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Gene: TMOD2 |
Gene summary for TMOD2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TMOD2 | Gene ID | 29767 |
| Gene name | tropomodulin 2 | |
| Gene Alias | N-TMOD | |
| Cytomap | 15q21.2 | |
| Gene Type | protein-coding | GO ID | GO:0003008 | UniProtAcc | Q9NZR1 |
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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 |
| 29767 | TMOD2 | HCC1 | Human | Liver | HCC | 2.29e-04 | 1.68e+00 | 0.5336 |
| 29767 | TMOD2 | HCC2 | Human | Liver | HCC | 4.23e-15 | 1.87e+00 | 0.5341 |
| 29767 | TMOD2 | HCC5 | Human | Liver | HCC | 5.87e-06 | 6.65e-01 | 0.4932 |
| 29767 | TMOD2 | S028 | Human | Liver | HCC | 5.94e-09 | 4.31e-01 | 0.2503 |
| 29767 | TMOD2 | S029 | Human | Liver | HCC | 3.01e-06 | 3.52e-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:002241112 | Liver | HCC | cellular component disassembly | 282/7958 | 443/18723 | 1.02e-19 | 1.38e-17 | 282 |
| GO:004325422 | Liver | HCC | regulation of protein-containing complex assembly | 264/7958 | 428/18723 | 5.47e-16 | 4.39e-14 | 264 |
| GO:005125822 | Liver | HCC | protein polymerization | 182/7958 | 297/18723 | 4.17e-11 | 1.58e-09 | 182 |
| GO:190290322 | Liver | HCC | regulation of supramolecular fiber organization | 224/7958 | 383/18723 | 1.54e-10 | 5.33e-09 | 224 |
| GO:000701522 | Liver | HCC | actin filament organization | 252/7958 | 442/18723 | 3.83e-10 | 1.25e-08 | 252 |
| GO:001063912 | Liver | HCC | negative regulation of organelle organization | 204/7958 | 348/18723 | 7.67e-10 | 2.37e-08 | 204 |
| GO:003298411 | Liver | HCC | protein-containing complex disassembly | 138/7958 | 224/18723 | 5.59e-09 | 1.46e-07 | 138 |
| GO:003253522 | Liver | HCC | regulation of cellular component size | 217/7958 | 383/18723 | 1.28e-08 | 3.14e-07 | 217 |
| GO:003227122 | Liver | HCC | regulation of protein polymerization | 141/7958 | 233/18723 | 2.00e-08 | 4.72e-07 | 141 |
| GO:003297022 | Liver | HCC | regulation of actin filament-based process | 222/7958 | 397/18723 | 3.81e-08 | 8.30e-07 | 222 |
| GO:003295622 | Liver | HCC | regulation of actin cytoskeleton organization | 202/7958 | 358/18723 | 6.18e-08 | 1.29e-06 | 202 |
| GO:003133312 | Liver | HCC | negative regulation of protein-containing complex assembly | 91/7958 | 141/18723 | 1.01e-07 | 1.98e-06 | 91 |
| GO:000815422 | Liver | HCC | actin polymerization or depolymerization | 130/7958 | 218/18723 | 2.31e-07 | 4.14e-06 | 130 |
| GO:003004122 | Liver | HCC | actin filament polymerization | 116/7958 | 191/18723 | 2.66e-07 | 4.68e-06 | 116 |
| GO:011005322 | Liver | HCC | regulation of actin filament organization | 158/7958 | 278/18723 | 9.01e-07 | 1.37e-05 | 158 |
| GO:003083212 | Liver | HCC | regulation of actin filament length | 113/7958 | 189/18723 | 1.16e-06 | 1.71e-05 | 113 |
| GO:003083322 | Liver | HCC | regulation of actin filament polymerization | 104/7958 | 172/18723 | 1.46e-06 | 2.08e-05 | 104 |
| GO:000806412 | Liver | HCC | regulation of actin polymerization or depolymerization | 112/7958 | 188/18723 | 1.65e-06 | 2.31e-05 | 112 |
| GO:003103222 | Liver | HCC | actomyosin structure organization | 109/7958 | 196/18723 | 1.39e-04 | 1.13e-03 | 109 |
| GO:190290412 | Liver | HCC | negative regulation of supramolecular fiber organization | 90/7958 | 167/18723 | 1.90e-03 | 9.69e-03 | 90 |
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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 |
| 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 |
| TMOD2 | SNV | Missense_Mutation | c.769N>G | p.Thr257Ala | p.T257A | Q9NZR1 | protein_coding | deleterious(0) | benign(0.007) | TCGA-AA-3966-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| TMOD2 | SNV | Missense_Mutation | rs760070721 | c.1024N>T | p.Arg342Cys | p.R342C | Q9NZR1 | protein_coding | deleterious(0) | possibly_damaging(0.777) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| TMOD2 | SNV | Missense_Mutation | c.340N>G | p.Thr114Ala | p.T114A | Q9NZR1 | protein_coding | deleterious(0.05) | benign(0.03) | TCGA-CA-6718-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | PD | |
| TMOD2 | SNV | Missense_Mutation | c.401T>A | p.Leu134His | p.L134H | Q9NZR1 | protein_coding | deleterious(0) | probably_damaging(0.988) | TCGA-G4-6311-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | oxaliplatin | SD | |
| TMOD2 | deletion | Frame_Shift_Del | c.39delN | p.Asn14ThrfsTer16 | p.N14Tfs*16 | Q9NZR1 | protein_coding | TCGA-D5-6926-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | 5-fluorouracil | SD | |||
| TMOD2 | SNV | Missense_Mutation | c.709N>T | p.Arg237Cys | p.R237C | Q9NZR1 | protein_coding | deleterious(0.02) | probably_damaging(0.978) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
| TMOD2 | SNV | Missense_Mutation | c.1052G>T | p.Arg351Met | p.R351M | Q9NZR1 | protein_coding | deleterious_low_confidence(0.01) | benign(0.332) | TCGA-AP-A051-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| TMOD2 | SNV | Missense_Mutation | novel | c.850N>A | p.Leu284Met | p.L284M | Q9NZR1 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AP-A1DV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| TMOD2 | SNV | Missense_Mutation | c.887T>C | p.Leu296Ser | p.L296S | Q9NZR1 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AX-A0J0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| TMOD2 | SNV | Missense_Mutation | c.709N>T | p.Arg237Cys | p.R237C | Q9NZR1 | protein_coding | deleterious(0.02) | probably_damaging(0.978) | TCGA-B5-A11E-01 | Endometrium | uterine corpus endometrioid carcinoma | 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 |
| Page: 1 |
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