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Gene: TTC39A |
Gene summary for TTC39A |
Gene summary. |
Gene information | Species | Human | Gene symbol | TTC39A | Gene ID | 22996 |
Gene name | tetratricopeptide repeat domain 39A | |
Gene Alias | C1orf34 | |
Cytomap | 1p32.3 | |
Gene Type | protein-coding | GO ID | GO:0008150 | UniProtAcc | A0A140VJY6 |
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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 |
22996 | TTC39A | P130T-E | Human | Esophagus | ESCC | 1.78e-42 | 9.52e-01 | 0.1676 |
22996 | TTC39A | HCC1_Meng | Human | Liver | HCC | 1.77e-41 | 1.12e-01 | 0.0246 |
22996 | TTC39A | HCC2_Meng | Human | Liver | HCC | 7.14e-15 | 1.31e-01 | 0.0107 |
22996 | TTC39A | HCC2 | Human | Liver | HCC | 1.70e-05 | 2.81e+00 | 0.5341 |
22996 | TTC39A | S014 | Human | Liver | HCC | 9.20e-18 | 6.64e-01 | 0.2254 |
22996 | TTC39A | S015 | Human | Liver | HCC | 2.05e-16 | 1.01e+00 | 0.2375 |
22996 | TTC39A | S016 | Human | Liver | HCC | 1.09e-26 | 9.15e-01 | 0.2243 |
22996 | TTC39A | S027 | Human | Liver | HCC | 7.39e-21 | 1.06e+00 | 0.2446 |
22996 | TTC39A | S028 | Human | Liver | HCC | 3.32e-27 | 9.06e-01 | 0.2503 |
22996 | TTC39A | S029 | Human | Liver | HCC | 1.27e-22 | 9.89e-01 | 0.2581 |
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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 |
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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 |
TTC39A | SNV | Missense_Mutation | novel | c.1658C>G | p.Ala553Gly | p.A553G | Q5SRH9 | protein_coding | tolerated(0.77) | benign(0.013) | TCGA-A1-A0SH-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | tc | SD |
TTC39A | SNV | Missense_Mutation | c.1382N>C | p.Met461Thr | p.M461T | Q5SRH9 | protein_coding | deleterious(0) | possibly_damaging(0.771) | TCGA-A8-A0A1-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | |
TTC39A | SNV | Missense_Mutation | c.1338C>G | p.Phe446Leu | p.F446L | Q5SRH9 | protein_coding | tolerated(0.49) | benign(0.001) | TCGA-C8-A26Y-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
TTC39A | SNV | Missense_Mutation | rs774585007 | c.1171N>G | p.Ile391Val | p.I391V | Q5SRH9 | protein_coding | tolerated(1) | benign(0.006) | TCGA-D8-A1XL-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine+cyclophosphamide+tamoxifen | SD |
TTC39A | insertion | Frame_Shift_Ins | novel | c.239_240insAAGTGGTGTGGGT | p.Ala81SerfsTer43 | p.A81Sfs*43 | Q5SRH9 | protein_coding | TCGA-BH-A0BJ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | ||
TTC39A | insertion | Nonsense_Mutation | novel | c.237_238insTGATATTTCCGTTGGTTTTGAGCTTC | p.Leu80Ter | p.L80* | Q5SRH9 | protein_coding | TCGA-BH-A0BJ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | ||
TTC39A | SNV | Missense_Mutation | c.567N>G | p.Ile189Met | p.I189M | Q5SRH9 | protein_coding | tolerated(0.3) | benign(0.201) | TCGA-EK-A3GK-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
TTC39A | SNV | Missense_Mutation | rs746175223 | c.1573N>A | p.Glu525Lys | p.E525K | Q5SRH9 | protein_coding | deleterious(0) | probably_damaging(0.922) | TCGA-VS-A8EL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
TTC39A | SNV | Missense_Mutation | c.789G>T | p.Glu263Asp | p.E263D | Q5SRH9 | protein_coding | tolerated(0.12) | benign(0.118) | TCGA-A6-6781-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | oxaliplatin | SD | |
TTC39A | SNV | Missense_Mutation | rs368894146 | c.1559G>A | p.Arg520His | p.R520H | Q5SRH9 | protein_coding | tolerated(0.32) | benign(0.009) | TCGA-AA-3864-01 | Colorectum | colon adenocarcinoma | Male | >=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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