# List of intestinal epithelial differentiation genes

Table of genes implicated in development and differentiation of the intestinal epithelium
The table listed below is a running comprehensive list of all intestinal differential genes that have been reported in the literature. The PMID is the pubmed identification number of the papers that support the summarized information in the table corresponding to each row.
| Official | Common | Function/phenotype | PMID |
| APC | | Conditional deletion promotes Paneth cell differentiation at the expense of enterocyte, goblet and enteroendocrine cell differentiation. Negative regulator of beta-catenin | 15716339 |
| ATOH1 | Math1, HATH1 | Commitment to secretory lineage | 20691176 17570220 11739954 |
| BLIMP1 | PRDM1 | Postnatal epithelial maturation; suckling/weaning transition | 21878906 21670299 |
| BMPR1A | | Involved in terminal differentiation of secretory cells | 17678919 |
| CBFA2T2 | Mtgr1 | Required for maintenance of secretory lineage | 16227606 |
| CDH1 | E-cadherin | Required for maturation/localization of Paneth and goblet cells | 21179475 |
| CDX1 | Cdx1 | Induced expression promoted enterocyte differentiation in IEC6 cells | 19059241 10579974 |
| CDX2 | Cdx2 | Involves in epithelial cell maturation as well as goblet and Paneth cell differentiation. Required for the small intestinal identity during development. In IEC-6 cells, conditional expression induced enterocyte and goblet like cells | 21081128 19386267 8552090 |
| CTNNB1 | Catenin, beta | Paneth cell differentiation. Essential for stem cell/crypt maintenance. Villus and crypt morphogenesis with Tcf3 via c-Myc | 18948094 17785439 17681174 |
| DLL1 | | Functions as a cis acting element and required for goblet cell differentiation in the Notch inactive colonic epithelia. Notch ligand in intestine. Required for the maintenance of stem and progenitors | 20170633 21238454 |
| DLL4 | | Notch ligand in intestine. Required for the maintenance of stem and progenitors | 21238454 |
| ELF3 | ESE-1 | Terminal differentiation of absorptive enterocytes | 19801644 |
| EPHB3 | | Localization of Paneth cells to crypt base | 12408869 |
| FGF7 | KGF | Regulate epithelial growth and promote differentiation | 19326389 |
| FGFR3 | | Paneth cell specification through beta-catenin/Tcf4 dependent and independent pathway. Significant reduction in Paneth cell in knockout mice. Involved in crypt development and stem cell expansion | 19407216 |
| FOXA1 | HNF3A | Involved in goblet cell differentiation and enteroendocrine differentiation | 19737569 |
| FOXA2 | HNF3B | Involved in goblet cell differentiation and enteroendocrine differentiation | 19737569 |
| FZD5 | | Required for Paneth cell maturation. Loss of Paneth cell genes after conditional deletion | 15778706 |
| GADD45GIP1 | Crif1 | Essential Elf3 coactivator in differentiation of absorptive enterocytes | 19801644 |
| GATA6 | | Regulates proximal-distal identity in the intestines | 21262227 |
| GATA4 | | Required for proximal intestinal identity | 16940177 18812176 |
| GFI1 | | Required for proper allocation of secretory lineage | 16230531 |
| HES1 | Hes1 | Commitment to absorptive lineage | 10615124 |
| HNF1A | HNF1-α | Regulates terminal differentiation of enterocytes and secretory cells potentially by direct regulation of Atoh1 | 20133952 20388655 |
| HNF1B | HNF1-β | Regulates terminal differentiation of enterocytes and secretory cells potentially by direct regulation of Atoh1 | 20133952 20388655 |
| IHH | | Colonocytes differentiation | 14770182 |
| KLF4 | GKLF | Promotes goblet cell differentiation in colon | 21070761 12015290 |
| LGR4 | GPR48 | Promotes Paneth cell differentiation and crypt cell proliferation. Along with LGR5, acts as the receptor for R-Spondin, a WNT co-ligand that amplifies WNT signaling | 21508962 21909076 |
| LGR5 | GPR49 | Premature paneth cell differentiation in fetal intestine. Intestinal stem cell marker. Along with LGR4, acts as the receptor for R-Spondin, a WNT co-ligand that amplifies WNT signaling | 19394326 21727895 |
| MMP9 | | Negatively regulates terminal differentiation of goblet cells in colon | 17484881 |
| MSI1 | | Suppress paneth cell differentiation independent of Notch and Wnt signaling pathways | 19214660 |
| MYBL2 | | Regulates commitment of colon stem cells to differentiate | 20857481; 20133952 |
| MYC | | Crypt loss upon conditional deletion in the adult | 16954380 |
| NEUROD1 | BETA2 | Differentiation of Ngn3 enteroendocrine cells into CCK and secretin cells | 18022152; 15044355 |
| NEUROG3 | NGN3, ATOH5 | Commitment to the enteroendocrine cell lineage | 17706959; 12456641 |
| NKX2-2 | Nkx2.2 | Required for a subset of enteroendocrine cells differentiation | 18022152 |
| NOTCH1 | | Regulates absorptive cells vs secretory cells | 15959516; 18274550 |
| NOTCH2 | | Regulates absorptive cells vs secretory cells | 15959516; 18274550 |
| NOX1 | | Regulate ROS to activate Notch signaling and indirectly promote absorptive cell lineage in the colon | 20351171 |
| PAX6 | | Differentiation of GIP in enteroendocrine lineage | 18022152; 10478839 |
| PDX1 | IPF1 | Overexpression causes differentiation of immature intestinal epithelia to enteroendocrine cells. Conditional deletion alters enterocyte and enteroendocrine gene expression | 11408276; 19808654 |
| PPARD | PPAR-δ/β | Involves in Paneth cell maturation by modulating IHH expression | 16890607 |
| PTK6 | BRK | Promote cell cycle exit in Wnt independent pathway and promote enterocyte differentiation | 16782882 |
| RB1 | pRB | Required for enterocyte terminal differentiation in small intestine | 18981186 |
| RBPJ | CBF1 | Conversion of progenitors and differentiated cells into goblet cells by conditional deletion | 15959515 |
| REG4 | | Marker for enteroendocrine cells | 26287467 |
| SOX9 | | Required for paneth cell differentiation | 17698607; 17681175 |
| SPDEF | PDEF | Regulates terminal differentiation of goblet cells and Paneth cells | 19786015; 19549527 |
| STK11 | LKB1 | Required for normal differentiation of goblet and Paneth cells | 19165340 |
| TGFBR2 | Tgf-βRII | The critical downstream target of Elf3 for enterocyte differentiation | 17408644 |
| VAV | | Required for enterocyte differentiation in mouse cecum and colon | 19139088 |