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Gene: HDAC3 |
Gene summary for HDAC3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | HDAC3 | Gene ID | 8841 |
| Gene name | histone deacetylase 3 | |
| Gene Alias | HD3 | |
| Cytomap | 5q31.3 | |
| Gene Type | protein-coding | GO ID | GO:0000122 | UniProtAcc | O15379 |
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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 |
| 8841 | HDAC3 | LZE4T | Human | Esophagus | ESCC | 7.39e-08 | 8.01e-02 | 0.0811 |
| 8841 | HDAC3 | LZE7T | Human | Esophagus | ESCC | 4.69e-07 | 2.83e-01 | 0.0667 |
| 8841 | HDAC3 | LZE8T | Human | Esophagus | ESCC | 1.78e-05 | 1.33e-01 | 0.067 |
| 8841 | HDAC3 | LZE22T | Human | Esophagus | ESCC | 1.20e-03 | 2.83e-01 | 0.068 |
| 8841 | HDAC3 | LZE24T | Human | Esophagus | ESCC | 2.80e-15 | 4.39e-01 | 0.0596 |
| 8841 | HDAC3 | LZE21T | Human | Esophagus | ESCC | 1.73e-02 | 2.55e-01 | 0.0655 |
| 8841 | HDAC3 | LZE6T | Human | Esophagus | ESCC | 3.69e-02 | 1.78e-01 | 0.0845 |
| 8841 | HDAC3 | P1T-E | Human | Esophagus | ESCC | 7.67e-11 | 4.53e-01 | 0.0875 |
| 8841 | HDAC3 | P2T-E | Human | Esophagus | ESCC | 3.34e-44 | 7.66e-01 | 0.1177 |
| 8841 | HDAC3 | P4T-E | Human | Esophagus | ESCC | 2.30e-18 | 4.63e-01 | 0.1323 |
| 8841 | HDAC3 | P5T-E | Human | Esophagus | ESCC | 5.93e-25 | 4.47e-01 | 0.1327 |
| 8841 | HDAC3 | P8T-E | Human | Esophagus | ESCC | 2.30e-21 | 2.16e-01 | 0.0889 |
| 8841 | HDAC3 | P9T-E | Human | Esophagus | ESCC | 1.33e-20 | 2.69e-01 | 0.1131 |
| 8841 | HDAC3 | P10T-E | Human | Esophagus | ESCC | 2.27e-26 | 4.60e-01 | 0.116 |
| 8841 | HDAC3 | P11T-E | Human | Esophagus | ESCC | 1.68e-14 | 6.25e-01 | 0.1426 |
| 8841 | HDAC3 | P12T-E | Human | Esophagus | ESCC | 3.87e-44 | 8.30e-01 | 0.1122 |
| 8841 | HDAC3 | P15T-E | Human | Esophagus | ESCC | 7.74e-20 | 6.12e-01 | 0.1149 |
| 8841 | HDAC3 | P16T-E | Human | Esophagus | ESCC | 1.76e-24 | 4.09e-01 | 0.1153 |
| 8841 | HDAC3 | P17T-E | Human | Esophagus | ESCC | 6.15e-05 | 4.15e-01 | 0.1278 |
| 8841 | HDAC3 | P19T-E | Human | Esophagus | ESCC | 2.70e-05 | 7.67e-01 | 0.1662 |
| Page: 1 2 3 4 5 6 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid 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:0032386111 | Thyroid | PTC | regulation of intracellular transport | 202/5968 | 337/18723 | 1.12e-26 | 3.93e-24 | 202 |
| GO:0033157112 | Thyroid | PTC | regulation of intracellular protein transport | 149/5968 | 229/18723 | 3.83e-25 | 1.15e-22 | 149 |
| GO:0006913112 | Thyroid | PTC | nucleocytoplasmic transport | 181/5968 | 301/18723 | 2.93e-24 | 7.69e-22 | 181 |
| GO:0051169112 | Thyroid | PTC | nuclear transport | 181/5968 | 301/18723 | 2.93e-24 | 7.69e-22 | 181 |
| GO:0032388112 | Thyroid | PTC | positive regulation of intracellular transport | 132/5968 | 202/18723 | 1.10e-22 | 2.57e-20 | 132 |
| GO:0031647113 | Thyroid | PTC | regulation of protein stability | 174/5968 | 298/18723 | 2.05e-21 | 4.05e-19 | 174 |
| GO:0034504111 | Thyroid | PTC | protein localization to nucleus | 170/5968 | 290/18723 | 3.34e-21 | 6.38e-19 | 170 |
| GO:0090316110 | Thyroid | PTC | positive regulation of intracellular protein transport | 109/5968 | 160/18723 | 4.20e-21 | 7.79e-19 | 109 |
| GO:1903320113 | Thyroid | PTC | regulation of protein modification by small protein conjugation or removal | 148/5968 | 242/18723 | 4.49e-21 | 8.10e-19 | 148 |
| GO:1903829113 | Thyroid | PTC | positive regulation of cellular protein localization | 162/5968 | 276/18723 | 2.40e-20 | 3.52e-18 | 162 |
| GO:0031396113 | Thyroid | PTC | regulation of protein ubiquitination | 128/5968 | 210/18723 | 3.06e-18 | 3.27e-16 | 128 |
| GO:1904951113 | Thyroid | PTC | positive regulation of establishment of protein localization | 175/5968 | 319/18723 | 1.10e-17 | 1.12e-15 | 175 |
| GO:001657010 | Thyroid | PTC | histone modification | 235/5968 | 463/18723 | 1.17e-17 | 1.15e-15 | 235 |
| GO:004682223 | Thyroid | PTC | regulation of nucleocytoplasmic transport | 76/5968 | 106/18723 | 4.11e-17 | 3.70e-15 | 76 |
| GO:0051222113 | Thyroid | PTC | positive regulation of protein transport | 163/5968 | 303/18723 | 1.58e-15 | 1.16e-13 | 163 |
| GO:1900180111 | Thyroid | PTC | regulation of protein localization to nucleus | 84/5968 | 136/18723 | 6.52e-13 | 3.08e-11 | 84 |
| GO:004682420 | Thyroid | PTC | positive regulation of nucleocytoplasmic transport | 47/5968 | 62/18723 | 1.44e-12 | 6.50e-11 | 47 |
| GO:1900182110 | Thyroid | PTC | positive regulation of protein localization to nucleus | 59/5968 | 87/18723 | 6.13e-12 | 2.61e-10 | 59 |
| GO:0017038111 | Thyroid | PTC | protein import | 109/5968 | 206/18723 | 2.74e-10 | 8.96e-09 | 109 |
| GO:005117017 | Thyroid | PTC | import into nucleus | 85/5968 | 159/18723 | 1.30e-08 | 3.08e-07 | 85 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0520325 | Esophagus | ESCC | Viral carcinogenesis | 137/4205 | 204/8465 | 2.47e-07 | 1.88e-06 | 9.62e-07 | 137 |
| hsa0491928 | Esophagus | ESCC | Thyroid hormone signaling pathway | 78/4205 | 121/8465 | 6.79e-04 | 2.23e-03 | 1.14e-03 | 78 |
| hsa0520335 | Esophagus | ESCC | Viral carcinogenesis | 137/4205 | 204/8465 | 2.47e-07 | 1.88e-06 | 9.62e-07 | 137 |
| hsa04919113 | Esophagus | ESCC | Thyroid hormone signaling pathway | 78/4205 | 121/8465 | 6.79e-04 | 2.23e-03 | 1.14e-03 | 78 |
| hsa0491912 | Liver | HCC | Thyroid hormone signaling pathway | 75/4020 | 121/8465 | 8.76e-04 | 3.38e-03 | 1.88e-03 | 75 |
| hsa052032 | Liver | HCC | Viral carcinogenesis | 117/4020 | 204/8465 | 2.68e-03 | 8.98e-03 | 5.00e-03 | 117 |
| hsa0491913 | Liver | HCC | Thyroid hormone signaling pathway | 75/4020 | 121/8465 | 8.76e-04 | 3.38e-03 | 1.88e-03 | 75 |
| hsa052033 | Liver | HCC | Viral carcinogenesis | 117/4020 | 204/8465 | 2.68e-03 | 8.98e-03 | 5.00e-03 | 117 |
| hsa052038 | Oral cavity | OSCC | Viral carcinogenesis | 124/3704 | 204/8465 | 5.57e-07 | 3.28e-06 | 1.67e-06 | 124 |
| hsa0491926 | Oral cavity | OSCC | Thyroid hormone signaling pathway | 73/3704 | 121/8465 | 1.63e-04 | 5.52e-04 | 2.81e-04 | 73 |
| hsa0520314 | Oral cavity | OSCC | Viral carcinogenesis | 124/3704 | 204/8465 | 5.57e-07 | 3.28e-06 | 1.67e-06 | 124 |
| hsa04919112 | Oral cavity | OSCC | Thyroid hormone signaling pathway | 73/3704 | 121/8465 | 1.63e-04 | 5.52e-04 | 2.81e-04 | 73 |
| hsa0520324 | Oral cavity | LP | Viral carcinogenesis | 90/2418 | 204/8465 | 1.20e-06 | 1.38e-05 | 8.89e-06 | 90 |
| hsa0520334 | Oral cavity | LP | Viral carcinogenesis | 90/2418 | 204/8465 | 1.20e-06 | 1.38e-05 | 8.89e-06 | 90 |
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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 |
| ∗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 |
| HDAC3 | SNV | Missense_Mutation | c.597N>G | p.Phe199Leu | p.F199L | O15379 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-E2-A14V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD | |
| HDAC3 | SNV | Missense_Mutation | c.1012C>T | p.Leu338Phe | p.L338F | O15379 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-E2-A155-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | |
| HDAC3 | deletion | Frame_Shift_Del | novel | c.731delN | p.Val244GlyfsTer72 | p.V244Gfs*72 | O15379 | protein_coding | TCGA-LL-A6FQ-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | ||
| HDAC3 | SNV | Missense_Mutation | novel | c.445G>A | p.Asp149Asn | p.D149N | O15379 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| HDAC3 | SNV | Missense_Mutation | novel | c.38T>C | p.Val13Ala | p.V13A | O15379 | protein_coding | deleterious(0.01) | possibly_damaging(0.897) | TCGA-DG-A2KK-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Chemotherapy | cisplatin | SD |
| HDAC3 | SNV | Missense_Mutation | c.708C>G | p.Phe236Leu | p.F236L | O15379 | protein_coding | deleterious(0) | benign(0.366) | TCGA-EK-A2PG-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD | |
| HDAC3 | SNV | Missense_Mutation | c.803N>A | p.Cys268Tyr | p.C268Y | O15379 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-FU-A3HZ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| HDAC3 | SNV | Missense_Mutation | c.1271N>A | p.Ser424Asn | p.S424N | O15379 | protein_coding | tolerated(0.57) | benign(0) | TCGA-IR-A3LK-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | PD | |
| HDAC3 | SNV | Missense_Mutation | c.192N>T | p.Glu64Asp | p.E64D | O15379 | protein_coding | tolerated(1) | benign(0.003) | TCGA-A6-2686-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| HDAC3 | SNV | Missense_Mutation | novel | c.712C>T | p.Pro238Ser | p.P238S | O15379 | protein_coding | tolerated(0.08) | probably_damaging(0.95) | TCGA-AA-3930-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | capecitabine | 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 |
| 8841 | HDAC3 | ENZYME, TRANSCRIPTION FACTOR, DRUGGABLE GENOME | inhibitor | CUDC-101 | CUDC-101 | |
| 8841 | HDAC3 | ENZYME, TRANSCRIPTION FACTOR, DRUGGABLE GENOME | BELINOSTAT | BELINOSTAT | 25937017 | |
| 8841 | HDAC3 | ENZYME, TRANSCRIPTION FACTOR, DRUGGABLE GENOME | 7-ETHYL-10-HYDROXY-CAMPTOTHECIN | 7-ETHYL-10-HYDROXYCAMPTOTHECIN | 23622981 | |
| 8841 | HDAC3 | ENZYME, TRANSCRIPTION FACTOR, DRUGGABLE GENOME | inhibitor | 187051792 | PANOBINOSTAT | |
| 8841 | HDAC3 | ENZYME, TRANSCRIPTION FACTOR, DRUGGABLE GENOME | VALPROIC ACID | VALPROIC ACID | 18294844,16921367,25304896 | |
| 8841 | HDAC3 | ENZYME, TRANSCRIPTION FACTOR, DRUGGABLE GENOME | RG2833 | |||
| 8841 | HDAC3 | ENZYME, TRANSCRIPTION FACTOR, DRUGGABLE GENOME | PMID29671355-Compound-25 | |||
| 8841 | HDAC3 | ENZYME, TRANSCRIPTION FACTOR, DRUGGABLE GENOME | inhibitor | 252166579 | TACEDINALINE | |
| 8841 | HDAC3 | ENZYME, TRANSCRIPTION FACTOR, DRUGGABLE GENOME | inhibitor | VALPROIC ACID | DEPAKOTE | |
| 8841 | HDAC3 | ENZYME, TRANSCRIPTION FACTOR, DRUGGABLE GENOME | 2-ENE-VALPROATE | CHEMBL117487 | 17566732 |
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