264
Views
96
CrossRef citations to date
0
Altmetric
Original Research

Identifying miRNA and gene modules of colon cancer associated with pathological stage by weighted gene co-expression network analysis

, , , , , , & show all
Pages 2815-2830 | Published online: 15 May 2018

References

  • ArnoldMSierraMSLaversanneMSoerjomataramIJemalABrayFGlobal patterns and trends in colorectal cancer incidence and mortalityGut201766468369126818619
  • FlemingMRavulaSTatishchevSFWangHLColorectal carcinoma: Pathologic aspectsJ Gastrointest Oncol20123315317322943008
  • YangYBaiYHeYPTEN loss promotes intratumoral androgen synthesis and tumor microenvironment remodeling via aberrant activation of RUNX2 in castration-resistant prostate cancerClin Cancer Res201824483484629167276
  • ZhangYMaJZhangSA prognostic analysis of 895 cases of stage III colon cancer in different colon subsitesInt J Colorectal Dis20153091173118326054387
  • TutarLTutarEOzgurATutarYTherapeutic targeting of microRNAs in cancer: future perspectivesDrug Dev Res201576738238826435382
  • WangJYWangCLWangXMLiuFJComprehensive analysis of microRNA/mRNA signature in colon adenocarcinomaEur Rev Med Pharmacol Sci20172192114212928537673
  • WuFYuanGChenJWangCNetwork analysis based on TCGA reveals hub genes in colon cancerContemp Oncol (Pozn)201721213614428947883
  • JacobsenASilberJHarinathGHuseJTSchultzNSanderCAnalysis of microRNA-target interactions across diverse cancer typesNat Struct Mol Biol201320111325133224096364
  • CarlsonMRZhangBFangZMischelPSHorvathSNelsonSFGene connectivity, function, and sequence conservation: predictions from modular yeast co-expression networksBMC Genomics200674016515682
  • CarterSLBrechbuhlerCMGriffinMBondATGene co-expression network topology provides a framework for molecular characterization of cellular stateBioinformatics200420142242225015130938
  • LangfelderPHorvathSWGCNA: an R package for weighted correlation network analysisBMC Bioinformatics2008955919114008
  • OldhamMCKonopkaGIwamotoKFunctional organization of the transcriptome in human brainNat Neurosci200811111271128218849986
  • HeZSunMKeYIdentifying biomarkers of papillary renal cell carcinoma associated with pathological stage by weighted gene co-expression network analysisOncotarget2017817279042791428427189
  • SunQZhaoHZhangCGene co-expression network reveals shared modules predictive of stage and grade in serous ovarian cancersOncotarget2017826429834299628562334
  • LiuRZhangWLiuZQZhouHHAssociating transcriptional modules with colon cancer survival through weighted gene co-expression network analysisBMC Genomics201718136128486948
  • ZhaiXXueQLiuQGuoYChenZColon cancer recurrence associated genes revealed by WGCNA coexpression network analysisMol Med Rep20171656499650528901407
  • ChenDTHernandezJMShibataDComplementary strand microRNAs mediate acquisition of metastatic potential in colonic adenocarcinomaJ Gastrointest Surg2012165905912 discussion 912–91322362069
  • ReidJFSokolovaVZoniEmiRNA profiling in colorectal cancer highlights miR-1 involvement in MET-dependent proliferationMol Cancer Res201210450451522343615
  • MarisaLde ReyniesADuvalAGene expression classification of colon cancer into molecular subtypes: characterization, validation, and prognostic valuePLoS Med2013105e100145323700391
  • KozomaraAGriffiths-JonesSmiRBase: annotating high confidence microRNAs using deep sequencing dataNucl Acids Res201442Database issueD68D7324275495
  • RobinsonMDMcCarthyDJSmythGKedgeR: a Bioconductor package for differential expression analysis of digital gene expression dataBioinformatics201026113914019910308
  • ZhangBHorvathSA general framework for weighted gene co-expression network analysisStat Appl Genet Mol Biol20054 Article17
  • LangfelderPHorvathSEigengene networks for studying the relationships between co-expression modulesBMC Syst Biol200715418031580
  • LangfelderPLuoROldhamMCHorvathSIs my network module preserved and reproducible?PLoS Comput Biol201171e100105721283776
  • StoreyJDThe positive false discovery rate: A Bayesian interpretation and the q-valueAnn Stat200331620132035
  • Huang daWShermanBTLempickiRASystematic and integrative analysis of large gene lists using DAVID bioinformatics resourcesNat Protoc200941445719131956
  • VlachosISZagganasKParaskevopoulouMDDIANA-miRPath v3.0: deciphering microRNA function with experimental supportNucl Acids Res201543W1W460W46625977294
  • NishidaNNagaharaMSatoTMicroarray analysis of colorectal cancer stromal tissue reveals upregulation of two oncogenic miRNA clustersClin Cancer Res201218113054307022452939
  • CalonAEspinetEPalomo-PonceSDependency of colorectal cancer on a TGF-beta-driven program in stromal cells for metastasis initiationCancer Cell201222557158423153532
  • TangZLiCKangBGaoGLiCZhangZGEPIA: a web server for cancer and normal gene expression profiling and interactive analysesNucl Acids Res201745W1W98W10228407145
  • AnayaJOncoLnc: linking TCGA survival data to mRNAs, miRNAs, and lncRNAsPeerJ Comput Sci20162e67
  • AgarwalVBellGWNamJWBartelDPPredicting effective microRNA target sites in mammalian mRNAsElife20154
  • SzklarczykDMorrisJHCookHThe STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessibleNucleic Acids Res201745D1D362D36827924014
  • ShannonPMarkielAOzierOCytoscape: a software environment for integrated models of biomolecular interaction networksGenome Res200313112498250414597658
  • BaderGDHogueCWAn automated method for finding molecular complexes in large protein interaction networksBMC Bioinformatics20034212525261
  • PelusoGIncollingoPCalogeroACurrent tissue molecular markers in colorectal cancer: a literature reviewBiomed Res Int20172017260562829214162
  • SztefkoKHodorowicz-ZaniewskaDPopielaTRichterPIGF-I, IGF-II, IGFBP2, IGFBP3 and acid-labile subunit (ALS) in colorectal cancer patients before surgery and during one year follow up in relation to ageAdv Med Sci2009541515819482725
  • DasVKalitaJPalMPredictive and prognostic biomarkers in colorectal cancer: A systematic review of recent advances and challengesBiomed Pharmacother20178781928040600
  • LiDYanDTangHIMP3 is a novel prognostic marker that correlates with colon cancer progression and pathogenesisAnn Surg Oncol200916123499350619672661
  • TlstyTDCoussensLMTumor stroma and regulation of cancer developmentAnnu Rev Pathol2006111915018039110
  • BussardKMMutkusLStumpfKGomez-ManzanoCMariniFCTumor-associated stromal cells as key contributors to the tumor microenvironmentBreast Cancer Res20161818427515302
  • HanahanDCoussensLMAccessories to the crime: functions of cells recruited to the tumor microenvironmentCancer Cell201221330932222439926
  • BiYEhirchiouDKiltsTMIdentification of tendon stem/progenitor cells and the role of the extracellular matrix in their nicheNat Med200713101219122717828274
  • BornsteinPKyriakidesTRYangZArmstrongLCBirkDEThrombospondin 2 modulates collagen fibrillogenesis and angiogenesisJ Investig Dermatol Symp Proc2000516166
  • KolacnaLBakesovaJVargaFBiochemical and biophysical aspects of collagen nanostructure in the extracellular matrixPhysiol Res200756suppl 1S51S6017552894
  • ArnoldSARiveraLBMillerAFLack of host SPARC enhances vascular function and tumor spread in an orthotopic murine model of pancreatic carcinomaDis Model Mech201031–2577220007485
  • FangMYuanJPengCLiYCollagen as a double-edged sword in tumor progressionTumour Biol20143542871288224338768
  • FischerHStenlingRRubioCLindblomAColorectal carcinogenesis is associated with stromal expression of COL11A1 and COL5A2Carcinogenesis200122687587811375892
  • SmithMJCulhaneACDonovanMAnalysis of differential gene expression in colorectal cancer and stroma using fluorescence-activated cell sorting purificationBr J Cancer200910091452146419401702
  • KirklandSCType I collagen inhibits differentiation and promotes a stem cell-like phenotype in human colorectal carcinoma cellsBr J Cancer2009101232032619568234
  • BrabletzTSpadernaSKolbJDown-regulation of the homeodomain factor Cdx2 in colorectal cancer by collagen type I: an active role for the tumor environment in malignant tumor progressionCancer Res200464196973697715466189
  • ContiJAKendallTJBatemanAThe desmoplastic reaction surrounding hepatic colorectal adenocarcinoma metastases aids tumor growth and survival via alphav integrin ligationClin Cancer Res200814206405641318927279
  • VellingaTTden UilSRinkesIHCollagen-rich stroma in aggressive colon tumors induces mesenchymal gene expression and tumor cell invasionOncogene201635405263527126996663
  • MadarSGoldsteinIRotterV‘Cancer associated fibroblasts’ – more than meets the eyeTrends Mol Med201319844745323769623
  • LeventalKRYuHKassLMatrix crosslinking forces tumor progression by enhancing integrin signalingCell2009139589190619931152
  • YuBChenXLiJStromal fibroblasts in the microenvironment of gastric carcinomas promote tumor metastasis via upregulating TAGLN expressionBMC Cell Biol2013141723510049
  • BernauKTorrEEEvansMDAokiJKNgamCRSandboNTensin 1 is essential for myofibroblast differentiation and extracellular matrix formationAm J Respir Cell Mol Biol201756446547628005397
  • CalabroNEKristofikNJKyriakidesTRThrombospondin-2 and extracellular matrix assemblyBiochim Biophys Acta2014184082396240224440155
  • JohnsonSMGrosshansHShingaraJRAS is regulated by the let-7 microRNA familyCell2005120563564715766527
  • ShimizuSTakeharaTHikitaHThe let-7 family of microRNAs inhibits Bcl-xL expression and potentiates sorafenib-induced apoptosis in human hepatocellular carcinomaJ Hepatol201052569870420347499
  • MotoyamaKInoueHNakamuraYUetakeHSugiharaKMoriMClinical significance of high mobility group A2 in human gastric cancer and its relationship to let-7 microRNA familyClin Cancer Res20081482334234018413822
  • ShiWZhangZYangBOverexpression of microRNA let-7 correlates with disease progression and poor prognosis in hepatocellular carcinomaMedicine20179632e776428796071
  • RoushSSlackFJThe let-7 family of microRNAsTrends Cell Biol2008181050551618774294