Spreadsheet: 24a25b53-59cb-4450-9668-a2e6830e0149
Sheet: Summary-NK-work-overlap-SAM-UpI

Additional File 2: Targets of down microRNA: Predicted mRNA targets of downregulated miRNAs in ccRCC.
microRNA | Direct Gene target | P-value | [NAME]
miR-200bc/429 | ZNF26 | 0.00014 | zinc finger protein 26
miR-141/200a | VSIG1 | 0.0002576 | V-set and immunoglobulin domain containing 1
miR-200bc/429 | ATP2B4 | 0.0002949 | ATPase, Ca++ transporting, plasma membrane 4
miR-200bc/429 | FMNL2 | 0.0003073 | formin-like 2
miR-141/200a | ZAK | 0.0003479 | sterile alpha motif and leucine zipper containing kinase AZK
miR-204/211 | SERP1 | 0.0003985 | stress-associated endoplasmic reticulum protein 1
miR-141/200a | NEK6 | 0.00042 | NIMA (never in mitosis gene a)-related kinase 6
miR-135b | SLC6A8 | 0.00043 | solute carrier family 6 (neurotransmitter transporter, creatine), member 8
miR-200bc/429 | ZAK | 0.0005885 | sterile alpha motif and leucine zipper containing kinase AZK
miR-204/211 | PXDN | 0.0006205 | peroxidasin homolog (Drosophila)
miR-149 | COL11A1 | 0.0006217 | collagen, type XI, alpha 1
miR-200bc/429 | DIDO1 | 0.000659 | death inducer-obliterator 1
miR-141/200a | LOC285382 | 0.0007828 | hypothetical gene supported by AK091454
miR-204/211 | STS | 0.0007849 | steroid sulfatase (microsomal), isozyme S
miR-149 | CDH4 | 0.0007907 | cadherin 4, type 1, R-cadherin (retinal)
miR-204/211 | COL1A2 | 0.0008044 | collagen, type I, alpha 2
miR-200bc/429 | FKBP1A | 0.000906 | FK506 binding protein 1A, 12kDa
miR-141/200a | SEMA6A | 0.0009728 | sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A
miR-141/200a | [NAME] | 0.001088 | MOB1, [NAME] kinase activator-like 2B (yeast)
miR-135b | [NAME] | 0.0011517 | major histocompatibility complex, class II, DQ beta 2
miR-200bc/429 | FAM29A | 0.0012169 | family with sequence similarity 29, member A
miR-135b | C1QTNF6 | 0.0012479 | C1q and tumor necrosis factor related protein 6
miR-200bc/429 | VEGFA | 0.0013166 | vascular endothelial growth factor A
miR-204/211 | PSMB8 | 0.0013392 | proteasome (prosome, macropain) subunit, beta type, 8 (large multifunctional peptidase 7)
miR-141/200a | AURKB | 0.0014526 | [NAME]
miR-200bc/429 | DAGLB | 0.0014639 | [NAME], beta
miR-200bc/429 | CLK4 | 0.0015521 | CDC-like kinase 4
miR-204/211 | TRIM59 | 0.0016521 | tripartite motif-containing 59
miR-199a | COL11A1 | 0.0017138 | collagen, type XI, alpha 1
miR-204/211 | RAP2B | 0.0017298 | RAP2B, member of RAS oncogene family
miR-141/200a | RBM3 | 0.0017597 | RNA binding motif (RNP1, RRM) protein 3
miR-200bc/429 | SRP72 | 0.0017941 | signal recognition particle 72kDa
miR-204/211 | C14orf106 | 0.0017983 | chromosome 14 open reading frame 106
miR-200bc/429 | ACP1 | 0.0018123 | acid phosphatase 1, soluble
miR-200bc/429 | LOC285382 | 0.0019641 | hypothetical gene supported by AK091454
miR-149 | LOC285382 | 0.002017 | hypothetical gene supported by AK091454
miR-204/211 | [NAME] | 0.0020497 | laminin, gamma 1 (formerly LAMB2)
miR-218 | HIST1H2BK | 0.0020574 | histone cluster 1, H2bk
miR-200bc/429 | CLCC1 | 0.002068 | chloride channel CLIC-like 1
miR-200bc/429 | NMD3 | 0.002078 | NMD3 homolog (S. cerevisiae)
miR-135b | SOBP | 0.0021296 | Sine oculis binding protein homolog (Drosophila)
miR-149 | RBM3 | 0.0021544 | RNA binding motif (RNP1, RRM) protein 3
miR-149 | RFX2 | 0.0021634 | regulatory factor X, 2 (influences HLA class II expression)
miR-200bc/429 | PJA2 | 0.0021987 | praja 2, RING-H2 motif containing
miR-149 | IQGAP3 | 0.0022005 | IQ motif containing GTPase activating protein 3
miR-204/211 | HS2ST1 | 0.0022117 | heparan sulfate 2-O-sulfotransferase 1
miR-200bc/429 | GIT2 | 0.0022362 | G protein-coupled receptor kinase interactor 2
miR-141/200a | GRB10 | 0.0022969 | growth factor receptor-bound protein 10
miR-204/211 | CXorf23 | 0.002298 | chromosome X open reading frame 23
miR-200bc/429 | NFIA | 0.0023091 | nuclear factor I/A
miR-218 | [NAME] | 0.0023273 | pyruvate dehydrogenase kinase, isozyme 1
miR-200bc/429 | CANX | 0.0023978 | calnexin
miR-141/200a | ADAMTS5 | 0.0024134 | ADAM metallopeptidase with thrombospondin type 1 motif, 5 (aggrecanase-2)
miR-141/200a | ANKRD29 | 0.0024869 | ankyrin repeat domain 29
miR-200bc/429 | INTS8 | 0.0025069 | integrator complex subunit 8
miR-200bc/429 | KIAA0286 | 0.0025594 | KIAA0286 protein
miR-149 | KCNMA1 | 0.0025714 | potassium large conductance calcium-activated channel, subfamily M, alpha member 1
miR-141/200a | CENTA2 | 0.0025934 | centaurin, alpha 2
miR-200bc/429 | ENPP3 | 0.0025965 | Ectonucleotide pyrophosphatase/phosphodiesterase 3
miR-200bc/429 | IDS | 0.0026114 | iduronate 2-sulfatase ([NAME] syndrome)
miR-200bc/429 | N4BP1 | 0.0026438 | Nedd4 binding protein 1
miR-204/211 | ELF4 | 0.0026698 | E74-like factor 4 (ets domain transcription factor)
miR-141/200a | KCNMA1 | 0.0027749 | potassium large conductance calcium-activated channel, subfamily M, alpha member 1
miR-135b | FLJ37440 | 0.0028241 | hypothetical protein FLJ37440
miR-204/211 | [NAME] | 0.0028264 | calumenin
miR-149 | PDGFD | 0.0029677 | platelet derived growth factor D
miR-218 | SLC38A1 | 0.0029951 | solute carrier family 38, member 1
miR-149 | KCNAB1 | 0.003015 | potassium voltage-gated channel, shaker-related subfamily, beta member 1
miR-200bc/429 | [NAME] | 0.0030412 | translocation associated membrane protein 1
miR-218 | [NAME] | 0.0030536 | laminin, gamma 1 (formerly LAMB2)
miR-204/211 | CCDC50 | 0.0030773 | coiled-coil domain containing 50
miR-135b | STC2 | 0.0030921 | stanniocalcin 2
miR-200bc/429 | SPIRE1 | 0.0031406 | spire homolog 1 (Drosophila)
miR-200bc/429 | SIRPA | 0.003222 | signal-regulatory protein alpha
miR-200bc/429 | ADAMTS5 | 0.0033593 | ADAM metallopeptidase with thrombospondin type 1 motif, 5 (aggrecanase-2)
miR-200bc/429 | MCM6 | 0.0035565 | minichromosome maintenance complex component 6
miR-200bc/429 | ELOVL7 | 0.0035731 | ELOVL family member 7, elongation of long chain fatty acids (yeast)
miR-200bc/429 | HEATR2 | 0.0036173 | HEAT repeat containing 2
miR-200bc/429 | [NAME] | 0.0036231 | proline-rich coiled-coil 1
miR-200bc/429 | [NAME] | 0.0036489 | kelch-like 24 (Drosophila)
miR-200bc/429 | BTK | 0.0037096 | Bruton agammaglobulinemia tyrosine kinase
miR-200bc/429 | GRB10 | 0.0037286 | growth factor receptor-bound protein 10
miR-200bc/429 | CSNK1A1 | 0.0039429 | Casein kinase 1, alpha 1
miR-218 | IGFBP3 | 0.0039843 | insulin-like growth factor binding protein 3
miR-204/211 | TIFA | 0.0041546 | TRAF-interacting protein with a forkhead-associated domain
miR-149 | CENTA2 | 0.0042142 | centaurin, alpha 2
miR-135b | SPN | 0.0042845 | sialophorin (leukosialin, CD43)
miR-135b | AR | 0.0044177 | androgen receptor (dihydrotestosterone receptor; testicular feminization; spinal and bulbar muscular atrophy; [NAME] disease)
miR-200bc/429 | FRYL | 0.0044957 | FRY-like
miR-204/211 | ATM | 0.0045235 | [NAME] mutated
miR-135b | LOC285382 | 0.0045275 | hypothetical gene supported by AK091454
miR-200bc/429 | RBM3 | 0.0045341 | RNA binding motif (RNP1, RRM) protein 3
miR-149 | DOCK8 | 0.0045829 | dedicator of cytokinesis 8
miR-141/200a | BTK | 0.0045962 | Bruton agammaglobulinemia tyrosine kinase
miR-135b | RBM3 | 0.004649 | RNA binding motif (RNP1, RRM) protein 3
miR-204/211 | IFI44 | 0.0047421 | interferon-induced protein 44
miR-200bc/429 | GUCY1B3 | 0.0047655 | guanylate cyclase 1, soluble, beta 3
miR-204/211 | FN1 | 0.0047895 | fibronectin 1
miR-200bc/429 | [NAME] | 0.0050005 | ubiquitin-conjugating enzyme E2B (RAD6 homolog)
miR-200bc/429 | TAF9B | 0.005032 | TAF9B RNA polymerase II, TATA box binding protein (TBP)-associated factor, 31kDa
miR-200bc/429 | [NAME] | 0.0051242 | phosphoglycerate kinase 1
miR-200bc/429 | APC | 0.0051293 | adenomatosis polyposis coli
miR-200bc/429 | PSMD10 | 0.0052302 | proteasome (prosome, macropain) 26S subunit, non-ATPase, 10
miR-149 | NOL3 | 0.0052392 | nucleolar protein 3 (apoptosis repressor with CARD domain)
miR-149 | ZAK | 0.0052435 | sterile alpha motif and leucine zipper containing kinase AZK
miR-200bc/429 | RCHY1 | 0.0052877 | ring finger and CHY zinc finger domain containing 1
miR-149 | SEMA6A | 0.0055668 | sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A
miR-135b | SQSTM1 | 0.0055907 | sequestosome 1
miR-200bc/429 | VEGFC | 0.0056138 | vascular endothelial growth factor C
miR-204/211 | [NAME] | 0.0056858 | similar to RIKEN cDNA 2310016C16
miR-141/200a | VEGFC | 0.0057465 | vascular endothelial growth factor C
miR-135b | SLC16A1 | 0.005839 | solute carrier family 16, member 1 (monocarboxylic acid transporter 1)
miR-200bc/429 | PDGFD | 0.0059703 | platelet derived growth factor D
miR-200bc/429 | FAS | 0.005991 | Fas (TNF receptor superfamily, member 6)
miR-200bc/429 | CUL4B | 0.0059992 | cullin 4B
miR-200bc/429 | DYNC1LI2 | 0.0060139 | dynein, cytoplasmic 1, light intermediate chain 2
miR-141/200a | RFX2 | 0.0060353 | regulatory factor X, 2 (influences HLA class II expression)
miR-218 | LOXL2 | 0.0060574 | lysyl oxidase-like 2
miR-149 | [NAME] | 0.0060627 | MOB1, [NAME] kinase activator-like 2B (yeast)
miR-135b | KCNE3 | 0.0061638 | potassium voltage-gated channel, Isk-related family, member 3
miR-204/211 | IDS | 0.0062849 | iduronate 2-sulfatase ([NAME] syndrome)
miR-200bc/429 | PLDN | 0.0062889 | [NAME] homolog (mouse)
miR-204/211 | LOXL2 | 0.0063347 | lysyl oxidase-like 2
miR-149 | VEGFA | 0.0063858 | vascular endothelial growth factor A
miR-149 | PREX1 | 0.0064117 | phosphatidylinositol 3,4,5-trisphosphate-dependent RAC exchanger 1
miR-135b | DEPDC1 | 0.0064194 | DEP domain containing 1
miR-135b | COL11A1 | 0.0064415 | collagen, type XI, alpha 1
miR-200bc/429 | LIMS1 | 0.0066082 | LIM and senescent cell antigen-like domains 1
miR-204/211 | [NAME] | 0.0066391 | potassium channel tetramerisation domain containing 9
miR-200bc/429 | PREX1 | 0.0066502 | phosphatidylinositol 3,4,5-trisphosphate-dependent RAC exchanger 1
miR-200bc/429 | DENR | 0.006666 | density-regulated protein
miR-200bc/429 | VDP | 0.0068149 | vesicle docking protein p115
miR-204/211 | DENR | 0.0069321 | density-regulated protein
miR-200bc/429 | SIPA1L2 | 0.0070429 | signal-induced proliferation-associated 1 like 2
miR-149 | TMEPAI | 0.0071553 | [NAME], prostate androgen induced RNA
miR-204/211 | C3orf58 | 0.0071809 | chromosome 3 open reading frame 58
miR-135b | NEK6 | 0.0072444 | NIMA (never in mitosis gene a)-related kinase 6
miR-135b | TRIP13 | 0.0073959 | thyroid hormone receptor interactor 13
miR-200bc/429 | SULF1 | 0.0074139 | sulfatase 1
miR-141/200a | TMEPAI | 0.0074859 | [NAME], prostate androgen induced RNA
miR-200bc/429 | LIPA | 0.0075182 | lipase A, lysosomal acid, cholesterol esterase ([NAME] disease)
miR-200bc/429 | CDC40 | 0.0076849 | cell division cycle 40 homolog (S. cerevisiae)
miR-204/211 | PDCD4 | 0.0077392 | programmed cell death 4 (neoplastic transformation inhibitor)
miR-200bc/429 | YIPF5 | 0.0077508 | Yip1 domain family, member 5
miR-204/211 | CAST | 0.0077624 | calpastatin
miR-204/211 | ECT2 | 0.0078296 | epithelial cell transforming sequence 2 oncogene
miR-200bc/429 | FGD6 | 0.0079499 | FYVE, [NAME] and PH domain containing 6
miR-204/211 | WWC3 | 0.0079552 | WWC family member 3
miR-204/211 | PLD1 | 0.0081086 | phospholipase D1, phosphatidylcholine-specific
miR-200bc/429 | ARL2BP | 0.0081848 | ADP-ribosylation factor-like 2 binding protein
miR-135b | SUCLG2 | 0.0084979 | succinate-CoA ligase, GDP-forming, beta subunit
miR-200bc/429 | NBN | 0.0085506 | nibrin
miR-200bc/429 | RGS5 | 0.0087151 | regulator of G-protein signaling 5
miR-204/211 | TAP1 | 0.0087206 | transporter 1, ATP-binding cassette, sub-family B (MDR/TAP)
miR-149 | ACAN | 0.008726 | aggrecan
miR-200bc/429 | [NAME] | 0.0087446 | mastermind-like 2 (Drosophila)
miR-204/211 | PSMB9 | 0.0088206 | proteasome (prosome, macropain) subunit, beta type, 9 (large multifunctional peptidase 2)
miR-149 | TRIP13 | 0.0089635 | thyroid hormone receptor interactor 13
miR-135b | PLD1 | 0.0089726 | phospholipase D1, phosphatidylcholine-specific
miR-204/211 | DTX3L | 0.0090106 | deltex 3-like (Drosophila)
miR-200bc/429 | LRRC17 | 0.0090809 | leucine rich repeat containing 17
miR-204/211 | NRP2 | 0.0092689 | neuropilin 2
miR-149 | PMM2 | 0.0092912 | phosphomannomutase 2
miR-200bc/429 | KCNMA1 | 0.0094104 | potassium large conductance calcium-activated channel, subfamily M, alpha member 1
miR-149 | SLC17A4 | 0.0094158 | solute carrier family 17 (sodium phosphate), member 4
miR-204/211 | LHFPL2 | 0.0094981 | lipoma HMGIC fusion partner-like 2
miR-141/200a | PDGFD | 0.009573 | platelet derived growth factor D
miR-200bc/429 | CDH6 | 0.0096418 | cadherin 6, type 2, K-cadherin (fetal kidney)
miR-149 | LOX | 0.009716 | lysyl oxidase
miR-200bc/429 | FAM78A | 0.0098941 | family with sequence similarity 78, member A
miR-200bc/429 | SEMA6A | <0.0001 | sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A
miR-204/211 | STX6 | <0.0001 | syntaxin 6