Open Access Publication
Hamilton, Mark P.; Rajapakshe, Kimal; Hartig, Sean M.; Reva, Boris; McLellan, Michael D.; Kandoth, Cyriac; Ding, Li; Zack, Travis I.; Gunaratne, Preethi H.; Wheeler, David A.; Coarfa, Cristian; and McGuire, Sean E., ,"Identification of a pan-cancer oncogenic microRNA superfamily anchored by a central core seed motif." Nature Communications.4,. 2730. (2013).
Supplementary Figures S1-S3 and Supplementary Tables S1-S4
ncomms3730-s2.xlsx (16 kB)
AGO-CLIP SRR inventory. This file breaks down the AGO-CLIP experimental data used in this study into individual sequence read archives (SRR)
ncomms3730-s3.xlsx (1559 kB)
AGO-CLIP Cluster Gene Summary. This data file indicates the total number of AGO-PAR-CLIP clusters (representing 11 of 14 AGO-CLIP libraries
ncomms3730-s4.xlsx (24321 kB)
AGO-CLIP Seed Union. This file contains inferred seeds generated by the AGO-CLIP datasets (described in AGO-CLIP inventory file). Seeds are defined through the PARalyzer algorithm. All AGO-CLIP familes were included without filtering for total reads. Many clusters will infer more than one potential seed region, of these, all or only some may be the actual binding partner at the active site. Non-canonical seed matches are not considered in this iteration of the seed atlas.
ncomms3730-s5.xlsx (520 kB)
miRNA significant changes in tumour versus matched normal tissues. Unexpressed microRNAs in any given tissue are filtered during processing.
ncomms3730-s6.xlsx (112 kB)
Selection of Pan-Cancer microRNAs.
ncomms3730-s7.xlsx (1113 kB)
Target-Driver Scores. This data details the individual scores each gene received based on combined pan-cancer expression, SNV, and CNV data.
ncomms3730-s8.xlsx (90 kB)
Top 250 oncomiR-target interactions. Heat maps indicate miRNA-mRNA expression correlate across all tumour samples for the given miRNA-target interaction.
ncomms3730-s9.xlsx (66 kB)
Top 250 miR-suppressor-target interactions. Heat maps indicate miRNA-mRNA expression correlate across all tumour samples for the given miRNA-target interaction.
ncomms3730-s10.xlsx (949 kB)
Seed-SNV whitelist union. This file contains a complete summary of somatic mutations discovered in TCGA sequencing data that intersect with microRNA target sites identified in the AGO-CLIP atlas. Detailed individual analysis of target mutation sites as well as mRNA expression values associated with those sites is detailed in Synapse ID syn1720734.
ncomms3730-s11.xlsx (36 kB)
Validated microRNA target SNVs. Detailed data documenting validated microRNA target site mutations defined in this study.
ncomms3730-s12.xlsx (55 kB)
Unique Insert Sequences. Sequence inserts generated for microRNA target site analysis in this study.
ncomms3730-s13.xlsx (34 kB)
List of The Cancer Genome Atlas Research Network contributors.
ncomms3730-s14.zip (6 kB)