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Gene: HDC |
Gene summary for HDC |
Gene summary. |
Gene information | Species | Human | Gene symbol | HDC | Gene ID | 3067 |
Gene name | histidine decarboxylase | |
Gene Alias | HDC | |
Cytomap | 15q21.2 | |
Gene Type | protein-coding | GO ID | GO:0001692 | UniProtAcc | P19113 |
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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 |
3067 | HDC | CA_HPV_1 | Human | Cervix | CC | 1.90e-14 | -4.60e-01 | 0.0264 |
3067 | HDC | HSIL_HPV_2 | Human | Cervix | HSIL_HPV | 1.66e-04 | 3.33e-02 | 0.0208 |
3067 | HDC | N_HPV_2 | Human | Cervix | N_HPV | 1.76e-02 | -3.56e-01 | -0.0131 |
3067 | HDC | CCI_1 | Human | Cervix | CC | 2.11e-03 | -5.60e-01 | 0.528 |
3067 | HDC | CCI_2 | Human | Cervix | CC | 5.80e-03 | -5.60e-01 | 0.5249 |
3067 | HDC | CCI_3 | Human | Cervix | CC | 3.56e-05 | -5.60e-01 | 0.516 |
3067 | HDC | CCII_1 | Human | Cervix | CC | 6.78e-08 | -5.60e-01 | 0.3249 |
3067 | HDC | Tumor | Human | Cervix | CC | 2.52e-20 | -5.60e-01 | 0.1241 |
3067 | HDC | sample1 | Human | Cervix | CC | 2.70e-06 | -5.60e-01 | 0.0959 |
3067 | HDC | sample3 | Human | Cervix | CC | 4.65e-21 | -5.60e-01 | 0.1387 |
3067 | HDC | H2 | Human | Cervix | HSIL_HPV | 1.62e-17 | -5.49e-01 | 0.0632 |
3067 | HDC | L1 | Human | Cervix | CC | 7.67e-09 | -5.60e-01 | 0.0802 |
3067 | HDC | T1 | Human | Cervix | CC | 8.70e-16 | -5.60e-01 | 0.0918 |
3067 | HDC | T2 | Human | Cervix | CC | 1.07e-02 | -5.60e-01 | 0.0709 |
3067 | HDC | T3 | Human | Cervix | CC | 3.12e-19 | -5.60e-01 | 0.1389 |
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Transcriptomic changes along malignancy continuum. |
Tissue | Expression Dynamics | Abbreviation |
Cervix | CC: Cervix cancer | |
HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
N_HPV: HPV-infected normal cervix |
∗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). |
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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:001603210 | Cervix | CC | viral process | 109/2311 | 415/18723 | 5.40e-15 | 6.46e-12 | 109 |
GO:001905810 | Cervix | CC | viral life cycle | 87/2311 | 317/18723 | 2.20e-13 | 1.20e-10 | 87 |
GO:004440310 | Cervix | CC | biological process involved in symbiotic interaction | 71/2311 | 290/18723 | 7.94e-09 | 6.98e-07 | 71 |
GO:001907910 | Cervix | CC | viral genome replication | 35/2311 | 131/18723 | 6.11e-06 | 1.49e-04 | 35 |
GO:00457876 | Cervix | CC | positive regulation of cell cycle | 66/2311 | 313/18723 | 7.78e-06 | 1.81e-04 | 66 |
GO:00073466 | Cervix | CC | regulation of mitotic cell cycle | 88/2311 | 457/18723 | 1.26e-05 | 2.60e-04 | 88 |
GO:00346129 | Cervix | CC | response to tumor necrosis factor | 55/2311 | 253/18723 | 1.75e-05 | 3.32e-04 | 55 |
GO:002261310 | Cervix | CC | ribonucleoprotein complex biogenesis | 88/2311 | 463/18723 | 2.11e-05 | 3.82e-04 | 88 |
GO:002261810 | Cervix | CC | ribonucleoprotein complex assembly | 49/2311 | 220/18723 | 2.52e-05 | 4.29e-04 | 49 |
GO:007182610 | Cervix | CC | ribonucleoprotein complex subunit organization | 49/2311 | 227/18723 | 5.91e-05 | 8.54e-04 | 49 |
GO:000838010 | Cervix | CC | RNA splicing | 76/2311 | 434/18723 | 9.79e-04 | 8.19e-03 | 76 |
GO:00457862 | Cervix | CC | negative regulation of cell cycle | 67/2311 | 385/18723 | 2.21e-03 | 1.59e-02 | 67 |
GO:00459302 | Cervix | CC | negative regulation of mitotic cell cycle | 44/2311 | 235/18723 | 3.02e-03 | 1.99e-02 | 44 |
GO:000037710 | Cervix | CC | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 55/2311 | 320/18723 | 6.71e-03 | 3.70e-02 | 55 |
GO:000039810 | Cervix | CC | mRNA splicing, via spliceosome | 55/2311 | 320/18723 | 6.71e-03 | 3.70e-02 | 55 |
GO:000037510 | Cervix | CC | RNA splicing, via transesterification reactions | 55/2311 | 324/18723 | 8.61e-03 | 4.44e-02 | 55 |
GO:0018958 | Cervix | HSIL_HPV | phenol-containing compound metabolic process | 12/737 | 110/18723 | 1.31e-03 | 1.50e-02 | 12 |
GO:0016032 | Colorectum | AD | viral process | 168/3918 | 415/18723 | 4.67e-20 | 3.66e-17 | 168 |
GO:0008380 | Colorectum | AD | RNA splicing | 169/3918 | 434/18723 | 3.59e-18 | 2.04e-15 | 169 |
GO:0000377 | Colorectum | AD | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 130/3918 | 320/18723 | 5.88e-16 | 2.16e-13 | 130 |
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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 |
∗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 |
HDC | SNV | Missense_Mutation | rs751827833 | c.446N>T | p.Thr149Met | p.T149M | P19113 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AG-3887-01 | Colorectum | rectum adenocarcinoma | Male | >=65 | I/II | Chemotherapy | irinotecan | SD |
HDC | SNV | Missense_Mutation | c.1869G>T | p.Met623Ile | p.M623I | P19113 | protein_coding | tolerated_low_confidence(0.11) | benign(0.001) | TCGA-AG-3892-01 | Colorectum | rectum adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
HDC | SNV | Missense_Mutation | c.1708T>C | p.Phe570Leu | p.F570L | P19113 | protein_coding | deleterious_low_confidence(0.01) | benign(0.014) | TCGA-AG-3892-01 | Colorectum | rectum adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
HDC | SNV | Missense_Mutation | novel | c.275N>T | p.Gly92Val | p.G92V | P19113 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
HDC | SNV | Missense_Mutation | c.121N>A | p.Ala41Thr | p.A41T | P19113 | protein_coding | tolerated(0.55) | benign(0.003) | TCGA-AG-A00Y-01 | Colorectum | rectum adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
HDC | SNV | Missense_Mutation | c.627N>T | p.Lys209Asn | p.K209N | P19113 | protein_coding | deleterious(0) | benign(0.291) | TCGA-EF-5830-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
HDC | SNV | Missense_Mutation | c.1815G>C | p.Lys605Asn | p.K605N | P19113 | protein_coding | deleterious_low_confidence(0.01) | benign(0.075) | TCGA-EI-6506-01 | Colorectum | rectum adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
HDC | SNV | Missense_Mutation | c.203N>A | p.Gly68Glu | p.G68E | P19113 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-F5-6810-01 | Colorectum | rectum adenocarcinoma | Unknown | Unknown | I/II | Unknown | Unknown | Unknown | |
HDC | SNV | Missense_Mutation | rs143849528 | c.355G>A | p.Val119Ile | p.V119I | P19113 | protein_coding | deleterious(0.03) | benign(0.098) | TCGA-A5-A7WJ-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
HDC | SNV | Missense_Mutation | novel | c.1003N>T | p.Leu335Phe | p.L335F | P19113 | protein_coding | deleterious(0.01) | probably_damaging(1) | TCGA-AJ-A3EK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR |
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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 |
3067 | HDC | DRUGGABLE GENOME, ENZYME | BF-DERM1 | |||
3067 | HDC | DRUGGABLE GENOME, ENZYME | inhibitor | 178101877 | ||
3067 | HDC | DRUGGABLE GENOME, ENZYME | Lixivaptan | LIXIVAPTAN | ||
3067 | HDC | DRUGGABLE GENOME, ENZYME | inhibitor | 178101826 | ||
3067 | HDC | DRUGGABLE GENOME, ENZYME | OMEPRAZOLE | OMEPRAZOLE | 8187977 | |
3067 | HDC | DRUGGABLE GENOME, ENZYME | ALPHA-FMH |
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