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Gene: CDX1 |
Gene summary for CDX1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CDX1 | Gene ID | 1044 |
| Gene name | caudal type homeobox 1 | |
| Gene Alias | CDX1 | |
| Cytomap | 5q32 | |
| Gene Type | protein-coding | GO ID | GO:0001501 | UniProtAcc | P47902 |
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Malignant transformation analysis |
| Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells |
| Malignant transformation involving gene list. |
| Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
| 1044 | CDX1 | HTA11_2487_2000001011 | Human | Colorectum | SER | 5.97e-13 | 5.47e-01 | -0.1808 |
| 1044 | CDX1 | HTA11_2951_2000001011 | Human | Colorectum | AD | 3.41e-03 | 3.33e-01 | 0.0216 |
| 1044 | CDX1 | HTA11_1938_2000001011 | Human | Colorectum | AD | 2.96e-05 | 4.59e-01 | -0.0811 |
| 1044 | CDX1 | HTA11_78_2000001011 | Human | Colorectum | AD | 1.89e-07 | 4.48e-01 | -0.1088 |
| 1044 | CDX1 | HTA11_347_2000001011 | Human | Colorectum | AD | 4.91e-27 | 6.87e-01 | -0.1954 |
| 1044 | CDX1 | HTA11_411_2000001011 | Human | Colorectum | SER | 1.07e-11 | 1.07e+00 | -0.2602 |
| 1044 | CDX1 | HTA11_2112_2000001011 | Human | Colorectum | SER | 1.88e-09 | 1.05e+00 | -0.2196 |
| 1044 | CDX1 | HTA11_3361_2000001011 | Human | Colorectum | AD | 7.13e-14 | 6.35e-01 | -0.1207 |
| 1044 | CDX1 | HTA11_83_2000001011 | Human | Colorectum | SER | 4.74e-06 | 5.71e-01 | -0.1526 |
| 1044 | CDX1 | HTA11_696_2000001011 | Human | Colorectum | AD | 2.07e-34 | 7.98e-01 | -0.1464 |
| 1044 | CDX1 | HTA11_866_2000001011 | Human | Colorectum | AD | 5.89e-09 | 4.05e-01 | -0.1001 |
| 1044 | CDX1 | HTA11_1391_2000001011 | Human | Colorectum | AD | 1.41e-18 | 7.63e-01 | -0.059 |
| 1044 | CDX1 | HTA11_2992_2000001011 | Human | Colorectum | SER | 1.15e-09 | 8.89e-01 | -0.1706 |
| 1044 | CDX1 | HTA11_5212_2000001011 | Human | Colorectum | AD | 1.50e-12 | 7.25e-01 | -0.2061 |
| 1044 | CDX1 | HTA11_5216_2000001011 | Human | Colorectum | SER | 2.35e-03 | 6.16e-01 | -0.1462 |
| 1044 | CDX1 | HTA11_546_2000001011 | Human | Colorectum | AD | 7.99e-11 | 6.58e-01 | -0.0842 |
| 1044 | CDX1 | HTA11_866_3004761011 | Human | Colorectum | AD | 1.50e-05 | 3.64e-01 | 0.096 |
| 1044 | CDX1 | HTA11_8622_2000001021 | Human | Colorectum | SER | 8.40e-03 | 3.95e-01 | 0.0528 |
| 1044 | CDX1 | HTA11_7663_2000001011 | Human | Colorectum | SER | 2.03e-12 | 6.87e-01 | 0.0131 |
| 1044 | CDX1 | HTA11_10711_2000001011 | Human | Colorectum | AD | 3.53e-05 | 3.63e-01 | 0.0338 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer |
| ∗log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage. |
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Malignant transformation related pathway analysis |
| Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer |
| Figure of enriched GO biological processes. |
| Tissue | Disease Stage | Enriched GO biological Processes |
| Colorectum | AD |  |
| Colorectum | SER |  |
| Colorectum | MSS |  |
| Colorectum | MSI-H |  |
| Colorectum | FAP |  |
| ∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| Page: 1 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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Cell-cell communication analysis |
| Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states |
| Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
| Page: 1 |
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Single-cell gene regulatory network inference analysis |
| Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states |
| TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
| CDX1 | CD8TEXP | Colorectum | AD | CEP170B,LAD1,KRT19, etc. | 1.74e-01 |  |
| CDX1 | CD8TEXP | Colorectum | ADJ | CEP170B,LAD1,KRT19, etc. | 9.23e-02 |  |
| CDX1 | CD8TEXP | Colorectum | CRC | CEP170B,LAD1,KRT19, etc. | 3.71e-01 |  |
| CDX1 | CD8TEXP | Colorectum | FAP | CEP170B,LAD1,KRT19, etc. | 9.12e-02 |  |
| CDX1 | TH1 | Colorectum | FAP | CEP170B,LAD1,KRT19, etc. | 1.16e-01 | |
| CDX1 | CD8TEXP | Colorectum | Healthy | CEP170B,LAD1,KRT19, etc. | 1.66e-01 |  |
| CDX1 | CD8TEXP | Colorectum | MSI-H | CEP170B,LAD1,KRT19, etc. | 7.06e-02 |  |
| CDX1 | CD8TEXP | Colorectum | MSS | CEP170B,LAD1,KRT19, etc. | 2.53e-01 |  |
| CDX1 | CD8TEXP | Colorectum | SER | CEP170B,LAD1,KRT19, etc. | 2.07e-01 |  |
| CDX1 | INCAF | Colorectum | AD | ESRP1,TJP3,CDX2, etc. | 3.56e-01 | |
| ∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression. |
| Page: 1 2 |
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Somatic mutation of malignant transformation related genes |
| Annotation of somatic variants for genes involved in malignant transformation |
| Hugo Symbol | Variant Class | Variant Classification | dbSNP RS | HGVSc | HGVSp | HGVSp Short | SWISSPROT | BIOTYPE | SIFT | PolyPhen | Tumor Sample Barcode | Tissue | Histology | Sex | Age | Stage | Therapy Types | Drugs | Outcome |
| CDX1 | SNV | Missense_Mutation | rs771897143 | c.496C>T | p.Arg166Cys | p.R166C | P47902 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AJ-A3OL-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatin | PD |
| CDX1 | SNV | Missense_Mutation | novel | c.550N>G | p.Lys184Glu | p.K184E | P47902 | protein_coding | deleterious(0) | probably_damaging(0.992) | TCGA-AJ-A5DW-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| CDX1 | SNV | Missense_Mutation | rs140956520 | c.547N>T | p.Arg183Trp | p.R183W | P47902 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AX-A0J1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| CDX1 | SNV | Missense_Mutation | rs143202475 | c.586N>T | p.Arg196Trp | p.R196W | P47902 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AX-A1CE-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | SD |
| CDX1 | SNV | Missense_Mutation | novel | c.736A>G | p.Ser246Gly | p.S246G | P47902 | protein_coding | tolerated(0.22) | benign(0) | TCGA-AX-A2HJ-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| CDX1 | SNV | Missense_Mutation | rs758524697 | c.628C>T | p.Arg210Cys | p.R210C | P47902 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-DF-A2KU-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | Unknown | I/II | Unknown | Unknown | SD |
| CDX1 | SNV | Missense_Mutation | rs200074812 | c.530G>A | p.Arg177His | p.R177H | P47902 | protein_coding | deleterious(0) | possibly_damaging(0.698) | TCGA-DI-A2QU-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD |
| CDX1 | SNV | Missense_Mutation | rs777049283 | c.688N>A | p.Asp230Asn | p.D230N | P47902 | protein_coding | tolerated_low_confidence(0.72) | benign(0.015) | TCGA-E6-A1LX-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| CDX1 | SNV | Missense_Mutation | novel | c.698N>T | p.Ala233Val | p.A233V | P47902 | protein_coding | tolerated(0.09) | benign(0.023) | TCGA-FI-A2D5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatinum | PD |
| CDX1 | deletion | Frame_Shift_Del | novel | c.704delC | p.Pro235GlnfsTer25 | p.P235Qfs*25 | P47902 | protein_coding | TCGA-D1-A177-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
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Related drugs of malignant transformation related genes |
| Identification of chemicals and drugs interact with genes involved in malignant transfromation |
| (DGIdb 4.0) |
| Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
| Page: 1 |
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