Table 1.
TGFβ SIGNATURE IN CHOLANGIOCARCINOMA CELL LINES
| (A) Genes induced by TGFβ | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Agilent Probe | Gene Name | Gene Symbol | Accession No. | HuCCT1 (TGFβ/Ctrl) | Huh28 (TGFβ/Ctrl) | Huh28/HuCCT1 | Known TGFβ Target | |||
| P Value | FC | P Value | FC | P Value | FC | |||||
| A_24_P411561 | Hepatitis A virus cellular receptor 2 | HAVCR2 | NM_032782 | 1.00E‐07 | 38.46 | 5.00E‐07 | 7.14 | 1.40E‐06 | 11.25 | yes |
| A_24_P158089 | Serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1 | SERPINE1 | NM_000602 | < 1e‐07 | 20.83 | 7.00E‐07 | 3.33 | 1.00E‐07 | 6.63 | yes |
| A_21_P0011334 | na | XLOC_l2_004757 | BC043257 | 4.50E‐05 | 18.52 | < 1e‐07 | 5.88 | 8.21E‐04 | 5.20 | no |
| A_33_P3243887 | Interleukin 11 | IL11 | NM_000641 | < 1e‐07 | 17.24 | < 1e‐07 | 7.14 | 1.40E‐06 | 3.54 | yes |
| A_21_P0001676 | na | XLOC_000166 | na | < 1e‐07 | 15.15 | 5.10E‐06 | 2.08 | < 1e‐07 | 300.67 | no |
| A_23_P153571 | IGF‐like family member 2 | IGFL2 | NM_001002915 | 3.40E‐06 | 12.82 | 5.35E‐05 | 2.27 | 4.69E‐05 | 5.42 | no |
| A_33_P3243454 | IGF‐like family member 3 | IGFL3 | NM_207393 | 5.30E‐06 | 11.76 | 1.00E‐07 | 3.70 | 4.00E‐07 | 57.37 | no |
| A_33_P3255384 | BPI Fold Containing Family C | BPIFC | NM_174932 | 1.00E‐07 | 10.20 | 7.56E‐05 | 2.78 | 2.00E‐07 | 12.20 | no |
| A_32_P185637 | Collagen, type XX, alpha 1 | COL20A1 | NM_020882 | 1.50E‐06 | 10.10 | < 1e‐07 | 6.25 | 3.10E‐06 | 8.09 | no |
| A_23_P110777 | Leukocyte cell‐derived chemotaxin 2 | LECT2 | NM_002302 | 2.57E‐04 | 8.33 | 1.23E‐05 | 7.69 | 2.30E‐06 | 7.21 | no |
| A_33_P3345534 | Keratin 14 | KRT14 | NM_000526 | 1.00E‐07 | 7.69 | 9.30E‐06 | 2.70 | 1.00E‐07 | 10.82 | no |
| A_23_P96158 | Keratin 17 | KRT17 | NM_000422 | < 1e‐07 | 7.69 | 8.70E‐06 | 2.63 | < 1e‐07 | 9.50 | no |
| A_24_P887857 | na | na | na | < 1e‐07 | 7.69 | 1.65E‐05 | 2.70 | 1.00E‐07 | 9.67 | no |
| A_23_P205074 | Solute carrier family 46, member 3 | SLC46A3 | NM_181785 | 3.15E‐04 | 7.69 | 1.00E‐06 | 2.33 | 3.55E‐04 | 7.54 | no |
| A_24_P882732 | na | na | DR007925 | < 1e‐07 | 7.14 | 2.28E‐05 | 2.70 | 1.00E‐07 | 9.50 | no |
| A_21_P0011578 | na | XLOC_l2_006021 | DB117598 | 3.00E‐07 | 7.14 | 3.00E‐05 | 2.70 | 4.00E‐07 | 8.77 | no |
| A_33_P3857239 | Keratin 42 pseudogene | KRT42P | NR_033415 | < 1e‐07 | 6.67 | 9.70E‐06 | 2.86 | 1.00E‐07 | 8.69 | no |
| A_33_P3235905 | na | na | na | 6.20E‐05 | 6.67 | 6.82E‐05 | 2.44 | 3.22E‐04 | 3.90 | no |
| A_21_P0008663 | na | XLOC_011331 | na | 2.90E‐06 | 6.67 | < 1e‐07 | 5.56 | 3.00E‐07 | 19.21 | no |
| A_32_P62963 | Keratin 16 pseudogene 2 | KRT16P2 | NR_029392 | 1.00E‐07 | 5.88 | 2.19E‐05 | 2.70 | 4.00E‐07 | 5.88 | no |
| A_23_P381489 | Long intergenic nonprotein coding RNA 313 | LINC00313 | NR_026863 | 4.10E‐06 | 5.88 | 8.91E‐05 | 2.08 | 2.19E‐04 | 2.29 | no |
| A_23_P166779 | Long intergenic nonprotein coding RNA 312 | LINC00312 | NR_024065 | 3.06E‐05 | 4.17 | 1.00E‐07 | 5.00 | 1.36E‐04 | 2.86 | no |
| A_23_P19663 | Connective tissue growth factor | CTGF | NM_001901 | 4.00E‐07 | 4.00 | 1.91E‐05 | 2.22 | 1.00E‐07 | 11.67 | yes |
| A_19_P00321671 | na | na | na | 1.56E‐04 | 4.00 | 3.60E‐06 | 3.03 | 5.06E‐05 | 5.57 | no |
| A_21_P0012601 | na | XLOC_l2_010751 | na | 1.20E‐06 | 4.00 | 6.60E‐06 | 3.03 | 5.00E‐07 | 5.23 | no |
| A_32_P76627 | na | na | CR597597 | 1.00E‐07 | 3.70 | 2.60E‐06 | 2.78 | 3.00E‐07 | 4.00 | no |
| A_23_P379649 | Bcl2 modifying factor | BMF | NM_001003940 | 1.65E‐05 | 3.57 | 3.00E‐07 | 2.56 | 8.00E‐07 | 10.75 | yes |
| A_21_P0009087 | na | XLOC_012049 | na | 1.72E‐04 | 3.45 | 1.06E‐05 | 3.03 | 2.81E‐05 | 5.86 | no |
| A_19_P00318323 | Long intergenic nonprotein coding RNA 340 | LINC00340 | NR_015410 | 2.06E‐05 | 3.33 | 8.60E‐06 | 2.27 | 1.00E‐07 | 19.17 | no |
| A_23_P107744 | Sphingosine‐1‐phosphate receptor 5 | S1PR5 | NM_030760 | 6.04E‐04 | 3.03 | 1.50E‐06 | 3.57 | 1.35E‐05 | 12.24 | no |
| A_32_P309404 | Solute carrier family 22 (extraneuronal monoamine transporter), member 3 | SLC22A3 | NM_021977 | 5.00E‐07 | 3.03 | 1.78E‐05 | 2.04 | 1.60E‐06 | 3.48 | no |
| A_24_P838448 | Long intergenic nonprotein coding RNA 340 | LINC00340 | NR_015410 | 1.04E‐04 | 2.86 | 1.30E‐06 | 2.44 | 2.00E‐07 | 12.50 | no |
| A_23_P124642 | RAS guanyl releasing protein 1 (calcium and DAG‐regulated) | RASGRP1 | NM_005739 | 1.40E‐05 | 2.70 | 1.32E‐05 | 2.08 | < 1e‐07 | 27.00 | no |
| A_23_P344531 | Synaptopodin | SYNPO | NM_007286 | 7.10E‐06 | 2.50 | 1.60E‐06 | 2.56 | < 1e‐07 | 24.38 | no |
| A_23_P303548 | Nucleolar protein 4‐like | NOL4L | XM_003403733 | 2.34E‐04 | 2.44 | 5.14E‐05 | 2.08 | 4.81E‐04 | 2.31 | no |
| A_24_P239606 | Growth arrest and DNA‐damage‐inducible, beta | GADD45B | NM_015675 | 3.00E‐06 | 2.33 | 6.10E‐05 | 2.44 | 3.69E‐05 | 2.93 | yes |
| A_23_P131846 | Snail homolog 1 (Drosophila) | SNAI1 | NM_005985 | 4.20E‐06 | 2.33 | 1.00E‐07 | 5.26 | < 1e‐07 | 9.48 | yes |
| A_21_P0009196 | na | XLOC_012515 | na | 6.91E‐04 | 2.27 | 2.06E‐05 | 2.08 | 8.00E‐06 | 7.67 | no |
| (B) Genes repressed by TGFβ | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Agilent Probe | Gene Name | Gene Symbol | Accession No. | HuCCT1 (TGFβ/Ctrl) | Huh28 (TGFβ/Ctrl) | Huh28 / HuCCT1 | Known TGFβ Target | |||
| P Value | FC | P Value | FC | P Value | FC | |||||
| A_33_P3663974 | Thyroid hormone receptor beta | THRB | NM_001128177 | 8.10E‐06 | 0.49 | 1.75E‐04 | 0.47 | 1.70E‐06 | 0.42 | no |
| A_21_P0010449 | na | XLOC_014399 | XR_109732 | 2.70E‐06 | 0.47 | 1.05E‐04 | 0.38 | 1.00E‐07 | 0.08 | no |
| A_21_P0000841 | Hypothetical LOC100505483 | LOC100505483 | NR_038926 | 7.60E‐06 | 0.45 | 3.13E‐05 | 0.40 | 2.25E‐05 | 0.43 | no |
| A_23_P121064 | Pentraxin 3, long | PTX3 | NM_002852 | 1.50E‐06 | 0.45 | 2.00E‐06 | 0.32 | 4.90E‐06 | 0.42 | yes |
| A_23_P121657 | Heparan sulfate (glucosamine) 3‐O‐sulfotransferase 1 | HS3ST1 | NM_005114 | 3.00E‐07 | 0.42 | 3.07E‐04 | 0.45 | < 1e‐07 | 0.00 | no |
| A_23_P52266 | Interferon‐induced protein with tetratricopeptide repeats 1 | IFIT1 | NM_001548 | 1.19E‐04 | 0.40 | 1.66E‐05 | 0.36 | 1.72E‐05 | 0.27 | no |
| A_23_P345460 | Pleckstrin homology domain‐containing, family G (with RhoGef domain) member 4 | PLEKHG4 | NM_015432 | 6.00E‐07 | 0.36 | 2.90E‐04 | 0.50 | 1.00E‐07 | 0.21 | no |
| A_23_P98350 | Baculoviral inhibitor of apoptosis protein repeat‐containing 3 | BIRC3 | NM_001165 | 1.00E‐07 | 0.29 | 2.70E‐06 | 0.45 | < 1e‐07 | 0.17 | yes |
| A_33_P3398181 | Hypothetical LOC100127909 | LOC100127909 | XR_111781 | 8.81E‐05 | 0.26 | 7.13E‐05 | 0.35 | 1.89E‐05 | 0.27 | no |
| A_23_P415021 | Methyltransferase‐like 7A | METTL7A | NM_014033 | 2.00E‐07 | 0.22 | 4.00E‐06 | 0.32 | 1.00E‐07 | 0.19 | no |
Abbreviations: Ctrl, control; FC, fold change; na, not applicable.