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Gene: HGD |
Gene summary for HGD |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | HGD | Gene ID | 3081 |
| Gene name | homogentisate 1,2-dioxygenase | |
| Gene Alias | AKU | |
| Cytomap | 3q13.33 | |
| Gene Type | protein-coding | GO ID | GO:0006082 | UniProtAcc | Q93099 |
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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 |
| 3081 | HGD | NAFLD1 | Human | Liver | NAFLD | 6.30e-10 | 1.22e+00 | -0.04 |
| 3081 | HGD | S41 | Human | Liver | Cirrhotic | 1.91e-03 | 6.05e-01 | -0.0343 |
| 3081 | HGD | S43 | Human | Liver | Cirrhotic | 1.33e-12 | -3.28e-01 | -0.0187 |
| 3081 | HGD | S44 | Human | Liver | HCC | 3.23e-04 | 6.29e-01 | -0.0083 |
| 3081 | HGD | HCC1_Meng | Human | Liver | HCC | 3.36e-113 | -5.89e-02 | 0.0246 |
| 3081 | HGD | HCC2_Meng | Human | Liver | HCC | 7.40e-40 | -3.09e-01 | 0.0107 |
| 3081 | HGD | cirrhotic1 | Human | Liver | Cirrhotic | 1.12e-15 | -7.50e-02 | 0.0202 |
| 3081 | HGD | cirrhotic2 | Human | Liver | Cirrhotic | 1.43e-14 | -2.04e-01 | 0.0201 |
| 3081 | HGD | cirrhotic3 | Human | Liver | Cirrhotic | 7.34e-06 | -2.90e-01 | 0.0215 |
| 3081 | HGD | HCC1 | Human | Liver | HCC | 2.11e-20 | 5.26e+00 | 0.5336 |
| 3081 | HGD | HCC2 | Human | Liver | HCC | 9.73e-08 | 4.42e+00 | 0.5341 |
| 3081 | HGD | Pt13.a | Human | Liver | HCC | 8.10e-05 | -1.95e-01 | 0.021 |
| 3081 | HGD | Pt13.b | Human | Liver | HCC | 1.57e-18 | -1.30e-01 | 0.0251 |
| 3081 | HGD | Pt13.c | Human | Liver | HCC | 3.64e-04 | -4.79e-01 | 0.0076 |
| 3081 | HGD | Pt14.a | Human | Liver | HCC | 7.13e-05 | 4.89e-02 | 0.0169 |
| 3081 | HGD | Pt14.b | Human | Liver | HCC | 1.51e-06 | 1.52e-01 | 0.018 |
| 3081 | HGD | Pt14.c | Human | Liver | HCC | 1.10e-10 | 9.03e-01 | 0.0054 |
| 3081 | HGD | Pt14.d | Human | Liver | HCC | 4.54e-06 | -5.33e-02 | 0.0143 |
| 3081 | HGD | S028 | Human | Liver | HCC | 2.83e-04 | 5.57e-01 | 0.2503 |
| 3081 | HGD | S029 | Human | Liver | HCC | 4.56e-09 | 9.85e-01 | 0.2581 |
| Page: 1 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease |
| ∗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:00075653 | Breast | Precancer | female pregnancy | 29/1080 | 193/18723 | 2.07e-06 | 7.31e-05 | 29 |
| GO:00447063 | Breast | Precancer | multi-multicellular organism process | 31/1080 | 220/18723 | 3.73e-06 | 1.19e-04 | 31 |
| GO:00329709 | Breast | Precancer | regulation of actin filament-based process | 42/1080 | 397/18723 | 1.11e-04 | 2.01e-03 | 42 |
| GO:00075663 | Breast | Precancer | embryo implantation | 11/1080 | 53/18723 | 1.82e-04 | 2.95e-03 | 11 |
| GO:00016678 | Breast | Precancer | ameboidal-type cell migration | 47/1080 | 475/18723 | 2.19e-04 | 3.35e-03 | 47 |
| GO:00329569 | Breast | Precancer | regulation of actin cytoskeleton organization | 36/1080 | 358/18723 | 8.56e-04 | 9.88e-03 | 36 |
| GO:000609113 | Breast | IDC | generation of precursor metabolites and energy | 103/1434 | 490/18723 | 1.53e-21 | 1.74e-18 | 103 |
| GO:002290013 | Breast | IDC | electron transport chain | 51/1434 | 175/18723 | 2.23e-17 | 8.43e-15 | 51 |
| GO:000756511 | Breast | IDC | female pregnancy | 39/1434 | 193/18723 | 1.81e-08 | 1.27e-06 | 39 |
| GO:00447061 | Breast | IDC | multi-multicellular organism process | 41/1434 | 220/18723 | 8.58e-08 | 5.19e-06 | 41 |
| GO:003297014 | Breast | IDC | regulation of actin filament-based process | 56/1434 | 397/18723 | 6.37e-06 | 1.99e-04 | 56 |
| GO:000166714 | Breast | IDC | ameboidal-type cell migration | 64/1434 | 475/18723 | 6.65e-06 | 2.05e-04 | 64 |
| GO:000756611 | Breast | IDC | embryo implantation | 14/1434 | 53/18723 | 3.14e-05 | 7.32e-04 | 14 |
| GO:003295614 | Breast | IDC | regulation of actin cytoskeleton organization | 48/1434 | 358/18723 | 1.03e-04 | 1.96e-03 | 48 |
| GO:00512712 | Breast | IDC | negative regulation of cellular component movement | 48/1434 | 367/18723 | 1.88e-04 | 3.12e-03 | 48 |
| GO:20001462 | Breast | IDC | negative regulation of cell motility | 46/1434 | 359/18723 | 4.01e-04 | 5.60e-03 | 46 |
| GO:004206311 | Breast | IDC | gliogenesis | 39/1434 | 301/18723 | 8.63e-04 | 1.00e-02 | 39 |
| GO:00303362 | Breast | IDC | negative regulation of cell migration | 43/1434 | 344/18723 | 1.01e-03 | 1.13e-02 | 43 |
| GO:00100011 | Breast | IDC | glial cell differentiation | 31/1434 | 225/18723 | 1.04e-03 | 1.15e-02 | 31 |
| GO:00400132 | Breast | IDC | negative regulation of locomotion | 47/1434 | 391/18723 | 1.39e-03 | 1.43e-02 | 47 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 |
| 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 |
| ∗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 |
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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 |
| HGD | SNV | Missense_Mutation | novel | c.1219N>T | p.Ala407Ser | p.A407S | Q93099 | protein_coding | tolerated(0.66) | benign(0.009) | TCGA-AQ-A54N-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| HGD | SNV | Missense_Mutation | c.30N>G | p.Phe10Leu | p.F10L | Q93099 | protein_coding | tolerated(0.05) | possibly_damaging(0.509) | TCGA-D8-A13Y-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| HGD | SNV | Missense_Mutation | c.1226N>T | p.Thr409Ile | p.T409I | Q93099 | protein_coding | deleterious(0) | probably_damaging(0.969) | TCGA-D8-A1XQ-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| HGD | SNV | Missense_Mutation | rs756255206 | c.559C>T | p.Arg187Trp | p.R187W | Q93099 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| HGD | SNV | Missense_Mutation | c.229G>A | p.Asp77Asn | p.D77N | Q93099 | protein_coding | tolerated(0.29) | benign(0) | TCGA-DG-A2KK-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Chemotherapy | cisplatin | SD | |
| HGD | SNV | Missense_Mutation | novel | c.697N>C | p.Trp233Arg | p.W233R | Q93099 | protein_coding | tolerated(0.26) | benign(0.301) | TCGA-DS-A0VN-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
| HGD | SNV | Missense_Mutation | novel | c.287N>C | p.Arg96Thr | p.R96T | Q93099 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-MA-AA41-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| HGD | SNV | Missense_Mutation | novel | c.1142C>T | p.Ala381Val | p.A381V | Q93099 | protein_coding | deleterious(0) | possibly_damaging(0.774) | TCGA-AA-3966-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| HGD | SNV | Missense_Mutation | c.173G>T | p.Arg58Ile | p.R58I | Q93099 | protein_coding | deleterious(0) | probably_damaging(0.948) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR | |
| HGD | SNV | Missense_Mutation | c.173N>T | p.Arg58Ile | p.R58I | Q93099 | protein_coding | deleterious(0) | probably_damaging(0.948) | TCGA-CA-6718-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | PD |
| Page: 1 2 3 4 5 6 |
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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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