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Gene: CDX2 |
Gene summary for CDX2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CDX2 | Gene ID | 1045 |
| Gene name | caudal type homeobox 2 | |
| Gene Alias | CDX-3 | |
| Cytomap | 13q12.2 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | Q99626 |
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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 |
| 1045 | CDX2 | HTA11_3410_2000001011 | Human | Colorectum | AD | 6.71e-23 | 6.18e-01 | 0.0155 |
| 1045 | CDX2 | HTA11_2487_2000001011 | Human | Colorectum | SER | 1.58e-17 | 8.87e-01 | -0.1808 |
| 1045 | CDX2 | HTA11_2951_2000001011 | Human | Colorectum | AD | 2.22e-06 | 9.33e-01 | 0.0216 |
| 1045 | CDX2 | HTA11_1938_2000001011 | Human | Colorectum | AD | 2.55e-26 | 1.29e+00 | -0.0811 |
| 1045 | CDX2 | HTA11_78_2000001011 | Human | Colorectum | AD | 7.14e-18 | 1.12e+00 | -0.1088 |
| 1045 | CDX2 | HTA11_347_2000001011 | Human | Colorectum | AD | 6.27e-56 | 1.46e+00 | -0.1954 |
| 1045 | CDX2 | HTA11_2112_2000001011 | Human | Colorectum | SER | 9.38e-04 | 8.87e-01 | -0.2196 |
| 1045 | CDX2 | HTA11_3361_2000001011 | Human | Colorectum | AD | 2.94e-25 | 1.15e+00 | -0.1207 |
| 1045 | CDX2 | HTA11_83_2000001011 | Human | Colorectum | SER | 2.48e-27 | 1.40e+00 | -0.1526 |
| 1045 | CDX2 | HTA11_696_2000001011 | Human | Colorectum | AD | 1.08e-60 | 1.57e+00 | -0.1464 |
| 1045 | CDX2 | HTA11_866_2000001011 | Human | Colorectum | AD | 3.85e-33 | 1.07e+00 | -0.1001 |
| 1045 | CDX2 | HTA11_1391_2000001011 | Human | Colorectum | AD | 3.01e-41 | 1.36e+00 | -0.059 |
| 1045 | CDX2 | HTA11_2992_2000001011 | Human | Colorectum | SER | 1.01e-06 | 9.02e-01 | -0.1706 |
| 1045 | CDX2 | HTA11_5212_2000001011 | Human | Colorectum | AD | 2.02e-14 | 1.12e+00 | -0.2061 |
| 1045 | CDX2 | HTA11_5216_2000001011 | Human | Colorectum | SER | 2.21e-12 | 1.30e+00 | -0.1462 |
| 1045 | CDX2 | HTA11_546_2000001011 | Human | Colorectum | AD | 1.33e-18 | 1.23e+00 | -0.0842 |
| 1045 | CDX2 | HTA11_7862_2000001011 | Human | Colorectum | AD | 5.49e-15 | 1.08e+00 | -0.0179 |
| 1045 | CDX2 | HTA11_866_3004761011 | Human | Colorectum | AD | 1.51e-43 | 1.50e+00 | 0.096 |
| 1045 | CDX2 | HTA11_4255_2000001011 | Human | Colorectum | SER | 7.40e-04 | 8.88e-01 | 0.0446 |
| 1045 | CDX2 | HTA11_9408_2000001011 | Human | Colorectum | AD | 3.47e-02 | 7.46e-01 | 0.0451 |
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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 |
| GO:0007034 | Colorectum | AD | vacuolar transport | 60/3918 | 157/18723 | 4.97e-07 | 1.85e-05 | 60 |
| GO:0007163 | Colorectum | AD | establishment or maintenance of cell polarity | 77/3918 | 218/18723 | 5.72e-07 | 2.08e-05 | 77 |
| GO:0001701 | Colorectum | AD | in utero embryonic development | 110/3918 | 367/18723 | 2.36e-05 | 4.62e-04 | 110 |
| GO:0001890 | Colorectum | AD | placenta development | 51/3918 | 144/18723 | 3.99e-05 | 7.16e-04 | 51 |
| GO:0001892 | Colorectum | AD | embryonic placenta development | 33/3918 | 82/18723 | 5.30e-05 | 9.01e-04 | 33 |
| GO:0007041 | Colorectum | AD | lysosomal transport | 42/3918 | 114/18723 | 6.61e-05 | 1.07e-03 | 42 |
| GO:0045197 | Colorectum | AD | establishment or maintenance of epithelial cell apical/basal polarity | 20/3918 | 44/18723 | 2.26e-04 | 2.94e-03 | 20 |
| GO:0035088 | Colorectum | AD | establishment or maintenance of apical/basal cell polarity | 21/3918 | 49/18723 | 4.31e-04 | 4.82e-03 | 21 |
| GO:0061245 | Colorectum | AD | establishment or maintenance of bipolar cell polarity | 21/3918 | 49/18723 | 4.31e-04 | 4.82e-03 | 21 |
| GO:0060711 | Colorectum | AD | labyrinthine layer development | 19/3918 | 44/18723 | 7.13e-04 | 7.21e-03 | 19 |
| GO:0061458 | Colorectum | AD | reproductive system development | 116/3918 | 427/18723 | 1.11e-03 | 1.01e-02 | 116 |
| GO:0048608 | Colorectum | AD | reproductive structure development | 114/3918 | 424/18723 | 1.78e-03 | 1.47e-02 | 114 |
| GO:0048568 | Colorectum | AD | embryonic organ development | 112/3918 | 427/18723 | 4.60e-03 | 3.14e-02 | 112 |
| GO:00071631 | Colorectum | SER | establishment or maintenance of cell polarity | 60/2897 | 218/18723 | 3.45e-06 | 1.33e-04 | 60 |
| GO:00018901 | Colorectum | SER | placenta development | 43/2897 | 144/18723 | 9.10e-06 | 3.03e-04 | 43 |
| GO:00018921 | Colorectum | SER | embryonic placenta development | 28/2897 | 82/18723 | 2.24e-05 | 6.43e-04 | 28 |
| GO:00070341 | Colorectum | SER | vacuolar transport | 43/2897 | 157/18723 | 8.92e-05 | 1.93e-03 | 43 |
| GO:00451971 | Colorectum | SER | establishment or maintenance of epithelial cell apical/basal polarity | 16/2897 | 44/18723 | 5.64e-04 | 7.83e-03 | 16 |
| GO:00607111 | Colorectum | SER | labyrinthine layer development | 16/2897 | 44/18723 | 5.64e-04 | 7.83e-03 | 16 |
| GO:00350881 | Colorectum | SER | establishment or maintenance of apical/basal cell polarity | 17/2897 | 49/18723 | 7.17e-04 | 9.44e-03 | 17 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
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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 |
| CDX2 | ABS | Colorectum | MSS | CD24,C10orf99,URAD, etc. | 9.20e-02 |  |
| CDX2 | ABS | Colorectum | SER | CD24,C10orf99,URAD, etc. | 2.79e-01 |  |
| CDX2 | CD8TEXP | Colorectum | AD | LGALS4,CD24,PHGR1, etc. | 1.76e-01 |  |
| CDX2 | CD8TEXP | Colorectum | ADJ | LGALS4,CD24,PHGR1, etc. | 1.06e-01 |  |
| CDX2 | CD8TEXP | Colorectum | CRC | LGALS4,CD24,PHGR1, etc. | 3.47e-01 |  |
| CDX2 | CD8TEXP | Colorectum | FAP | LGALS4,CD24,PHGR1, etc. | 9.38e-02 |  |
| CDX2 | TH1 | Colorectum | FAP | LGALS4,CD24,PHGR1, etc. | 9.73e-02 | |
| CDX2 | CD8TEXP | Colorectum | Healthy | LGALS4,CD24,PHGR1, etc. | 1.77e-01 |  |
| CDX2 | CD8TEXP | Colorectum | MSI-H | LGALS4,CD24,PHGR1, etc. | 6.77e-02 |  |
| CDX2 | CD8TEXP | Colorectum | MSS | LGALS4,CD24,PHGR1, etc. | 2.38e-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. |
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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 |
| CDX2 | SNV | Missense_Mutation | novel | c.277G>A | p.Ala93Thr | p.A93T | Q99626 | protein_coding | tolerated(0.45) | possibly_damaging(0.503) | TCGA-UL-AAZ6-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | herceptin | SD |
| CDX2 | SNV | Missense_Mutation | novel | c.881G>A | p.Gly294Asp | p.G294D | Q99626 | protein_coding | deleterious(0.01) | possibly_damaging(0.72) | TCGA-C5-A8YR-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | PD |
| CDX2 | SNV | Missense_Mutation | c.616N>T | p.His206Tyr | p.H206Y | Q99626 | protein_coding | deleterious(0) | possibly_damaging(0.506) | TCGA-EK-A2RJ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| CDX2 | SNV | Missense_Mutation | c.257N>T | p.Ala86Val | p.A86V | Q99626 | protein_coding | tolerated(0.28) | benign(0.119) | TCGA-EK-A3GN-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD | |
| CDX2 | SNV | Missense_Mutation | c.34N>T | p.Ser12Cys | p.S12C | Q99626 | protein_coding | deleterious(0.01) | probably_damaging(0.922) | TCGA-A6-5665-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| CDX2 | SNV | Missense_Mutation | c.716C>T | p.Ala239Val | p.A239V | Q99626 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-AD-6889-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Chemotherapy | xeloda | PD | |
| CDX2 | SNV | Missense_Mutation | novel | c.753G>T | p.Gln251His | p.Q251H | Q99626 | protein_coding | deleterious(0) | benign(0.021) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| CDX2 | SNV | Missense_Mutation | rs763139212 | c.626G>A | p.Arg209His | p.R209H | Q99626 | protein_coding | deleterious(0) | possibly_damaging(0.883) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| CDX2 | SNV | Missense_Mutation | novel | c.713N>A | p.Arg238Lys | p.R238K | Q99626 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AJ-A3EK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR |
| CDX2 | SNV | Missense_Mutation | novel | c.14N>G | p.Tyr5Cys | p.Y5C | Q99626 | protein_coding | tolerated(0.12) | possibly_damaging(0.455) | TCGA-BG-A222-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
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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 |
| 1045 | CDX2 | CLINICALLY ACTIONABLE, TRANSCRIPTION FACTOR | TPN | 10712262 |
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