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Gene: TMOD1 |
Gene summary for TMOD1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TMOD1 | Gene ID | 7111 |
| Gene name | tropomodulin 1 | |
| Gene Alias | D9S57E | |
| Cytomap | 9q22.33 | |
| Gene Type | protein-coding | GO ID | GO:0001654 | UniProtAcc | P28289 |
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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 |
| 7111 | TMOD1 | HTA11_4255_2000001011 | Human | Colorectum | SER | 3.03e-06 | 3.30e-01 | 0.0446 |
| 7111 | TMOD1 | HTA11_8622_2000001021 | Human | Colorectum | SER | 1.95e-07 | 2.81e-01 | 0.0528 |
| 7111 | TMOD1 | HTA11_7663_2000001011 | Human | Colorectum | SER | 6.29e-03 | 2.25e-01 | 0.0131 |
| 7111 | TMOD1 | HTA11_10623_2000001011 | Human | Colorectum | AD | 8.98e-03 | 1.61e-01 | -0.0177 |
| 7111 | TMOD1 | HTA11_6818_2000001011 | Human | Colorectum | AD | 6.21e-21 | 8.35e-01 | 0.0112 |
| 7111 | TMOD1 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 1.82e-03 | 1.05e-01 | 0.3859 |
| 7111 | TMOD1 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 2.24e-13 | 2.34e-01 | 0.3005 |
| 7111 | TMOD1 | HTA12-15-2 | Human | Pancreas | PDAC | 4.58e-06 | 5.74e-01 | 0.2315 |
| 7111 | TMOD1 | HTA12-23-1 | Human | Pancreas | PDAC | 3.96e-05 | 6.36e-01 | 0.3405 |
| 7111 | TMOD1 | HTA12-25-1 | Human | Pancreas | PDAC | 2.48e-10 | 8.24e-01 | 0.313 |
| 7111 | TMOD1 | HTA12-26-1 | Human | Pancreas | PDAC | 3.69e-12 | 6.32e-01 | 0.3728 |
| 7111 | TMOD1 | HTA12-29-1 | Human | Pancreas | PDAC | 2.01e-48 | 9.76e-01 | 0.3722 |
| 7111 | TMOD1 | HTA12-30-1 | Human | Pancreas | PDAC | 4.45e-02 | 8.25e-01 | 0.3671 |
| 7111 | TMOD1 | HTA12-32-1 | Human | Pancreas | PDAC | 1.09e-02 | 8.55e-01 | 0.3624 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer |
| ∗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:19029031 | Colorectum | SER | regulation of supramolecular fiber organization | 114/2897 | 383/18723 | 7.32e-13 | 1.95e-10 | 114 |
| GO:00308321 | Colorectum | SER | regulation of actin filament length | 69/2897 | 189/18723 | 9.76e-13 | 2.39e-10 | 69 |
| GO:00308331 | Colorectum | SER | regulation of actin filament polymerization | 64/2897 | 172/18723 | 2.42e-12 | 5.70e-10 | 64 |
| GO:00329701 | Colorectum | SER | regulation of actin filament-based process | 115/2897 | 397/18723 | 4.16e-12 | 8.80e-10 | 115 |
| GO:00322711 | Colorectum | SER | regulation of protein polymerization | 78/2897 | 233/18723 | 5.71e-12 | 1.17e-09 | 78 |
| GO:00512581 | Colorectum | SER | protein polymerization | 91/2897 | 297/18723 | 2.72e-11 | 5.06e-09 | 91 |
| GO:00432541 | Colorectum | SER | regulation of protein-containing complex assembly | 119/2897 | 428/18723 | 3.34e-11 | 5.86e-09 | 119 |
| GO:00329561 | Colorectum | SER | regulation of actin cytoskeleton organization | 104/2897 | 358/18723 | 3.68e-11 | 6.11e-09 | 104 |
| GO:00224111 | Colorectum | SER | cellular component disassembly | 114/2897 | 443/18723 | 1.17e-08 | 9.59e-07 | 114 |
| GO:00020641 | Colorectum | SER | epithelial cell development | 64/2897 | 220/18723 | 1.96e-07 | 1.10e-05 | 64 |
| GO:00106391 | Colorectum | SER | negative regulation of organelle organization | 90/2897 | 348/18723 | 3.14e-07 | 1.69e-05 | 90 |
| GO:00322721 | Colorectum | SER | negative regulation of protein polymerization | 31/2897 | 80/18723 | 3.67e-07 | 1.96e-05 | 31 |
| GO:00308371 | Colorectum | SER | negative regulation of actin filament polymerization | 27/2897 | 65/18723 | 4.00e-07 | 2.06e-05 | 27 |
| GO:19029041 | Colorectum | SER | negative regulation of supramolecular fiber organization | 50/2897 | 167/18723 | 1.63e-06 | 7.23e-05 | 50 |
| GO:00329841 | Colorectum | SER | protein-containing complex disassembly | 61/2897 | 224/18723 | 4.17e-06 | 1.60e-04 | 61 |
| GO:00514941 | Colorectum | SER | negative regulation of cytoskeleton organization | 48/2897 | 163/18723 | 4.34e-06 | 1.63e-04 | 48 |
| GO:00313331 | Colorectum | SER | negative regulation of protein-containing complex assembly | 43/2897 | 141/18723 | 5.03e-06 | 1.86e-04 | 43 |
| GO:00300421 | Colorectum | SER | actin filament depolymerization | 23/2897 | 59/18723 | 1.02e-05 | 3.34e-04 | 23 |
| GO:00308341 | Colorectum | SER | regulation of actin filament depolymerization | 21/2897 | 54/18723 | 2.57e-05 | 7.07e-04 | 21 |
| GO:00516931 | Colorectum | SER | actin filament capping | 16/2897 | 41/18723 | 2.21e-04 | 3.89e-03 | 16 |
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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 |
| TMOD1 | SNV | Missense_Mutation | c.199C>A | p.Leu67Ile | p.L67I | P28289 | protein_coding | deleterious(0) | probably_damaging(0.991) | TCGA-BH-A0E7-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| TMOD1 | SNV | Missense_Mutation | c.724N>C | p.Tyr242His | p.Y242H | P28289 | protein_coding | tolerated(0.54) | benign(0) | TCGA-BH-A18G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| TMOD1 | SNV | Missense_Mutation | rs767885123 | c.718N>A | p.Val240Met | p.V240M | P28289 | protein_coding | deleterious(0.04) | possibly_damaging(0.761) | TCGA-EK-A2PG-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD |
| TMOD1 | SNV | Missense_Mutation | novel | c.895N>A | p.Glu299Lys | p.E299K | P28289 | protein_coding | deleterious(0.01) | probably_damaging(0.998) | TCGA-VS-A959-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD |
| TMOD1 | SNV | Missense_Mutation | rs771595062 | c.398N>T | p.Ala133Val | p.A133V | P28289 | protein_coding | deleterious(0) | probably_damaging(0.938) | TCGA-AA-3971-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | folinic | CR |
| TMOD1 | SNV | Missense_Mutation | rs770906034 | c.178G>A | p.Gly60Ser | p.G60S | P28289 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
| TMOD1 | SNV | Missense_Mutation | rs760447981 | c.341C>T | p.Pro114Leu | p.P114L | P28289 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-AA-A01D-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Chemotherapy | capecitabine | PD |
| TMOD1 | SNV | Missense_Mutation | novel | c.460T>C | p.Ser154Pro | p.S154P | P28289 | protein_coding | tolerated(0.11) | benign(0.071) | TCGA-AY-6196-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Unknown | Unknown | SD |
| TMOD1 | SNV | Missense_Mutation | c.247N>T | p.Asp83Tyr | p.D83Y | P28289 | protein_coding | deleterious(0.01) | probably_damaging(1) | TCGA-AY-A69D-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| TMOD1 | SNV | Missense_Mutation | novel | c.24G>T | p.Glu8Asp | p.E8D | P28289 | protein_coding | tolerated(0.18) | benign(0.191) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
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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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