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Gene: HACD3 |
Gene summary for HACD3 |
Gene summary. |
Gene information | Species | Human | Gene symbol | HACD3 | Gene ID | 51495 |
Gene name | 3-hydroxyacyl-CoA dehydratase 3 | |
Gene Alias | B-IND1 | |
Cytomap | 15q22.31 | |
Gene Type | protein-coding | GO ID | GO:0000038 | UniProtAcc | Q9P035 |
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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 |
51495 | HACD3 | GSM4909282 | Human | Breast | IDC | 7.06e-24 | 5.52e-01 | -0.0288 |
51495 | HACD3 | GSM4909285 | Human | Breast | IDC | 3.41e-06 | 1.47e-01 | 0.21 |
51495 | HACD3 | GSM4909291 | Human | Breast | IDC | 3.15e-09 | 5.08e-01 | 0.1753 |
51495 | HACD3 | GSM4909293 | Human | Breast | IDC | 4.69e-06 | 1.59e-01 | 0.1581 |
51495 | HACD3 | GSM4909296 | Human | Breast | IDC | 1.27e-02 | 7.02e-02 | 0.1524 |
51495 | HACD3 | GSM4909297 | Human | Breast | IDC | 5.79e-04 | -2.64e-02 | 0.1517 |
51495 | HACD3 | GSM4909298 | Human | Breast | IDC | 5.58e-09 | 2.79e-01 | 0.1551 |
51495 | HACD3 | GSM4909306 | Human | Breast | IDC | 2.66e-10 | 4.07e-01 | 0.1564 |
51495 | HACD3 | GSM4909307 | Human | Breast | IDC | 8.65e-04 | 2.12e-01 | 0.1569 |
51495 | HACD3 | GSM4909308 | Human | Breast | IDC | 1.78e-12 | 4.93e-01 | 0.158 |
51495 | HACD3 | GSM4909311 | Human | Breast | IDC | 6.80e-14 | -1.47e-01 | 0.1534 |
51495 | HACD3 | GSM4909312 | Human | Breast | IDC | 1.74e-05 | 1.17e-01 | 0.1552 |
51495 | HACD3 | GSM4909317 | Human | Breast | IDC | 3.32e-05 | 3.56e-01 | 0.1355 |
51495 | HACD3 | GSM4909319 | Human | Breast | IDC | 8.31e-17 | -2.49e-01 | 0.1563 |
51495 | HACD3 | GSM4909321 | Human | Breast | IDC | 2.54e-11 | 2.04e-01 | 0.1559 |
51495 | HACD3 | brca2 | Human | Breast | Precancer | 4.63e-13 | 3.07e-01 | -0.024 |
51495 | HACD3 | NCCBC14 | Human | Breast | DCIS | 1.92e-06 | 4.56e-02 | 0.2021 |
51495 | HACD3 | NCCBC5 | Human | Breast | DCIS | 1.95e-09 | -6.55e-02 | 0.2046 |
51495 | HACD3 | P1 | Human | Breast | IDC | 1.05e-09 | 3.15e-02 | 0.1527 |
51495 | HACD3 | P2 | Human | Breast | IDC | 3.19e-02 | -1.78e-01 | 0.21 |
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Transcriptomic changes along malignancy continuum. |
∗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:000724914 | Breast | IDC | I-kappaB kinase/NF-kappaB signaling | 37/1434 | 281/18723 | 8.58e-04 | 9.98e-03 | 37 |
GO:007233012 | Breast | IDC | monocarboxylic acid biosynthetic process | 29/1434 | 214/18723 | 1.91e-03 | 1.83e-02 | 29 |
GO:001605313 | Breast | IDC | organic acid biosynthetic process | 39/1434 | 316/18723 | 2.13e-03 | 1.99e-02 | 39 |
GO:000663312 | Breast | IDC | fatty acid biosynthetic process | 23/1434 | 163/18723 | 3.21e-03 | 2.70e-02 | 23 |
GO:004639413 | Breast | IDC | carboxylic acid biosynthetic process | 38/1434 | 314/18723 | 3.39e-03 | 2.83e-02 | 38 |
GO:001603224 | Breast | DCIS | viral process | 73/1390 | 415/18723 | 3.40e-12 | 6.88e-10 | 73 |
GO:001905824 | Breast | DCIS | viral life cycle | 59/1390 | 317/18723 | 4.05e-11 | 5.74e-09 | 59 |
GO:001907923 | Breast | DCIS | viral genome replication | 30/1390 | 131/18723 | 2.12e-08 | 1.45e-06 | 30 |
GO:005079222 | Breast | DCIS | regulation of viral process | 34/1390 | 164/18723 | 3.58e-08 | 2.30e-06 | 34 |
GO:190390022 | Breast | DCIS | regulation of viral life cycle | 28/1390 | 148/18723 | 3.79e-06 | 1.16e-04 | 28 |
GO:004852421 | Breast | DCIS | positive regulation of viral process | 16/1390 | 65/18723 | 1.56e-05 | 3.79e-04 | 16 |
GO:004506923 | Breast | DCIS | regulation of viral genome replication | 18/1390 | 85/18723 | 4.23e-05 | 8.98e-04 | 18 |
GO:004507012 | Breast | DCIS | positive regulation of viral genome replication | 8/1390 | 30/18723 | 1.21e-03 | 1.28e-02 | 8 |
GO:000724923 | Breast | DCIS | I-kappaB kinase/NF-kappaB signaling | 35/1390 | 281/18723 | 1.80e-03 | 1.74e-02 | 35 |
GO:001605322 | Breast | DCIS | organic acid biosynthetic process | 38/1390 | 316/18723 | 2.22e-03 | 2.04e-02 | 38 |
GO:007233022 | Breast | DCIS | monocarboxylic acid biosynthetic process | 28/1390 | 214/18723 | 2.43e-03 | 2.18e-02 | 28 |
GO:004639422 | Breast | DCIS | carboxylic acid biosynthetic process | 37/1390 | 314/18723 | 3.56e-03 | 2.92e-02 | 37 |
GO:000663322 | Breast | DCIS | fatty acid biosynthetic process | 22/1390 | 163/18723 | 4.62e-03 | 3.52e-02 | 22 |
GO:0016032111 | Esophagus | ESCC | viral process | 301/8552 | 415/18723 | 3.34e-29 | 1.32e-26 | 301 |
GO:0019058111 | Esophagus | ESCC | viral life cycle | 226/8552 | 317/18723 | 1.17e-20 | 1.76e-18 | 226 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa012129 | Esophagus | ESCC | Fatty acid metabolism | 41/4205 | 57/8465 | 5.13e-04 | 1.75e-03 | 8.98e-04 | 41 |
hsa0121214 | Esophagus | ESCC | Fatty acid metabolism | 41/4205 | 57/8465 | 5.13e-04 | 1.75e-03 | 8.98e-04 | 41 |
hsa012126 | Liver | NAFLD | Fatty acid metabolism | 17/1043 | 57/8465 | 3.43e-04 | 5.93e-03 | 4.78e-03 | 17 |
hsa0121211 | Liver | NAFLD | Fatty acid metabolism | 17/1043 | 57/8465 | 3.43e-04 | 5.93e-03 | 4.78e-03 | 17 |
hsa012122 | Liver | Cirrhotic | Fatty acid metabolism | 32/2530 | 57/8465 | 3.12e-05 | 2.47e-04 | 1.52e-04 | 32 |
hsa01040 | Liver | Cirrhotic | Biosynthesis of unsaturated fatty acids | 14/2530 | 27/8465 | 1.36e-02 | 4.25e-02 | 2.62e-02 | 14 |
hsa012123 | Liver | Cirrhotic | Fatty acid metabolism | 32/2530 | 57/8465 | 3.12e-05 | 2.47e-04 | 1.52e-04 | 32 |
hsa010401 | Liver | Cirrhotic | Biosynthesis of unsaturated fatty acids | 14/2530 | 27/8465 | 1.36e-02 | 4.25e-02 | 2.62e-02 | 14 |
hsa012124 | Liver | HCC | Fatty acid metabolism | 45/4020 | 57/8465 | 1.05e-06 | 1.10e-05 | 6.09e-06 | 45 |
hsa000622 | Liver | HCC | Fatty acid elongation | 20/4020 | 27/8465 | 4.58e-03 | 1.36e-02 | 7.55e-03 | 20 |
hsa010402 | Liver | HCC | Biosynthesis of unsaturated fatty acids | 19/4020 | 27/8465 | 1.37e-02 | 3.33e-02 | 1.85e-02 | 19 |
hsa012125 | Liver | HCC | Fatty acid metabolism | 45/4020 | 57/8465 | 1.05e-06 | 1.10e-05 | 6.09e-06 | 45 |
hsa0006211 | Liver | HCC | Fatty acid elongation | 20/4020 | 27/8465 | 4.58e-03 | 1.36e-02 | 7.55e-03 | 20 |
hsa010403 | Liver | HCC | Biosynthesis of unsaturated fatty acids | 19/4020 | 27/8465 | 1.37e-02 | 3.33e-02 | 1.85e-02 | 19 |
hsa012128 | Oral cavity | OSCC | Fatty acid metabolism | 35/3704 | 57/8465 | 5.37e-03 | 1.29e-02 | 6.55e-03 | 35 |
hsa0121213 | Oral cavity | OSCC | Fatty acid metabolism | 35/3704 | 57/8465 | 5.37e-03 | 1.29e-02 | 6.55e-03 | 35 |
hsa012127 | Prostate | BPH | Fatty acid metabolism | 19/1718 | 57/8465 | 1.44e-02 | 4.17e-02 | 2.58e-02 | 19 |
hsa0121212 | Prostate | BPH | Fatty acid metabolism | 19/1718 | 57/8465 | 1.44e-02 | 4.17e-02 | 2.58e-02 | 19 |
hsa0121221 | Prostate | Tumor | Fatty acid metabolism | 23/1791 | 57/8465 | 7.60e-04 | 3.59e-03 | 2.23e-03 | 23 |
hsa010404 | Prostate | Tumor | Biosynthesis of unsaturated fatty acids | 12/1791 | 27/8465 | 5.53e-03 | 1.93e-02 | 1.19e-02 | 12 |
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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 |
HACD3 | SNV | Missense_Mutation | rs775563054 | c.233N>G | p.Val78Gly | p.V78G | Q9P035 | protein_coding | deleterious(0) | probably_damaging(0.969) | TCGA-A2-A1G4-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | adriamycin | SD |
HACD3 | SNV | Missense_Mutation | rs775563054 | c.233T>G | p.Val78Gly | p.V78G | Q9P035 | protein_coding | deleterious(0) | probably_damaging(0.969) | TCGA-BH-A1EX-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
HACD3 | SNV | Missense_Mutation | rs775563054 | c.233N>G | p.Val78Gly | p.V78G | Q9P035 | protein_coding | deleterious(0) | probably_damaging(0.969) | TCGA-C8-A12X-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
HACD3 | SNV | Missense_Mutation | rs775563054 | c.233N>G | p.Val78Gly | p.V78G | Q9P035 | protein_coding | deleterious(0) | probably_damaging(0.969) | TCGA-D8-A1Y3-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicine+cyclophosphamide | SD |
HACD3 | SNV | Missense_Mutation | rs775563054 | c.233N>G | p.Val78Gly | p.V78G | Q9P035 | protein_coding | deleterious(0) | probably_damaging(0.969) | TCGA-EW-A1IW-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | aromasin | SD |
HACD3 | SNV | Missense_Mutation | novel | c.231N>T | p.Gln77His | p.Q77H | Q9P035 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-JL-A3YW-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
HACD3 | deletion | Frame_Shift_Del | novel | c.736delN | p.Phe246LeufsTer19 | p.F246Lfs*19 | Q9P035 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
HACD3 | deletion | Frame_Shift_Del | novel | c.767delN | p.Phe257SerfsTer8 | p.F257Sfs*8 | Q9P035 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | ||
HACD3 | SNV | Missense_Mutation | c.1074G>T | p.Lys358Asn | p.K358N | Q9P035 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-VS-A9V3-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PD | |
HACD3 | deletion | Frame_Shift_Del | novel | c.1073delA | p.Lys358ArgfsTer17 | p.K358Rfs*17 | Q9P035 | protein_coding | TCGA-EA-A410-01 | Cervix | cervical & endocervical cancer | 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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