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Gene: KCTD3 |
Gene summary for KCTD3 |
Gene summary. |
Gene information | Species | Human | Gene symbol | KCTD3 | Gene ID | 51133 |
Gene name | potassium channel tetramerization domain containing 3 | |
Gene Alias | NY-REN-45 | |
Cytomap | 1q41 | |
Gene Type | protein-coding | GO ID | GO:0008150 | UniProtAcc | Q9Y597 |
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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 |
51133 | KCTD3 | GSM4909298 | Human | Breast | IDC | 3.98e-14 | 3.47e-01 | 0.1551 |
51133 | KCTD3 | GSM4909308 | Human | Breast | IDC | 1.40e-05 | 2.72e-01 | 0.158 |
51133 | KCTD3 | GSM4909311 | Human | Breast | IDC | 7.05e-06 | -1.19e-01 | 0.1534 |
51133 | KCTD3 | GSM4909319 | Human | Breast | IDC | 2.63e-06 | -7.90e-02 | 0.1563 |
51133 | KCTD3 | M5 | Human | Breast | IDC | 2.25e-03 | 6.24e-01 | 0.1598 |
51133 | KCTD3 | NCCBC14 | Human | Breast | DCIS | 9.01e-05 | 3.87e-01 | 0.2021 |
51133 | KCTD3 | DCIS2 | Human | Breast | DCIS | 1.55e-65 | 4.03e-01 | 0.0085 |
51133 | KCTD3 | CCI_1 | Human | Cervix | CC | 1.92e-06 | 6.35e-01 | 0.528 |
51133 | KCTD3 | CCI_3 | Human | Cervix | CC | 2.38e-13 | 6.97e-01 | 0.516 |
51133 | KCTD3 | LZE2T | Human | Esophagus | ESCC | 2.08e-04 | 5.14e-01 | 0.082 |
51133 | KCTD3 | LZE7T | Human | Esophagus | ESCC | 4.96e-03 | 2.41e-01 | 0.0667 |
51133 | KCTD3 | P1T-E | Human | Esophagus | ESCC | 5.49e-05 | 3.38e-01 | 0.0875 |
51133 | KCTD3 | P2T-E | Human | Esophagus | ESCC | 4.48e-29 | 2.28e-01 | 0.1177 |
51133 | KCTD3 | P5T-E | Human | Esophagus | ESCC | 7.23e-15 | 1.68e-01 | 0.1327 |
51133 | KCTD3 | P8T-E | Human | Esophagus | ESCC | 3.87e-10 | 1.75e-01 | 0.0889 |
51133 | KCTD3 | P9T-E | Human | Esophagus | ESCC | 6.63e-09 | 1.78e-01 | 0.1131 |
51133 | KCTD3 | P10T-E | Human | Esophagus | ESCC | 1.61e-15 | 1.51e-01 | 0.116 |
51133 | KCTD3 | P11T-E | Human | Esophagus | ESCC | 8.91e-05 | 2.95e-01 | 0.1426 |
51133 | KCTD3 | P12T-E | Human | Esophagus | ESCC | 2.46e-17 | 1.40e-01 | 0.1122 |
51133 | KCTD3 | P15T-E | Human | Esophagus | ESCC | 3.36e-06 | 1.91e-01 | 0.1149 |
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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 |
Esophagus | ESCC | |
Skin | AK | |
Skin | SCCIS | |
Skin | cSCC | |
Thyroid | HT |
∗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:00512592 | Esophagus | ESCC | protein complex oligomerization | 130/8552 | 238/18723 | 3.29e-03 | 1.36e-02 | 130 |
GO:0051259 | Oral cavity | OSCC | protein complex oligomerization | 121/7305 | 238/18723 | 1.29e-04 | 9.21e-04 | 121 |
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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 |
KCTD3 | SNV | Missense_Mutation | c.553N>G | p.Arg185Gly | p.R185G | Q9Y597 | protein_coding | tolerated(0.55) | benign(0.006) | TCGA-A1-A0SP-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | SD | ||
KCTD3 | SNV | Missense_Mutation | c.1541N>C | p.Arg514Thr | p.R514T | Q9Y597 | protein_coding | deleterious(0.02) | probably_damaging(0.999) | TCGA-A8-A06Q-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
KCTD3 | SNV | Missense_Mutation | c.260G>A | p.Gly87Glu | p.G87E | Q9Y597 | protein_coding | tolerated(0.11) | benign(0.345) | TCGA-A8-A08S-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | SD | |
KCTD3 | SNV | Missense_Mutation | c.725N>T | p.Pro242Leu | p.P242L | Q9Y597 | protein_coding | deleterious(0.01) | benign(0.244) | TCGA-B6-A0X4-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
KCTD3 | SNV | Missense_Mutation | novel | c.1385N>G | p.Ser462Cys | p.S462C | Q9Y597 | protein_coding | deleterious(0) | probably_damaging(0.993) | TCGA-BH-A0DK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD |
KCTD3 | SNV | Missense_Mutation | novel | c.1649N>C | p.Arg550Thr | p.R550T | Q9Y597 | protein_coding | deleterious(0) | probably_damaging(0.99) | TCGA-LQ-A4E4-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | anastrozole | PD |
KCTD3 | deletion | Frame_Shift_Del | c.146_158delNNNNNNNNNNNNN | p.Ser49LysfsTer23 | p.S49Kfs*23 | Q9Y597 | protein_coding | TCGA-D8-A1JP-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | |||
KCTD3 | SNV | Missense_Mutation | c.481N>A | p.Gly161Arg | p.G161R | Q9Y597 | protein_coding | tolerated(0.53) | benign(0.001) | TCGA-A6-6653-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
KCTD3 | SNV | Missense_Mutation | rs566861222 | c.410N>A | p.Arg137His | p.R137H | Q9Y597 | protein_coding | tolerated(0.09) | benign(0.007) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR |
KCTD3 | SNV | Missense_Mutation | c.1910C>T | p.Thr637Ile | p.T637I | Q9Y597 | protein_coding | tolerated_low_confidence(0.11) | benign(0.021) | TCGA-AA-A022-01 | Colorectum | colon adenocarcinoma | 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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