Supplementary Figure and Tables

Figure S1 Schematic representation of a miRNA-FFL and TF-FFL.

miRNA miRNA

miRNA-FFL TF-FFL

Figure S2 Overview of data collection and annotation in miRFFLDB Database

Figure S3: Shows quartile distribution of the occurrences of miRNAs in MYC -FFLs that are identified from miRFFLDB.

Figure S4: Frequency chart of textmining results of ‘miRNAs interacting with MYC during cancer’.

Table S1: KEGG pathway enrichment of MYC-miR-92a-3p and MYC-hsa-miR-16-5p TF- FFLs regulated targets.

MYC-hsa-miR-16-5p Category Term Coun % PValue Fold t Enrichme nt KEGG_PATHWA hsa03010: 16 17.7777 1.82E- RPSA, 13.71685 Y 8 13 MRPL3, RPL13, RPS6, RPS2, RPS5, MRPL20, RPS25, RPL9, RPLP0, RPL21, RPS12, RPL10, RPL5, RPL12, RPS24 KEGG_PATHWA hsa04066:HIF-1 5 5.55555 0.00850 EIF4E, 6.072564 Y signaling pathway 6 1 TFRC, VEGFA, RPS6KB 1, RPS6 KEGG_PATHWA hsa04150:mTOR 3 3.33333 0.08557 EIF4E, 6.030684 Y signaling pathway 3 8 RPS6KB 1, RPS6 KEGG_PATHWA hsa04910:Insulin 6 6.66666 0.00590 EIF4E, 5.06927 Y signaling pathway 7 5 CRKL, FASN, RPS6KB 1, PCK2, RPS6 KEGG_PATHWA hsa04152:AMPK 4 4.44444 0.08478 PPP2R5C 3.791649 Y signaling pathway 4 8 , FASN, RPS6KB 1, PCK2 KEGG_PATHWA hsa04151:PI3K-Akt 7 7.77777 0.06907 EIF4E, 2.36566 Y signaling pathway 8 1 CCND2, VEGFA, PPP2R5C , RPS6KB 1, PCK2, RPS6 MYC-hsa-miR-92a-5p Category Term Coun % PValue Genes Fold t Enrichme nt KEGG_PATHWA hsa03010:Ribosome 12 0.07301 3.64E- RPS25, 11.45228 Y 9 09 RPS28, MRPL3, RPL23, RPL13A, RPL22, RPL9, RPL15, RPL8, RPS15A, RPS5, RPS24 KEGG_PATHWA hsa00970:Aminoac 4 0.02434 0.01334 CARS, 7.866209 Y yl-tRNA 1 LARS, biosynthesis VARS, EARS2 KEGG_PATHWA hsa03013:RNA 5 0.03042 0.04033 XPOT, 3.773036 Y transport 5 3 EIF3B, NUP205, RANBP2, KPNB1

Table S2: The table shows 16 MYC-hsa-miR-16-5p and 14 MYC/MYCN- hsa-miR-92a-3p TF-FFLs co-regulating ribosomal targets obtained from miRFFLDB database.

TF miRNA gene MYC hsa-miR-16-5p MRPL20 MYC hsa-miR-16-5p RPS6 MYC hsa-miR-16-5p RPL10 MYC hsa-miR-16-5p RPL12 MYC hsa-miR-16-5p RPL9 MYC hsa-miR-16-5p MRPL3 MYC hsa-miR-16-5p RPL5 MYC hsa-miR-16-5p RPS2 MYC hsa-miR-16-5p RPLP0 MYC hsa-miR-16-5p RPS12 MYC hsa-miR-16-5p RPL13 MYC hsa-miR-16-5p RPS25 MYC hsa-miR-16-5p RPL21 MYC hsa-miR-16-5p RPSA MYC hsa-miR-16-5p RPS24 MYC hsa-miR-16-5p RPS5 MYC hsa-miR-92a-3p RPS24 MYC hsa-miR-92a-3p RPS5 MYC hsa-miR-92a-3p HLA-E MYCN hsa-miR-92a-3p HLA-E MYC hsa-miR-92a-3p RPL9 MYC hsa-miR-92a-3p RPL15 MYC hsa-miR-92a-3p RPL8 MYC hsa-miR-92a-3p RPS15A MYC hsa-miR-92a-3p RPL22 MYC hsa-miR-92a-3p RPS25 MYC hsa-miR-92a-3p MRPL3 MYC hsa-miR-92a-3p RPL13A MYC hsa-miR-92a-3p RPS28 MYC hsa-miR-92a-3p RPL23

Table S3: Shows comparison of regulatory interaction data of miRFFLDB database and RegNetwork database using example search of hsa-miR-141-3p.

miRFFLDB RegNetwork Regulator symbol Target Experimental Regulator Target symbol Evidence symbol validation symbol hsa-miR-141-3p QKI validated E2F1 hsa-miR-141-3p Predicted hsa-miR-141-3p CHML validated EGR1 hsa-miR-141-3p Predicted hsa-miR-141-3p PTPRD validated FOS hsa-miR-141-3p Predicted hsa-miR-141-3p GNA13 validated GABPA hsa-miR-141-3p Predicted hsa-miR-141-3p STXBP2 validated JUN hsa-miR-141-3p Predicted hsa-miR-141-3p CELF1 validated MAX hsa-miR-141-3p Predicted hsa-miR-141-3p CDV3 validated MXI1::CL hsa-miR-141-3p Predicted EC5A hsa-miR-141-3p CDC25C validated MYC hsa-miR-141-3p Predicted hsa-miR-141-3p CDC25A validated NFYA hsa-miR-141-3p Predicted hsa-miR-141-3p PRELID2 validated PAX5 hsa-miR-141-3p Predicted hsa-miR-141-3p MCL1 validated PPARG hsa-miR-141-3p Predicted hsa-miR-141-3p PPP1R15 validated SP1 hsa-miR-141-3p Predicted B hsa-miR-141-3p SPRYD4 validated SPI1 hsa-miR-141-3p Predicted hsa-miR-141-3p FUT11 validated TAL1 hsa-miR-141-3p Predicted hsa-miR-141-3p ZMPSTE2 validated TCF3 hsa-miR-141-3p Predicted 4 hsa-miR-141-3p MAP4K4 validated TFAP2A hsa-miR-141-3p Predicted hsa-miR-141-3p CCDC71L validated TFAP2C hsa-miR-141-3p Predicted hsa-miR-141-3p CCDC18 validated USF1 hsa-miR-141-3p Predicted hsa-miR-141-3p MALAT1 validated hsa-miR-141-3p YWHAG validated hsa-miR-141-3p YRDC validated hsa-miR-141-3p YME1L1 validated hsa-miR-141-3p XPOT validated hsa-miR-141-3p PIGW validated hsa-miR-141-3p PHLPP2 validated hsa-miR-141-3p PHLPP1 validated hsa-miR-141-3p SLC35D1 validated hsa-miR-141-3p WDR37 validated hsa-miR-141-3p C18orf25 validated hsa-miR-141-3p C16orf58 validated hsa-miR-141-3p PGK1 validated hsa-miR-141-3p PGAM4 validated hsa-miR-141-3p PEX11A validated hsa-miR-141-3p VAC14 validated hsa-miR-141-3p ERO1A validated hsa-miR-141-3p KLHL20 validated hsa-miR-141-3p USP53 validated hsa-miR-141-3p EPHA7 validated hsa-miR-141-3p EPHA2 validated hsa-miR-141-3p BICRAL validated hsa-miR-141-3p UQCRFS1 validated hsa-miR-141-3p SHC1 validated hsa-miR-141-3p KIAA154 validated 9L hsa-miR-141-3p KIAA114 validated 7 hsa-miR-141-3p PAPPA validated hsa-miR-141-3p ELMO2 validated hsa-miR-141-3p BAP1 validated hsa-miR-141-3p EIF4E validated hsa-miR-141-3p UBAP1 validated hsa-miR-141-3p ATXN7L1 validated hsa-miR-141-3p TROVE2 validated hsa-miR-141-3p IPO5 validated hsa-miR-141-3p TRMT112 validated hsa-miR-141-3p DPY19L1 validated hsa-miR-141-3p ARL5B validated hsa-miR-141-3p DNAJC28 validated hsa-miR-141-3p S100A6 validated hsa-miR-141-3p TRAPPC2 validated B hsa-miR-141-3p TRAM1 validated hsa-miR-141-3p IGF1R validated hsa-miR-141-3p APOOL validated hsa-miR-141-3p HSPA4 validated hsa-miR-141-3p TNKS2 validated hsa-miR-141-3p RPL12 validated hsa-miR-141-3p TNFRSF1 validated 0B hsa-miR-141-3p ANGPTL validated 7 hsa-miR-141-3p TMOD3 validated hsa-miR-141-3p HNRNPF validated hsa-miR-141-3p NDST4 validated hsa-miR-141-3p CYP1B1 validated hsa-miR-141-3p RIN2 validated hsa-miR-141-3p TM4SF1 validated hsa-miR-141-3p ACVR2B validated hsa-miR-141-3p TIAM1 validated hsa-miR-141-3p COX6B1 validated hsa-miR-141-3p RASSF2 validated hsa-miR-141-3p RAP2C validated hsa-miR-141-3p TGFB2 validated hsa-miR-141-3p RAB8B validated hsa-miR-141-3p CLDND1 validated hsa-miR-141-3p A1BG validated hsa-miR-141-3p TAZ validated hsa-miR-141-3p KIAA154 validated 9 hsa-miR-141-3p ELAVL4 validated hsa-miR-141-3p KEAP1 validated hsa-miR-141-3p ZNF621 validated hsa-miR-141-3p ELAVL2 validated hsa-miR-141-3p SFPQ validated hsa-miR-141-3p PTEN validated hsa-miR-141-3p PSMD11 validated hsa-miR-141-3p CDYL validated hsa-miR-141-3p E2F3 validated hsa-miR-141-3p OGT validated hsa-miR-141-3p STK3 validated hsa-miR-141-3p STAT5A validated hsa-miR-141-3p STAT4 validated hsa-miR-141-3p IRF2BPL validated hsa-miR-141-3p SCD5 validated hsa-miR-141-3p MED13 validated hsa-miR-141-3p MDM4 validated hsa-miR-141-3p ZNF292 validated hsa-miR-141-3p PRKAA2 validated hsa-miR-141-3p GATA6 validated hsa-miR-141-3p NR0B2 validated hsa-miR-141-3p DLX5 validated hsa-miR-141-3p MAPK9 validated hsa-miR-141-3p ZMAT3 validated hsa-miR-141-3p MAPK14 validated hsa-miR-141-3p ZFPM2 validated hsa-miR-141-3p PPARA validated hsa-miR-141-3p ZEB2 validated hsa-miR-141-3p ZEB1 validated hsa-miR-141-3p POLR3F validated hsa-miR-141-3p MALT1 validated hsa-miR-141-3p MACC1 validated hsa-miR-141-3p ZBTB34 validated hsa-miR-141-3p HOXB5 validated hsa-miR-141-3p HNRNPD validated hsa-miR-141-3p HNRNPA validated B hsa-miR-141-3p LPP validated hsa-miR-141-3p YAP1 validated hsa-miR-141-3p CTBP2 validated hsa-miR-141-3p LHX1 validated hsa-miR-141-3p HIPK2 validated hsa-miR-141-3p ADNP2 validated hsa-miR-141-3p PHB2 validated hsa-miR-141-3p RBM28 validated hsa-miR-141-3p HDGF validated hsa-miR-141-3p RB1 validated hsa-miR-141-3p H2AFZ validated hsa-miR-141-3p TFDP2 validated hsa-miR-141-3p BRD3 validated hsa-miR-141-3p TET3 validated hsa-miR-141-3p TET1 validated hsa-miR-141-3p ZNF805 validated hsa-miR-141-3p ERBIN validated hsa-miR-141-3p KLF5 validated hsa-miR-141-3p TCF7L1 validated hsa-miR-141-3p KLF12 validated hsa-miR-141-3p KLF11 validated hsa-miR-141-3p BICD2 validated hsa-miR-141-3p CLOCK validated ZEB1 CYP1B1 validated MYC EIF4E validated MYC hsa-miR- validated 141-3p EP300 RASSF2 validated EP300 hsa-miR- validated 141-3p MYC CDC25C validated EP300 TM4SF1 validated MYC CDC25A validated EP300 PPP1R15 validated B EP300 RAB8B validated EP300 QKI validated MYC QKI validated MYC SPRYD4 validated EP300 PGK1 validated MYC PGK1 validated EP300 IPO5 validated EP300 CYP1B1 validated KAT2B CYP1B1 validated KAT2B hsa-miR- validated 141-3p ZEB1 hsa-miR- validated 141-3p EP300 USP53 validated EP300 HNRNPF validated MYC HNRNPF validated MYC PIGW validated MYC XPOT validated EP300 RPL12 validated MYC RPL12 validated EP300 TROVE2 validated MYC HSPA4 validated EP300 MALAT1 validated MYC MALAT1 validated MYC TNFRSF1 validated 0B