Table 1

Keywords used for literature mining
Gene/pathway Association with CRC Ref
hMLH1/DNA repair Genetic or epigenetic inactivation [3,98]
MSH2/DNA repair Genetic or epigenetic inactivation [2]
MLH3/DNA repair Dominant negative mutations inhibit hMLH1 function [30,31]
MYH/Development Attenuate CRC in association with FAP [4,99]
CDK8/cell cycle regulation CDK8 Inhibition activates Wnt/b-catenin pathway [100,101]
DCC Genetic loss [102]
IGF-IR/IGF-IR, EGFR and HER2 receptor tyrosine kinase signalling Co-expression in advanced stages [36]
TGFBR1/TGF-beta signalling pathway Inhibits/prevents CRC [103,104]
Axin2/Cytoskeleton remodelling Mutations activates Wnt signalling [34]
APC/Cell cycle Genetic loss [105,106]
b-Raf/Ras signalling pathway Mutations are prognostic [107,108]
MSH6/DNA damage Mutations in HNPCC [109,110]
PTEN/cell signalling Genetic loss or functional inactivation linked to poor survival [32,33]
CXCL12 and CXCR4/Immune response – signalling pathway Inverse relationship between CXCL12 and CXCR4, with over-expression of CXCL12 and down-regulation of CXCR4 are linked to tumor progression [111]
RAD18/DNA damage Polymorphism at Arg302Gln [112,113]
c-Met/HGF signalling pathway Over-expression linked to tumor progression [114]
HG/HGF signalling pathway Over-expression HGF in association with c-Met linked to metastasis [115]
MACC1/signalling pathway Over-expression associated with metastasis [116]
CASPASE-3/apoptosis-FAS signalling/TNFR1/caspase-cascade [117][118]
CASP10/caspase-cascade Somatic mutations linked to pathogenesis [119]
NAT1/metabolic pathways Genetic mutations [120,121]
GSTM1/detoxification pathway GSTM1 expression associated with tumor progression [122]
GSTT1/cell cycle GSTT1 expression associated with high risk of CRC [122]
CYP2C9/lipid metabolism High risk associated with CYP2C9*1 gene [123], [124]
Bcl-2/Apoptosis-FAS signalling/TNFR1 signalling Loss of expression associated with stage II relapse [125]
PRMT1/DNA repair Expression of gene variant associated with CRC [126,127]
SMAD3/Cytoskeleton remodelling Expression is associated with the survival rate of CRC [128]
IGFBP1/IGF Beta receptor signalling pathway Expression is inversely proportional to survival rate in CRC [129]
PDGFBB/PDGF signalling pathway Higher expression associated with low survival rate [130]
PDGFRB/PDGF signalling pathway Higher expression associated with CRC tumor stroma [131]
PLK1/cell cycle Higher expression and a prognostic factor in CRC [132]
IFITM1/Beta-catenin signalling pathway Expression identified in CRC, important for pathogenesis, metastasis and potential biomarker [133]
MBL2/lectin pathway Very population specific. Two school of thought (yes/no) NCI bulletin-April-17,2007
PMS2/DNA repair Loss in expression associated with CRC [134]
CXCL2/Apoptotic pathways Elevated expression associated with CRC [135]
IGF1R/IGFR signalling pathway Regulates the expression of VEGF expression. Can be used as prognostic factor. [136]
CYP27B1/Vitamin D pathway Enzyme identified to be associated with CRC- but more studies need to be performed [137]
CYP24/Vitamin D pathway Useful gene/SNP/precursor for chemotherapy [138]
MUCINS/mucin expression pathway Useful therapeutic target [139,140]

Pradhan et al.

Pradhan et al. BMC Cancer 2012 12:331   doi:10.1186/1471-2407-12-331

Open Data