Virus Expression Database

GSE46611

MicroRNA Target Site Identification by Integrating Sequence and Binding Information

Submitted by Neelanjan Mukherjee (MDC Berlin, Germany) on May 03 2013

Platform: ngs – Illumina HiSeq 2000 (Homo sapiens)

Pubmed: 23708386

Summary High-throughput sequencing has opened numerous possibilities for the identification of regulatory RNA-binding events. Cross-linking and immunoprecipitation of Argonaute protein members can pinpoint microRNA target sites within tens of bases, but leaves the identity of the microRNA unresolved. A flexible computational framework that integrates sequence with cross-linking features reliably identifies the microRNA family involved in each binding event, considerably outperforms sequence-only approaches, and quantifies the prevalence of noncanonical binding modes.

5 Samples

ID Title Cell Type Timepoint Reported Virus Virus Species Exclusion Reason
GSM1133247 LCLBACWT lymphoblastoid cell line  4 mos EBV Human gammaherpesvirus 4
GSM1133248 LCLBACD1_1 lymphoblastoid cell line  4 mos EBV Human gammaherpesvirus 4 Extra interventions
EBV missing a mir
GSM1133249 LCLBACD1_2 lymphoblastoid cell line  4 mos EBV Human gammaherpesvirus 4 Extra interventions
EBV missing a mir
GSM1133250 LCLBACD2 lymphoblastoid cell line  4 mos EBV Human gammaherpesvirus 4 Extra interventions
EBV missing a mir
GSM1133251 LCLBACD3 lymphoblastoid cell line  4 mos EBV Human gammaherpesvirus 4 Extra interventions
EBV missing a mir