Table 1.

MicroRNAs required for clustering of tumor cell lines based on tissues of origin

microRNA *Confidence interval for tumor cell line clusters
Hematologic (95) Colon (95) Melanoma (96) CNS (97)
miR-127, miR-3829595960,X
miR-130aN70708194
miR-200a, miR-141, miR-141N, miR-200c, miR-200cN, miR-200b, miR-200bN96969273,X
miR-100, miR-125b, miR-99a89899490
miR-10b96969681
miR-106a, miR-17-3p, miR-17-5p, miR-18, miR-19a, miR-19b, miR-20, miR-20N, miR-92N95959585
miR-9294949695
miR-10a96969686
miR-14694949487,X
miR-20395959588
miR-33510088,X9296,X
miR-30a-3p10094,X9191,X
miR-34210095,X9395
miR-108, miR-18596969595
miR-142-3p, miR-142-5p9697,X9596,X
miR-135b96969598
miR-148a93939798
miR-20494949894
miR-319595,X9796
miR-9594949492
miR-15195959594
miR-15395959594
miR-18494949395
miR-148b94949597
miR-21894949596
miR-128a, miR-129, miR-133a, miR-302a, miR-302b, miR-302c, miR-302d, miR-367, miR-32694949496
miR-182, miR-183, miR-9694949496
miR-378, miR-422a, miR-422b95959497
miR-13795959596
miR-25, miR-23bN, miR-27b, miR-93, miR-3295959596
miR-194, miR-21592929397
miR-7, miR-7N92929297
miR-22493939597
miR-33093939496
miR-34b94949398
miR-372, miR-37393939398
miR-19290909599
miR-196b90909599
miR-14991919696
miR-34a, miR-34aN91919596
  • NOTE: Among the 81 microRNAs that were selected as being sufficient to define the four statistically significant clusters ( Fig. 3), 38 microRNAs were determined to be expressed in a pattern similar to that of at least one other microRNA based on a Pearson coefficient of correlation >0.8 at a P ≤ 0.05, and hence, only one representative of each such group was taken for further analysis. We evaluated the remaining 43 microRNAs (shown in boldface), which were expressed in unique patterns, in a leave-one-out sensitivity analysis. Of the 43 tested, 36 exhibited a critical contribution to the clustering: when any one of these 36 and their correlated microRNAs listed in the table were removed from a multiscale bootstrap/hierarchical cluster analysis of the NCI-60 cell lines, the confidence interval either dropped to <95% or changed the cluster memberships by two or more cell lines. The effect on all four of the clusters in the absence of any one of the 31 microRNAs is shown by a change in the confidence interval or a change in the cell lines making up the clusters. The microRNAs in each of the correlated expression groups are identified and listed together with the microRNAs that were tested in the analysis. Seven microRNAs (highlighted in gray) were those that upon being left out of the analysis, did not cause a decrease or an increase in the confidence interval or change the dissimilarity distance between cell lines.

  • * MicroRNAs in boldface were tested in the leave-one-out analysis. MicroRNAs with correlated expression patterns are listed adjacent to the ones that were tested.

  • MicroRNAs listed here exhibited the following behavior in a leave-one-out multiscale bootstrap resampling analysis (see Materials and Methods): Leaving out the indicated microRNA caused a decrease in the confidence interval assignment, and/or changed the dissimilarity distance between cell lines (indicated by an X) leading to gain or loss of cell line members in a cluster.

  • Starting confidence interval for the individual clusters as calculated by multiscale bootstrap resampling analyses.