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Table 3 Overview of the most relevant genes associated with metastasis during liver colonisation (FDR < 5%)

From: The adaptation of colorectal cancer cells when forming metastases in the liver: expression of associated genes and pathways in a mouse model

Gene Ensembl ID Gene Symbol Functional Gene Group p-value Mean intensity CMT-93 Mean intensity liver metastases logFC* logFC^ FDR
Matrix metallopepti-dase 7 ENSMUSG00000018623 MMP7 Extracellular Matrix Proteins 1,7 × 10−180 0,02 72,56 8,97 11,69 4,9 × 10−178
Keratin 20 ENSMUSG00000035775 KRT20 CRC-Related Genes 2,9 × 10−174 0,81 51,99 5,8 6,12 7,7 × 10−172
Wnt inhibitory factor 1 ENSMUSG00000020218 WIF1 Wnt Signalling (canonical) 3,7 × 10−126 0,00 20,68 7,37 12,85 3,3 × 10−124
Matrix metallopepti-dase 9 ENSMUSG00000017737 MMP9 Extracellular Matrix Proteins 3,8 × 10−72 0,10 14,16 5,95 7,92 9 × 10−71
Chemokine (C-X-C motif) receptor 4 ENSMUSG00000045382 CXCR4 Cell Growth and Proliferation Genes 1,5 × 10−71 0,02 19,29 7,06 10,50 3,4 × 10−70
Matrix metallopepti-dase 2 ENSMUSG00000031740 MMP2 Extracellular Matrix Proteins 1,8 × 10−70 0,09 27,83 7,04 8,33 4,2 × 10−69
Eph receptor B2 ENSMUSG00000028664 EPHB2 Cell Growth and Proliferation Genes 4,8 × 10−59 1,06 10,86 3,2 3,65 8 × 10−58
Chemokine (C-X-C motif) receptor 2 ENSMUSG00000026180 CXCR2 Cell Growth and Proliferation Genes 1,1 10−40 0,04 7,53 5,51 7,75 9,7 × 10−40
Cadherin 11 ENSMUSG00000031673 CDH11 Cell Adhesion Genes 8,8 × 10−40 0,12 6,32 4,67 5,75 7,9 × 10−39
Axin2 ENSMUSG00000000142 AXIN2 Wnt Signalling (canonical) 2,2 × 10−39 20,31 72,10 1,82 1,87 2 × 10−38
Integrin beta 3 ENSMUSG00000020689 ITGB3 Cell Adhesion Genes 1,6 × 10−33 5,54 25,48 2,17 2,35 1,2 × 10−32
Matrix metallopeptidase 13 ENSMUSG00000050578 MMP13 Extracellular Matrix Proteins 8,1 × 10−29 0,22 7,45 4,43 5,20 4,8 × 10−28
Glycoprotein (transmembrane) nmb ENSMUSG00000029816 GPNMB Cell Adhesion Genes 3,9 × 10−27 0,21 14,50 5,45 6,25 2,1 × 10−26
Snail family zinc finger 1 ENSMUSG00000042821 SNAI1 EMT Transition 2,9 × 10−26 0,12 3,05 3,62 4,66 1,5 × 10−25
Plasminogen activator, urokinase receptor ENSMUSG00000046223 PLAUR Cell Growth and Proliferation Genes 8,9 × 10−20 191,38 71,50 −1,42 −1,28 3,6 × 10−19
Matrix metallopeptidase 3 ENSMUSG00000043613 MMP3 Extracellular Matrix Proteins 3,7 × 10−17 0,05 2,70 3,95 5,74 1,3 × 10−16
Integrin alpha 6 ENSMUSG00000027111 ITGA6 Cell Adhesion Genes 5 × 10−17 12,03 31,23 1,36 1,32 1,8 × 10−16
Matrix metallopeptidase 10 ENSMUSG00000047562 MMP10 Extracellular Matrix Proteins 7,6 × 10−17 0,06 2,68 3,83 5,37 2,7 × 10−16
Somatostatin receptor 2 ENSMUSG00000047904 SSTR2 Cell Growth and Proliferation Genes 5,7 × 10−15 0,22 1,57 2,19 3,17 1,8 × 10−14
Jun proto-oncogene ENSMUSG00000052684 JUN Transcription Factors and Regulators 7,8 × 10−13 22,13 44,89 1,01 1,16 2,3 × 10−12
Frizzled homolog 2 (Drosophila) ENSMUSG00000050288 FZD2 Wnt Signalling (canonical) 1,1 × 10−12 6,88 2,16 -1,7 -1,54 3 × 10−12
Chemokine (C-C motif) ligand 7 ENSMUSG00000035373 CCL7 Cell Growth and Proliferation Genes 2,4 × 10−12 0,98 9,98 3,18 3,47 6,9 × 10−12
Nuclear receptor subfamily 4, group A, member 3 ENSMUSG00000028341 NR4A3 Transcription Factors and Regulators 3,5 × 10−12 0,16 1,22 2,1 3,31 1 × 10−11
RAR-related orphan receptor beta ENSMUSG00000036192 RORB Cell Growth and Proliferation Genes 2,6 × 10−11 2,57 0,70 -1,94 -1,68 7 × 10−11
Cyclin-dependent kinase inhibitor 2A ENSMUSG00000044303 CDKN2A Transcription Factors and Regulators 1,9 × 10−8 179,73 91,40 −0,98 −0,84 4,4 × 10−8
Matrix metallopeptidase 11 ENSMUSG00000000901 MMP11 Extracellular Matrix Proteins 6,6 × 10−7 12,30 5,36 −1,21 −1,19 1,4 × 10−6
Ets variant 4 ENSMUSG00000017724 ETV4 Transcription Factors and Regulators 9,5 × 10−7 21,60 10,13 −1,1 −0,93 1,9 × 10−6
Lymphoid enhancer binding factor 1 ENSMUSG00000027985 LEF1 EMT Transition 5,3 × 10−5 0,37 1,19 1,26 1,69 9,3 × 10−5
Caspase 3 ENSMUSG00000031628 CASP3 Apoptosis Genes 0,00027 48,58 29,55 −0,72 −0,57 0,00045
Fibronectin 1 ENSMUSG00000026193 FN1 EMT Transition 0,00085 1051,50 805,60 −0,38 −0,74 0,00134
B cell CLL/lymphoma 9 ENSMUSG00000038256 BCL9 Wnt Signalling (canonical) 0,00222 15,50 19,20 0,3 0,42 0,00336
Dickkopf homolog 2 (Xenopus laevis) ENSMUSG00000028031 DKK2 Wnt Signalling (canonical) 0,02671 9,31 6,03 −0,65 −0,50 0,03566
  1. LogFC* describes changes between/comparing the mean intensities calculated as the log fold changes of base 2 referring to the TPM-values, logFC^ represents the log fold change of base 2 from the R package EdgeR