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Gene: TMEM38A |
Gene summary for TMEM38A |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TMEM38A | Gene ID | 79041 |
| Gene name | transmembrane protein 38A | |
| Gene Alias | TRIC-A | |
| Cytomap | 19p13.11 | |
| Gene Type | protein-coding | GO ID | GO:0003008 | UniProtAcc | Q9H6F2 |
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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 |
| 79041 | TMEM38A | HCC1_Meng | Human | Liver | HCC | 2.87e-30 | 7.24e-02 | 0.0246 |
| 79041 | TMEM38A | HCC2_Meng | Human | Liver | HCC | 3.68e-06 | 7.11e-02 | 0.0107 |
| 79041 | TMEM38A | HCC1 | Human | Liver | HCC | 4.04e-09 | 1.11e+00 | 0.5336 |
| 79041 | TMEM38A | HCC2 | Human | Liver | HCC | 5.76e-22 | 2.44e+00 | 0.5341 |
| 79041 | TMEM38A | HCC5 | Human | Liver | HCC | 1.53e-08 | 1.09e+00 | 0.4932 |
| 79041 | TMEM38A | S028 | Human | Liver | HCC | 1.67e-09 | 3.94e-01 | 0.2503 |
| 79041 | TMEM38A | S029 | Human | Liver | HCC | 1.25e-06 | 3.57e-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). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:000702911 | Liver | HCC | endoplasmic reticulum organization | 64/7958 | 87/18723 | 3.92e-09 | 1.04e-07 | 64 |
| GO:005123521 | Liver | HCC | maintenance of location | 185/7958 | 327/18723 | 1.70e-07 | 3.12e-06 | 185 |
| GO:005165112 | Liver | HCC | maintenance of location in cell | 119/7958 | 214/18723 | 7.11e-05 | 6.39e-04 | 119 |
| GO:001407421 | Liver | HCC | response to purine-containing compound | 84/7958 | 148/18723 | 3.19e-04 | 2.26e-03 | 84 |
| GO:00432791 | Liver | HCC | response to alkaloid | 62/7958 | 115/18723 | 8.79e-03 | 3.42e-02 | 62 |
| GO:0010882 | Liver | HCC | regulation of cardiac muscle contraction by calcium ion signaling | 18/7958 | 27/18723 | 9.75e-03 | 3.66e-02 | 18 |
| GO:0010881 | Liver | HCC | regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion | 15/7958 | 22/18723 | 1.35e-02 | 4.80e-02 | 15 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| Page: 1 |
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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. |
| Page: 1 |
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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 |
| TMEM38A | SNV | Missense_Mutation | novel | c.262N>A | p.Leu88Met | p.L88M | Q9H6F2 | protein_coding | deleterious(0.04) | probably_damaging(0.939) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| TMEM38A | SNV | Missense_Mutation | novel | c.698N>G | p.His233Arg | p.H233R | Q9H6F2 | protein_coding | tolerated(0.41) | probably_damaging(0.998) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| TMEM38A | SNV | Missense_Mutation | novel | c.272N>T | p.Ser91Leu | p.S91L | Q9H6F2 | protein_coding | deleterious(0) | possibly_damaging(0.666) | TCGA-C5-A1MP-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| TMEM38A | SNV | Missense_Mutation | c.394N>A | p.Val132Met | p.V132M | Q9H6F2 | protein_coding | deleterious(0.04) | benign(0.054) | TCGA-CK-6746-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| TMEM38A | SNV | Missense_Mutation | rs577226448 | c.802N>A | p.Gly268Ser | p.G268S | Q9H6F2 | protein_coding | tolerated(0.94) | benign(0.029) | TCGA-D5-6529-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Chemotherapy | oxaliplatinum+ | SD |
| TMEM38A | SNV | Missense_Mutation | rs147713228 | c.827N>T | p.Ser276Leu | p.S276L | Q9H6F2 | protein_coding | tolerated(0.06) | benign(0.028) | TCGA-D5-6928-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| TMEM38A | SNV | Missense_Mutation | c.387N>T | p.Lys129Asn | p.K129N | Q9H6F2 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-AG-3892-01 | Colorectum | rectum adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| TMEM38A | SNV | Missense_Mutation | novel | c.90C>A | p.Phe30Leu | p.F30L | Q9H6F2 | protein_coding | deleterious(0) | benign(0.003) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| TMEM38A | SNV | Missense_Mutation | novel | c.319A>G | p.Lys107Glu | p.K107E | Q9H6F2 | protein_coding | deleterious(0.03) | probably_damaging(0.992) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| TMEM38A | SNV | Missense_Mutation | rs374515747 | c.866G>A | p.Gly289Asp | p.G289D | Q9H6F2 | protein_coding | tolerated(0.17) | probably_damaging(0.999) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | 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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