Skip to main content

Table 1 List of the inferred clusters in the presence of recurrent trans-factors

From: PTRcombiner: mining combinatorial regulation of gene expression from post-transcriptional interaction maps

Class Cluster Trans-factors
RBP Clust R01 AGO1, AGO2, ELAVL1, FMR1_iso1, FMR1_iso7,
   FXR2, LIN28A, LIN28B, MOV10, TIA1, TIAL1,
   ZC3H7B
RBP Clust R02 AGO1, AGO2, ELAVL1, IGF2BP1, IGF2BP2,
   IGF2BP3, TIAL1
Singleton Clust R03 AGO1
RBP Clust R04 ELAVL1, HNRNPD
RBP Clust R05 AGO1, AGO2, ELAVL1, EWSR1, FMR1_iso1,
   FUS, LIN28A, LIN28B, TAF15, TIA1, TIAL1,
   ZC3H7B
RBP Clust R06 AGO1, ELAVL1, TIA1, TIAL1
RBP Clust R07 AGO1, FMR1_iso1, FMR1_iso7
RBP Clust R08 AGO1, AGO2, CAPRIN1, ELAVL1, FMR1_iso1,
   FMR1_iso7, LIN28B, TIA1, TIAL1, ZC3H7B
RBP Clust R09 AGO1, AGO2, C22ORF28, ELAVL1, FMR1_iso1,
   FMR1_iso7, LIN28B, TIA1, TIAL1, ZC3H7B
RBP-miRNA Clust R10 LIN28A, LIN28B, hsa-miR-221*
RBP Clust R11 AGO1, HNRNPH
RBP Clust R12 AGO1, AGO2, ELAVL1, FMR1_iso1, HNRNPC,
   TIA1, TIAL1
Singleton Clust R13 PUM1
RBP Clust R14 AGO1, AGO2, ELAVL1, FMR1_iso1, FMR1_iso7,
   HNRNPU, TIA1, TIAL1
RBP Clust R15 AGO1, AGO2, ELAVL1, FMR1_iso1, FMR1_iso7,
   HNRNPF, TIA1, TIAL1
RBP Clust R16 AGO1, AGO2, ELAVL1, EWSR1, FMR1_iso1,
   FMR1_iso7, FXR1, FXR2, LIN28A, LIN28B, TIA1,
   TIAL1, ZC3H7B
RBP Clust R17 AGO1, AGO2, ELAVL1, FMR1_iso1, IGF2BP1,
   IGF2BP2, IGF2BP3, PUM2, TIA1, TIAL1
Singleton Clust R18 PABPC1
Singleton Clust R19 U2AF2
RBP-miRNA Clust R20 AGO1, AGO2, ELAVL1, FMR1_iso1, IGF2BP1,
   IGF2BP2, IGF2BP3, TIA1, TIAL1, hsa-miR-130a,
   hsa-miR-130b, hsa-miR-148a, hsa-miR-148b,
   hsa-miR-301a, hsa-miR-301b
RBP-miRNA Clust R21 AGO1, AGO2, ELAVL1, FMR1_iso1, IGF2BP1,
   IGF2BP2, IGF2BP3, TIA1, TIAL1, hsa-miR-15a,
   hsa-miR-15b, hsa-miR-16, hsa-miR-424
Singleton Clust R22 DGCR8
RBP-miRNA Clust R23 AGO1, AGO2, ELAVL1, FMR1_iso1, IGF2BP1,
   IGF2BP2, IGF2BP3, TIA1, TIAL1, hsa-miR-106b,
   hsa-miR-17, hsa-miR-20a, hsa-miR-320,
   hsa-miR-93
RBP-miRNA Clust R24 AGO1, AGO2, ELAVL1, IGF2BP1, IGF2BP2,
   IGF2BP3, TIAL1, hsa-let-7a, hsa-let-7b,
   hsa-let-7c, hsa-let-7d, hsa-let-7e, hsa-let-7f,
   hsa-let-7g, hsa-let-7i
RBP Clust R25 AGO1, AGO2, ELAVL1, FMR1_iso1,
   HNRNPA2B1, TIA1, TIAL1
  1. Clusters were classified according to their composition: “RBP” for those composed exclusively of RBPs; “miRNA”, composed exclusively of miRNAs; “RBP-miRNA”, composed of both RBPs and miRNAs; and “Singleton”, composed of only one trans-factor.