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Gene: HDAC2 |
Gene summary for HDAC2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | HDAC2 | Gene ID | 3066 |
| Gene name | histone deacetylase 2 | |
| Gene Alias | HD2 | |
| Cytomap | 6q21 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | Q92769 |
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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 |
| 3066 | HDAC2 | GSM4909281 | Human | Breast | IDC | 3.44e-02 | 2.93e-01 | 0.21 |
| 3066 | HDAC2 | GSM4909285 | Human | Breast | IDC | 9.19e-30 | 6.25e-01 | 0.21 |
| 3066 | HDAC2 | GSM4909286 | Human | Breast | IDC | 6.81e-04 | 3.76e-01 | 0.1081 |
| 3066 | HDAC2 | GSM4909287 | Human | Breast | IDC | 6.52e-06 | 3.19e-01 | 0.2057 |
| 3066 | HDAC2 | GSM4909293 | Human | Breast | IDC | 3.45e-05 | 3.26e-01 | 0.1581 |
| 3066 | HDAC2 | GSM4909296 | Human | Breast | IDC | 5.60e-13 | -2.83e-01 | 0.1524 |
| 3066 | HDAC2 | GSM4909297 | Human | Breast | IDC | 1.69e-11 | -1.28e-01 | 0.1517 |
| 3066 | HDAC2 | GSM4909302 | Human | Breast | IDC | 8.95e-09 | -2.84e-01 | 0.1545 |
| 3066 | HDAC2 | GSM4909311 | Human | Breast | IDC | 2.08e-21 | -2.20e-01 | 0.1534 |
| 3066 | HDAC2 | GSM4909312 | Human | Breast | IDC | 1.46e-09 | -9.16e-02 | 0.1552 |
| 3066 | HDAC2 | GSM4909319 | Human | Breast | IDC | 5.75e-26 | -2.92e-01 | 0.1563 |
| 3066 | HDAC2 | GSM4909320 | Human | Breast | IDC | 1.46e-06 | -2.79e-01 | 0.1575 |
| 3066 | HDAC2 | GSM4909321 | Human | Breast | IDC | 2.26e-12 | -2.26e-01 | 0.1559 |
| 3066 | HDAC2 | brca3 | Human | Breast | Precancer | 3.44e-04 | 3.18e-01 | -0.0263 |
| 3066 | HDAC2 | M2 | Human | Breast | IDC | 1.30e-10 | 5.28e-01 | 0.21 |
| 3066 | HDAC2 | NCCBC14 | Human | Breast | DCIS | 4.60e-09 | -2.16e-02 | 0.2021 |
| 3066 | HDAC2 | NCCBC5 | Human | Breast | DCIS | 4.33e-10 | -7.12e-02 | 0.2046 |
| 3066 | HDAC2 | NCCBC6 | Human | Breast | DCIS | 2.73e-06 | 5.13e-01 | 0.2095 |
| 3066 | HDAC2 | P1 | Human | Breast | IDC | 1.01e-13 | -1.51e-01 | 0.1527 |
| 3066 | HDAC2 | P2 | Human | Breast | IDC | 2.24e-05 | 2.71e-01 | 0.21 |
| Page: 1 2 3 4 5 6 7 8 9 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| 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 | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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:00519605 | Oral cavity | OSCC | regulation of nervous system development | 205/7305 | 443/18723 | 9.80e-04 | 5.11e-03 | 205 |
| GO:000632510 | Oral cavity | OSCC | chromatin organization | 190/7305 | 409/18723 | 1.17e-03 | 5.97e-03 | 190 |
| GO:00107173 | Oral cavity | OSCC | regulation of epithelial to mesenchymal transition | 54/7305 | 99/18723 | 1.21e-03 | 6.10e-03 | 54 |
| GO:00100015 | Oral cavity | OSCC | glial cell differentiation | 110/7305 | 225/18723 | 1.56e-03 | 7.45e-03 | 110 |
| GO:000181910 | Oral cavity | OSCC | positive regulation of cytokine production | 213/7305 | 467/18723 | 1.93e-03 | 8.96e-03 | 213 |
| GO:00362962 | Oral cavity | OSCC | response to increased oxygen levels | 20/7305 | 30/18723 | 1.99e-03 | 9.23e-03 | 20 |
| GO:00456871 | Oral cavity | OSCC | positive regulation of glial cell differentiation | 26/7305 | 42/18723 | 2.22e-03 | 1.00e-02 | 26 |
| GO:0014013 | Oral cavity | OSCC | regulation of gliogenesis | 54/7305 | 103/18723 | 3.85e-03 | 1.57e-02 | 54 |
| GO:0070932 | Oral cavity | OSCC | histone H3 deacetylation | 14/7305 | 20/18723 | 4.95e-03 | 1.94e-02 | 14 |
| GO:0032963 | Oral cavity | OSCC | collagen metabolic process | 54/7305 | 104/18723 | 5.00e-03 | 1.96e-02 | 54 |
| GO:00313458 | Oral cavity | OSCC | negative regulation of cell projection organization | 89/7305 | 186/18723 | 8.51e-03 | 3.09e-02 | 89 |
| GO:001635810 | Oral cavity | OSCC | dendrite development | 113/7305 | 243/18723 | 1.00e-02 | 3.49e-02 | 113 |
| GO:0032526 | Oral cavity | OSCC | response to retinoic acid | 54/7305 | 107/18723 | 1.04e-02 | 3.54e-02 | 54 |
| GO:00609967 | Oral cavity | OSCC | dendritic spine development | 50/7305 | 99/18723 | 1.31e-02 | 4.34e-02 | 50 |
| GO:00487627 | Oral cavity | OSCC | mesenchymal cell differentiation | 109/7305 | 236/18723 | 1.43e-02 | 4.69e-02 | 109 |
| GO:0045862110 | Oral cavity | LP | positive regulation of proteolysis | 165/4623 | 372/18723 | 5.40e-17 | 8.46e-15 | 165 |
| GO:0006979110 | Oral cavity | LP | response to oxidative stress | 181/4623 | 446/18723 | 5.74e-14 | 6.10e-12 | 181 |
| GO:0000302110 | Oral cavity | LP | response to reactive oxygen species | 95/4623 | 222/18723 | 2.23e-09 | 9.98e-08 | 95 |
| GO:0051098110 | Oral cavity | LP | regulation of binding | 140/4623 | 363/18723 | 2.47e-09 | 1.10e-07 | 140 |
| GO:0042542110 | Oral cavity | LP | response to hydrogen peroxide | 68/4623 | 146/18723 | 6.95e-09 | 2.81e-07 | 68 |
| 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 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0501616 | Breast | Precancer | Huntington disease | 98/684 | 306/8465 | 2.85e-35 | 2.25e-33 | 1.72e-33 | 98 |
| hsa0516918 | Breast | Precancer | Epstein-Barr virus infection | 35/684 | 202/8465 | 1.15e-05 | 1.26e-04 | 9.64e-05 | 35 |
| hsa05031 | Breast | Precancer | Amphetamine addiction | 14/684 | 69/8465 | 1.05e-03 | 7.35e-03 | 5.63e-03 | 14 |
| hsa052036 | Breast | Precancer | Viral carcinogenesis | 27/684 | 204/8465 | 7.19e-03 | 4.06e-02 | 3.11e-02 | 27 |
| hsa0501617 | Breast | Precancer | Huntington disease | 98/684 | 306/8465 | 2.85e-35 | 2.25e-33 | 1.72e-33 | 98 |
| hsa0516919 | Breast | Precancer | Epstein-Barr virus infection | 35/684 | 202/8465 | 1.15e-05 | 1.26e-04 | 9.64e-05 | 35 |
| hsa050311 | Breast | Precancer | Amphetamine addiction | 14/684 | 69/8465 | 1.05e-03 | 7.35e-03 | 5.63e-03 | 14 |
| hsa0520312 | Breast | Precancer | Viral carcinogenesis | 27/684 | 204/8465 | 7.19e-03 | 4.06e-02 | 3.11e-02 | 27 |
| hsa0501623 | Breast | IDC | Huntington disease | 103/867 | 306/8465 | 5.14e-30 | 4.17e-28 | 3.12e-28 | 103 |
| hsa0516922 | Breast | IDC | Epstein-Barr virus infection | 45/867 | 202/8465 | 3.16e-07 | 6.05e-06 | 4.52e-06 | 45 |
| hsa050312 | Breast | IDC | Amphetamine addiction | 18/867 | 69/8465 | 1.42e-04 | 1.36e-03 | 1.01e-03 | 18 |
| hsa0491916 | Breast | IDC | Thyroid hormone signaling pathway | 23/867 | 121/8465 | 2.45e-03 | 1.69e-02 | 1.27e-02 | 23 |
| hsa0520322 | Breast | IDC | Viral carcinogenesis | 34/867 | 204/8465 | 2.82e-03 | 1.86e-02 | 1.39e-02 | 34 |
| hsa0522010 | Breast | IDC | Chronic myeloid leukemia | 15/867 | 76/8465 | 9.24e-03 | 4.37e-02 | 3.27e-02 | 15 |
| hsa0501633 | Breast | IDC | Huntington disease | 103/867 | 306/8465 | 5.14e-30 | 4.17e-28 | 3.12e-28 | 103 |
| hsa0516932 | Breast | IDC | Epstein-Barr virus infection | 45/867 | 202/8465 | 3.16e-07 | 6.05e-06 | 4.52e-06 | 45 |
| hsa050313 | Breast | IDC | Amphetamine addiction | 18/867 | 69/8465 | 1.42e-04 | 1.36e-03 | 1.01e-03 | 18 |
| hsa0491917 | Breast | IDC | Thyroid hormone signaling pathway | 23/867 | 121/8465 | 2.45e-03 | 1.69e-02 | 1.27e-02 | 23 |
| hsa0520332 | Breast | IDC | Viral carcinogenesis | 34/867 | 204/8465 | 2.82e-03 | 1.86e-02 | 1.39e-02 | 34 |
| hsa0522013 | Breast | IDC | Chronic myeloid leukemia | 15/867 | 76/8465 | 9.24e-03 | 4.37e-02 | 3.27e-02 | 15 |
| Page: 1 2 3 4 5 6 7 8 9 |
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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 |
| HDAC2 | STM | Colorectum | CRC | LINC01594,FMNL3,GRM8, etc. | 3.25e-01 |  |
| HDAC2 | ASC | Colorectum | CRC | LINC01594,FMNL3,GRM8, etc. | 3.29e-01 | |
| HDAC2 | ASC | Colorectum | FAP | LINC01594,FMNL3,GRM8, etc. | 2.90e-01 |  |
| HDAC2 | ASC | Colorectum | SER | ESD,MT-ND3,RPL39, etc. | 1.19e-01 |  |
| HDAC2 | AT2L | Lung | IAC | CD24,DBN1,SPINT2, etc. | 4.95e-01 |  |
| HDAC2 | STM | Prostate | Healthy | PHF10,ITGB1BP1,NSDHL, etc. | 4.66e-01 |  |
| HDAC2 | MESC | Stomach | SIM | RPARP-AS1,SLC38A11,SOX4, etc. | 1.20e-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 |
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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 |
| HDAC2 | SNV | Missense_Mutation | c.502N>T | p.His168Tyr | p.H168Y | Q92769 | protein_coding | deleterious(0.04) | possibly_damaging(0.828) | TCGA-A7-A0DA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| HDAC2 | SNV | Missense_Mutation | c.523N>A | p.Asp175Asn | p.D175N | Q92769 | protein_coding | deleterious(0.03) | probably_damaging(0.915) | TCGA-BH-A0BR-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| HDAC2 | deletion | Nonsense_Mutation | c.459_463delNNNNN | p.Tyr153Ter | p.Y153* | Q92769 | protein_coding | TCGA-AR-A0TU-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Doxorubicin | SD | |||
| HDAC2 | SNV | Missense_Mutation | novel | c.691G>A | p.Asp231Asn | p.D231N | Q92769 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-MA-AA3Z-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| HDAC2 | deletion | Frame_Shift_Del | novel | c.883_884delNN | p.Pro295IlefsTer13 | p.P295Ifs*13 | Q92769 | protein_coding | TCGA-MA-AA3Y-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | ||
| HDAC2 | SNV | Missense_Mutation | c.875N>G | p.Phe292Cys | p.F292C | Q92769 | protein_coding | deleterious(0) | probably_damaging(0.973) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR | |
| HDAC2 | SNV | Missense_Mutation | c.1229N>T | p.Ala410Val | p.A410V | Q92769 | protein_coding | tolerated(0.32) | benign(0.423) | TCGA-F4-6703-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| HDAC2 | SNV | Missense_Mutation | c.230T>C | p.Leu77Pro | p.L77P | Q92769 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-NH-A50T-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| HDAC2 | SNV | Missense_Mutation | novel | c.1001N>G | p.Tyr334Cys | p.Y334C | Q92769 | protein_coding | deleterious(0) | possibly_damaging(0.761) | TCGA-EI-6917-01 | Colorectum | rectum adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5fluorouracil+oxaciplatina+l-folinian | SD |
| HDAC2 | SNV | Missense_Mutation | novel | c.1271N>T | p.Ser424Phe | p.S424F | Q92769 | protein_coding | deleterious(0.01) | probably_damaging(0.997) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 |
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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 |
| 3066 | HDAC2 | DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME, TRANSCRIPTION FACTOR | 2-ENE-VALPROATE | CHEMBL117487 | 17566732 | |
| 3066 | HDAC2 | DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME, TRANSCRIPTION FACTOR | inhibitor | 187051807 | SCRIPTAID | |
| 3066 | HDAC2 | DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME, TRANSCRIPTION FACTOR | inhibitor | BELINOSTAT | BELINOSTAT | |
| 3066 | HDAC2 | DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME, TRANSCRIPTION FACTOR | inhibitor | 187051797 | APICIDIN | |
| 3066 | HDAC2 | DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME, TRANSCRIPTION FACTOR | PAZOPANIB | PAZOPANIB | 28221861 | |
| 3066 | HDAC2 | DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME, TRANSCRIPTION FACTOR | PRACINOSTAT | PRACINOSTAT | ||
| 3066 | HDAC2 | DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME, TRANSCRIPTION FACTOR | inhibitor | 187051798 | BELINOSTAT | |
| 3066 | HDAC2 | DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME, TRANSCRIPTION FACTOR | inhibitor | SODIUM PHENYLBUTYRATE | ||
| 3066 | HDAC2 | DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME, TRANSCRIPTION FACTOR | VORINOSTAT | VORINOSTAT | 24694055,19344175,19966789,26211462,23622981,22260166,17447750,20491440,21548582,24074025,23672185,19084294 | |
| 3066 | HDAC2 | DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME, TRANSCRIPTION FACTOR | PANOBINOSTAT | PANOBINOSTAT |
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