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Gene: PTMS |
Gene summary for PTMS |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PTMS | Gene ID | 5763 |
| Gene name | parathymosin | |
| Gene Alias | ParaT | |
| Cytomap | 12p13.31 | |
| Gene Type | protein-coding | GO ID | GO:0002376 | UniProtAcc | F5GXR3 |
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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 |
| 5763 | PTMS | C21 | Human | Oral cavity | OSCC | 2.23e-49 | 2.81e+00 | 0.2678 |
| 5763 | PTMS | C30 | Human | Oral cavity | OSCC | 3.99e-52 | 4.04e+00 | 0.3055 |
| 5763 | PTMS | C38 | Human | Oral cavity | OSCC | 1.93e-18 | 3.10e+00 | 0.172 |
| 5763 | PTMS | C43 | Human | Oral cavity | OSCC | 7.61e-57 | 1.73e+00 | 0.1704 |
| 5763 | PTMS | C46 | Human | Oral cavity | OSCC | 1.30e-44 | 1.91e+00 | 0.1673 |
| 5763 | PTMS | C51 | Human | Oral cavity | OSCC | 5.64e-28 | 2.61e+00 | 0.2674 |
| 5763 | PTMS | C57 | Human | Oral cavity | OSCC | 3.14e-05 | 1.44e+00 | 0.1679 |
| 5763 | PTMS | C06 | Human | Oral cavity | OSCC | 9.45e-23 | 3.42e+00 | 0.2699 |
| 5763 | PTMS | C07 | Human | Oral cavity | OSCC | 5.55e-19 | 2.88e+00 | 0.2491 |
| 5763 | PTMS | C08 | Human | Oral cavity | OSCC | 2.09e-66 | 2.60e+00 | 0.1919 |
| 5763 | PTMS | C86 | Human | Oral cavity | OSCC | 1.56e-10 | 1.49e+00 | 0.161 |
| 5763 | PTMS | C09 | Human | Oral cavity | OSCC | 8.49e-16 | 1.15e+00 | 0.1431 |
| 5763 | PTMS | LN22 | Human | Oral cavity | OSCC | 1.55e-14 | 2.01e+00 | 0.1733 |
| 5763 | PTMS | LN38 | Human | Oral cavity | OSCC | 2.08e-23 | 2.49e+00 | 0.168 |
| 5763 | PTMS | LN46 | Human | Oral cavity | OSCC | 1.24e-17 | 1.64e+00 | 0.1666 |
| 5763 | PTMS | LP15 | Human | Oral cavity | LP | 2.01e-20 | 2.74e+00 | 0.2174 |
| 5763 | PTMS | LP17 | Human | Oral cavity | LP | 1.98e-17 | 2.75e+00 | 0.2349 |
| 5763 | PTMS | EOLP-1 | Human | Oral cavity | EOLP | 1.17e-02 | -1.01e-01 | -0.0202 |
| 5763 | PTMS | NEOLP-3 | Human | Oral cavity | NEOLP | 1.06e-04 | 1.22e-01 | -0.0191 |
| 5763 | PTMS | SYSMH1 | Human | Oral cavity | OSCC | 1.48e-30 | 1.21e+00 | 0.1127 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| 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 | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid 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:00062602 | Cervix | CC | DNA replication | 48/2311 | 260/18723 | 2.70e-03 | 1.85e-02 | 48 |
| GO:0006260 | Colorectum | MSI-H | DNA replication | 31/1319 | 260/18723 | 2.83e-03 | 3.63e-02 | 31 |
| GO:00062604 | Esophagus | ESCC | DNA replication | 181/8552 | 260/18723 | 3.55e-15 | 2.05e-13 | 181 |
| GO:00062601 | Liver | HCC | DNA replication | 146/7958 | 260/18723 | 5.68e-06 | 7.02e-05 | 146 |
| GO:00062603 | Oral cavity | OSCC | DNA replication | 159/7305 | 260/18723 | 3.25e-13 | 1.59e-11 | 159 |
| GO:000626011 | Oral cavity | LP | DNA replication | 97/4623 | 260/18723 | 3.67e-06 | 7.75e-05 | 97 |
| GO:00062605 | Skin | AK | DNA replication | 40/1910 | 260/18723 | 5.49e-03 | 3.03e-02 | 40 |
| GO:000626012 | Skin | cSCC | DNA replication | 106/4864 | 260/18723 | 1.18e-07 | 2.77e-06 | 106 |
| GO:00062606 | Thyroid | PTC | DNA replication | 114/5968 | 260/18723 | 3.09e-05 | 2.95e-04 | 114 |
| GO:000626013 | Thyroid | ATC | DNA replication | 124/6293 | 260/18723 | 1.58e-06 | 1.93e-05 | 124 |
| Page: 1 |
| 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 |
| PTMS | SNV | Missense_Mutation | novel | c.181N>T | p.Pro61Ser | p.P61S | protein_coding | deleterious_low_confidence(0) | unknown(0) | TCGA-A8-A094-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PTMS | SNV | Missense_Mutation | c.293N>T | p.Arg98Met | p.R98M | protein_coding | unknown(0) | TCGA-AA-3715-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |||
| PTMS | SNV | Missense_Mutation | rs770854499 | c.311G>A | p.Arg104His | p.R104H | protein_coding | unknown(0) | TCGA-NH-A5IV-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| PTMS | SNV | Missense_Mutation | c.281N>G | p.Lys94Arg | p.K94R | protein_coding | unknown(0) | TCGA-WS-AB45-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |||
| PTMS | SNV | Missense_Mutation | rs763082021 | c.310N>T | p.Arg104Cys | p.R104C | protein_coding | unknown(0) | TCGA-A5-A0GW-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| PTMS | SNV | Missense_Mutation | c.60G>T | p.Lys20Asn | p.K20N | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.978) | TCGA-AX-A2HC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | PD | ||
| PTMS | SNV | Missense_Mutation | c.281N>G | p.Lys94Arg | p.K94R | protein_coding | unknown(0) | TCGA-AX-A2HJ-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |||
| PTMS | SNV | Missense_Mutation | rs372653257 | c.98G>A | p.Arg33Gln | p.R33Q | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.947) | TCGA-BK-A6W3-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| PTMS | SNV | Missense_Mutation | c.281N>G | p.Lys94Arg | p.K94R | protein_coding | unknown(0) | TCGA-D1-A16F-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |||
| PTMS | SNV | Missense_Mutation | novel | c.246N>T | p.Glu82Asp | p.E82D | protein_coding | unknown(0) | TCGA-EY-A215-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 |
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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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