 | STOML3 | stomatin like 3 | 2 | 2 | ||||||||
MIRT459801 | POTED | POTE ankyrin domain family member D | 2 | 10 | ||||||||
MIRT460911 | POLQ | DNA polymerase theta | 2 | 2 | ||||||||
MIRT468082 | SHOC2 | SHOC2, leucine rich repeat scaffold protein | 2 | 6 | ||||||||
MIRT470281 | PRKAA1 | protein kinase AMP-activated catalytic subunit alpha 1 | 2 | 2 | ||||||||
MIRT471876 | NUFIP2 | NUFIP2, FMR1 interacting protein 2 | 2 | 2 | ||||||||
MIRT476147 | GPR137C | G protein-coupled receptor 137C | 2 | 8 | ||||||||
MIRT478056 | DNAJC10 | DnaJ heat shock protein family (Hsp40) member C10 | 2 | 10 | ||||||||
MIRT501054 | SMCR8 | Smith-Magenis syndrome chromosome region, candidate 8 | 2 | 4 | ||||||||
MIRT501732 | OVOL1 | ovo like transcriptional repressor 1 | 2 | 2 | ||||||||
MIRT502214 | HSPB8 | heat shock protein family B (small) member 8 | 2 | 2 | ||||||||
MIRT505243 | UBE2D3 | ubiquitin conjugating enzyme E2 D3 | 2 | 2 | ||||||||
MIRT505957 | RAN | RAN, member RAS oncogene family | 2 | 6 | ||||||||
MIRT507996 | BCL2L13 | BCL2 like 13 | 2 | 4 | ||||||||
MIRT510433 | ZNF207 | zinc finger protein 207 | 2 | 6 | ||||||||
MIRT510827 | SBNO1 | strawberry notch homolog 1 | 2 | 4 | ||||||||
MIRT511493 | HNRNPA0 | heterogeneous nuclear ribonucleoprotein A0 | 2 | 4 | ||||||||
MIRT512129 | CREBL2 | cAMP responsive element binding protein like 2 | 2 | 8 | ||||||||
MIRT514512 | SHISA9 | shisa family member 9 | 2 | 4 | ||||||||
MIRT516482 | RAB32 | RAB32, member RAS oncogene family | 2 | 4 | ||||||||
MIRT519514 | RBM22 | RNA binding motif protein 22 | 2 | 4 | ||||||||
MIRT523367 | GTF2A1 | general transcription factor IIA subunit 1 | 2 | 2 | ||||||||
MIRT524217 | DDI2 | DNA damage inducible 1 homolog 2 | 2 | 6 | ||||||||
MIRT524649 | C4orf32 | family with sequence similarity 241 member A | 2 | 2 | ||||||||
MIRT528297 | ZNF76 | zinc finger protein 76 | 2 | 2 | ||||||||
MIRT528577 | ITGB3BP | integrin subunit beta 3 binding protein | 2 | 2 | ||||||||
MIRT530458 | SULT1B1 | sulfotransferase family 1B member 1 | 2 | 2 | ||||||||
MIRT535774 | MYCN | MYCN proto-oncogene, bHLH transcription factor | 2 | 2 | ||||||||
MIRT544239 | CCBL2 | kynurenine aminotransferase 3 | 2 | 2 | ||||||||
MIRT546733 | RNF217 | ring finger protein 217 | 2 | 2 | ||||||||
MIRT550360 | INCENP | inner centromere protein | 2 | 4 | ||||||||
MIRT553343 | TRPC3 | transient receptor potential cation channel subfamily C member 3 | 2 | 4 | ||||||||
MIRT556629 | LAPTM4A | lysosomal protein transmembrane 4 alpha | 2 | 2 | ||||||||
MIRT558006 | FAM122B | family with sequence similarity 122B | 2 | 2 | ||||||||
MIRT558994 | CA8 | carbonic anhydrase 8 | 2 | 2 | ||||||||
MIRT560418 | ENTPD1 | ectonucleoside triphosphate diphosphohydrolase 1 | 2 | 2 | ||||||||
MIRT565717 | SESN3 | sestrin 3 | 2 | 2 | ||||||||
MIRT566271 | PTAR1 | protein prenyltransferase alpha subunit repeat containing 1 | 2 | 2 | ||||||||
MIRT568161 | CCDC6 | coiled-coil domain containing 6 | 2 | 2 | ||||||||
MIRT569753 | C2orf71 | chromosome 2 open reading frame 71 | 2 | 2 | ||||||||
MIRT573959 | FIGNL1 | fidgetin like 1 | 2 | 2 | ||||||||
MIRT574530 | PEG10 | paternally expressed 10 | 2 | 2 | ||||||||
MIRT609453 | CCDC149 | coiled-coil domain containing 149 | 2 | 2 | ||||||||
MIRT614047 | THBS2 | thrombospondin 2 | 2 | 2 | ||||||||
MIRT628418 | ATMIN | ATM interactor | 2 | 2 | ||||||||
MIRT689556 | XPO6 | exportin 6 | 2 | 2 | ||||||||
MIRT725598 | CDH7 | cadherin 7 | 2 | 2 | ||||||||
MIRT735561 | TRIM7 | tripartite motif containing 7 | 3 | 0 |