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Gene: HOXA3 |
Gene summary for HOXA3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | HOXA3 | Gene ID | 3200 |
| Gene name | homeobox A3 | |
| Gene Alias | HOX1 | |
| Cytomap | 7p15.2 | |
| Gene Type | protein-coding | GO ID | GO:0001501 | UniProtAcc | A0A024RA33 |
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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 |
| 3200 | HOXA3 | HTA11_3410_2000001011 | Human | Colorectum | AD | 5.06e-22 | -7.14e-01 | 0.0155 |
| 3200 | HOXA3 | HTA11_2487_2000001011 | Human | Colorectum | SER | 1.82e-14 | -7.29e-01 | -0.1808 |
| 3200 | HOXA3 | HTA11_78_2000001011 | Human | Colorectum | AD | 6.43e-11 | -6.55e-01 | -0.1088 |
| 3200 | HOXA3 | HTA11_347_2000001011 | Human | Colorectum | AD | 9.64e-08 | -5.25e-01 | -0.1954 |
| 3200 | HOXA3 | HTA11_2112_2000001011 | Human | Colorectum | SER | 5.37e-04 | -7.69e-01 | -0.2196 |
| 3200 | HOXA3 | HTA11_3361_2000001011 | Human | Colorectum | AD | 3.52e-12 | -7.44e-01 | -0.1207 |
| 3200 | HOXA3 | HTA11_83_2000001011 | Human | Colorectum | SER | 4.65e-04 | -6.20e-01 | -0.1526 |
| 3200 | HOXA3 | HTA11_696_2000001011 | Human | Colorectum | AD | 1.18e-31 | -7.17e-01 | -0.1464 |
| 3200 | HOXA3 | HTA11_866_2000001011 | Human | Colorectum | AD | 1.48e-22 | -6.67e-01 | -0.1001 |
| 3200 | HOXA3 | HTA11_1391_2000001011 | Human | Colorectum | AD | 1.09e-09 | -6.06e-01 | -0.059 |
| 3200 | HOXA3 | HTA11_2992_2000001011 | Human | Colorectum | SER | 6.91e-04 | -7.40e-01 | -0.1706 |
| 3200 | HOXA3 | HTA11_5212_2000001011 | Human | Colorectum | AD | 2.09e-03 | -6.94e-01 | -0.2061 |
| 3200 | HOXA3 | HTA11_546_2000001011 | Human | Colorectum | AD | 4.80e-06 | -6.99e-01 | -0.0842 |
| 3200 | HOXA3 | HTA11_9341_2000001011 | Human | Colorectum | SER | 1.06e-02 | -7.69e-01 | -0.00410000000000005 |
| 3200 | HOXA3 | HTA11_7862_2000001011 | Human | Colorectum | AD | 1.08e-02 | -6.27e-01 | -0.0179 |
| 3200 | HOXA3 | HTA11_866_3004761011 | Human | Colorectum | AD | 4.50e-12 | -6.27e-01 | 0.096 |
| 3200 | HOXA3 | HTA11_10711_2000001011 | Human | Colorectum | AD | 9.50e-11 | -6.95e-01 | 0.0338 |
| 3200 | HOXA3 | HTA11_7696_3000711011 | Human | Colorectum | AD | 3.40e-20 | -6.58e-01 | 0.0674 |
| 3200 | HOXA3 | HTA11_6818_2000001011 | Human | Colorectum | AD | 2.48e-02 | -6.25e-01 | 0.0112 |
| 3200 | HOXA3 | HTA11_11156_2000001011 | Human | Colorectum | AD | 2.53e-02 | -7.69e-01 | 0.0397 |
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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:0048732 | Colorectum | AD | gland development | 149/3918 | 436/18723 | 6.07e-11 | 6.33e-09 | 149 |
| GO:0048568 | Colorectum | AD | embryonic organ development | 112/3918 | 427/18723 | 4.60e-03 | 3.14e-02 | 112 |
| GO:00487321 | Colorectum | SER | gland development | 112/2897 | 436/18723 | 1.75e-08 | 1.28e-06 | 112 |
| GO:00487322 | Colorectum | MSS | gland development | 143/3467 | 436/18723 | 3.85e-13 | 8.01e-11 | 143 |
| GO:00485681 | Colorectum | MSS | embryonic organ development | 100/3467 | 427/18723 | 6.00e-03 | 4.03e-02 | 100 |
| GO:00487324 | Colorectum | FAP | gland development | 103/2622 | 436/18723 | 3.61e-08 | 3.12e-06 | 103 |
| GO:00485682 | Colorectum | FAP | embryonic organ development | 79/2622 | 427/18723 | 5.32e-03 | 3.49e-02 | 79 |
| GO:0009952 | Colorectum | FAP | anterior/posterior pattern specification | 41/2622 | 201/18723 | 7.82e-03 | 4.63e-02 | 41 |
| GO:00487325 | Colorectum | CRC | gland development | 88/2078 | 436/18723 | 1.62e-08 | 2.79e-06 | 88 |
| GO:00099521 | Colorectum | CRC | anterior/posterior pattern specification | 36/2078 | 201/18723 | 2.56e-03 | 2.40e-02 | 36 |
| GO:0048771 | Colorectum | CRC | tissue remodeling | 32/2078 | 175/18723 | 3.08e-03 | 2.73e-02 | 32 |
| GO:00485683 | Colorectum | CRC | embryonic organ development | 65/2078 | 427/18723 | 5.15e-03 | 3.94e-02 | 65 |
| GO:0048705 | Colorectum | CRC | skeletal system morphogenesis | 37/2078 | 220/18723 | 6.58e-03 | 4.71e-02 | 37 |
| GO:0048706 | Colorectum | CRC | embryonic skeletal system development | 23/2078 | 121/18723 | 6.85e-03 | 4.81e-02 | 23 |
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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 |
| HOXA3 | MVA | Cervix | CC | RNF125,RRAGA,NRM, etc. | 8.36e-03 |  |
| HOXA3 | iATC | Thyroid | PTC | NEK5,ATXN7L2,AGBL2, etc. | 1.77e-02 |  |
| ∗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 |
| HOXA3 | SNV | Missense_Mutation | c.859N>A | p.Val287Ile | p.V287I | O43365 | protein_coding | tolerated(0.14) | probably_damaging(0.979) | TCGA-A2-A0SW-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | arimidex | PD | |
| HOXA3 | SNV | Missense_Mutation | c.797G>A | p.Arg266His | p.R266H | O43365 | protein_coding | tolerated(0.17) | benign(0.139) | TCGA-BH-A0BP-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| HOXA3 | SNV | Missense_Mutation | novel | c.698G>A | p.Arg233His | p.R233H | O43365 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| HOXA3 | SNV | Missense_Mutation | rs773785595 | c.1178N>T | p.Ser393Leu | p.S393L | O43365 | protein_coding | deleterious(0) | benign(0.137) | TCGA-FU-A23L-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| HOXA3 | SNV | Missense_Mutation | rs764656757 | c.124N>A | p.Asp42Asn | p.D42N | O43365 | protein_coding | deleterious(0) | benign(0.011) | TCGA-IR-A3LK-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | PD |
| HOXA3 | SNV | Missense_Mutation | c.868N>A | p.Glu290Lys | p.E290K | O43365 | protein_coding | deleterious(0.01) | possibly_damaging(0.549) | TCGA-VS-A958-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| HOXA3 | SNV | Missense_Mutation | novel | c.121N>A | p.Ala41Thr | p.A41T | O43365 | protein_coding | tolerated(0.19) | benign(0) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| HOXA3 | SNV | Missense_Mutation | c.539N>A | p.Ala180Asp | p.A180D | O43365 | protein_coding | tolerated(0.49) | benign(0.386) | TCGA-CK-4951-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| HOXA3 | SNV | Missense_Mutation | c.353C>T | p.Ala118Val | p.A118V | O43365 | protein_coding | tolerated(0.26) | benign(0) | TCGA-NH-A5IV-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| HOXA3 | SNV | Missense_Mutation | c.583C>T | p.Arg195Cys | p.R195C | O43365 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-QL-A97D-01 | Colorectum | colon adenocarcinoma | 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 |
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