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Gene: TUBGCP4 |
Gene summary for TUBGCP4 |
Gene summary. |
Gene information | Species | Human | Gene symbol | TUBGCP4 | Gene ID | 27229 |
Gene name | tubulin gamma complex associated protein 4 | |
Gene Alias | 76P | |
Cytomap | 15q15.3 | |
Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | Q9UGJ1 |
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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 |
27229 | TUBGCP4 | HCC1_Meng | Human | Liver | HCC | 7.83e-34 | 5.35e-02 | 0.0246 |
27229 | TUBGCP4 | HCC2_Meng | Human | Liver | HCC | 1.26e-14 | 7.61e-02 | 0.0107 |
27229 | TUBGCP4 | HCC1 | Human | Liver | HCC | 8.07e-11 | 2.41e+00 | 0.5336 |
27229 | TUBGCP4 | HCC2 | Human | Liver | HCC | 7.87e-21 | 2.82e+00 | 0.5341 |
27229 | TUBGCP4 | HCC5 | Human | Liver | HCC | 1.45e-15 | 1.21e+00 | 0.4932 |
27229 | TUBGCP4 | S015 | Human | Liver | HCC | 6.45e-03 | 1.68e-01 | 0.2375 |
27229 | TUBGCP4 | S016 | Human | Liver | HCC | 2.69e-02 | 1.57e-01 | 0.2243 |
27229 | TUBGCP4 | S027 | Human | Liver | HCC | 1.29e-04 | 4.01e-01 | 0.2446 |
27229 | TUBGCP4 | S028 | Human | Liver | HCC | 7.18e-13 | 4.12e-01 | 0.2503 |
27229 | TUBGCP4 | S029 | Human | Liver | HCC | 3.82e-03 | 2.02e-01 | 0.2581 |
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Transcriptomic changes along malignancy continuum. |
Tissue | Expression Dynamics | Abbreviation |
Liver | HCC: Hepatocellular carcinoma | |
NAFLD: Non-alcoholic fatty liver disease |
∗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:005125822 | Liver | HCC | protein polymerization | 182/7958 | 297/18723 | 4.17e-11 | 1.58e-09 | 182 |
GO:000705111 | Liver | HCC | spindle organization | 116/7958 | 184/18723 | 1.40e-08 | 3.40e-07 | 116 |
GO:005122511 | Liver | HCC | spindle assembly | 75/7958 | 117/18723 | 1.92e-06 | 2.67e-05 | 75 |
GO:0046785 | Liver | HCC | microtubule polymerization | 51/7958 | 83/18723 | 3.82e-04 | 2.61e-03 | 51 |
GO:0007020 | Liver | HCC | microtubule nucleation | 25/7958 | 35/18723 | 5.05e-04 | 3.29e-03 | 25 |
GO:00311222 | Liver | HCC | cytoplasmic microtubule organization | 35/7958 | 56/18723 | 2.00e-03 | 1.01e-02 | 35 |
GO:0031109 | Liver | HCC | microtubule polymerization or depolymerization | 68/7958 | 122/18723 | 2.14e-03 | 1.08e-02 | 68 |
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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 |
TUBGCP4 | SNV | Missense_Mutation | novel | c.259C>T | p.Arg87Trp | p.R87W | Q9UGJ1 | protein_coding | deleterious(0) | probably_damaging(0.993) | TCGA-4R-AA8I-01 | Liver | liver hepatocellular carcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
TUBGCP4 | SNV | Missense_Mutation | novel | c.213C>A | p.His71Gln | p.H71Q | Q9UGJ1 | protein_coding | tolerated(0.66) | benign(0.001) | TCGA-DD-AAVQ-01 | Liver | liver hepatocellular carcinoma | Male | <65 | I/II | Unknown | Unknown | PD |
TUBGCP4 | SNV | Missense_Mutation | c.1037A>T | p.Glu346Val | p.E346V | Q9UGJ1 | protein_coding | deleterious(0) | benign(0.262) | TCGA-50-5930-01 | Lung | lung adenocarcinoma | Male | <65 | III/IV | Chemotherapy | taxotere | PD | |
TUBGCP4 | SNV | Missense_Mutation | c.31N>A | p.Gly11Arg | p.G11R | Q9UGJ1 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-75-7027-01 | Lung | lung adenocarcinoma | Male | Unknown | I/II | Unknown | Unknown | PD | |
TUBGCP4 | SNV | Missense_Mutation | novel | c.661N>C | p.Asp221His | p.D221H | Q9UGJ1 | protein_coding | deleterious(0.01) | benign(0.373) | TCGA-86-A4JF-01 | Lung | lung adenocarcinoma | Male | <65 | I/II | Chemotherapy | unknown | PD |
TUBGCP4 | SNV | Missense_Mutation | rs776182570 | c.1546N>T | p.Arg516Cys | p.R516C | Q9UGJ1 | protein_coding | deleterious(0.02) | possibly_damaging(0.739) | TCGA-21-1080-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
TUBGCP4 | SNV | Missense_Mutation | c.1576N>C | p.Asp526His | p.D526H | Q9UGJ1 | protein_coding | deleterious(0) | probably_damaging(0.984) | TCGA-43-6770-01 | Lung | lung squamous cell carcinoma | Female | <65 | I/II | Vaccine | recprame+as15 | SD | |
TUBGCP4 | SNV | Missense_Mutation | novel | c.328N>C | p.Glu110Gln | p.E110Q | Q9UGJ1 | protein_coding | tolerated(0.09) | possibly_damaging(0.674) | TCGA-60-2721-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
TUBGCP4 | SNV | Missense_Mutation | novel | c.379N>T | p.Asp127Tyr | p.D127Y | Q9UGJ1 | protein_coding | deleterious(0.01) | benign(0.065) | TCGA-77-8136-01 | Lung | lung squamous cell carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
TUBGCP4 | SNV | Missense_Mutation | novel | c.733N>C | p.Glu245Gln | p.E245Q | Q9UGJ1 | protein_coding | tolerated(0.12) | possibly_damaging(0.727) | TCGA-92-7340-01 | Lung | lung squamous cell carcinoma | Female | <65 | I/II | Chemotherapy | cisplatin | 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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