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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 | GSM4909282 | Human | Breast | IDC | 5.23e-07 | 3.66e-01 | -0.0288 |
5763 | PTMS | GSM4909286 | Human | Breast | IDC | 9.66e-09 | 2.37e-01 | 0.1081 |
5763 | PTMS | GSM4909287 | Human | Breast | IDC | 6.56e-29 | 6.00e-01 | 0.2057 |
5763 | PTMS | GSM4909288 | Human | Breast | IDC | 1.24e-09 | 4.49e-01 | 0.0988 |
5763 | PTMS | GSM4909293 | Human | Breast | IDC | 4.57e-59 | 8.13e-01 | 0.1581 |
5763 | PTMS | GSM4909294 | Human | Breast | IDC | 3.32e-15 | 3.02e-01 | 0.2022 |
5763 | PTMS | GSM4909296 | Human | Breast | IDC | 2.96e-27 | -5.83e-01 | 0.1524 |
5763 | PTMS | GSM4909297 | Human | Breast | IDC | 1.17e-15 | -3.29e-01 | 0.1517 |
5763 | PTMS | GSM4909298 | Human | Breast | IDC | 7.62e-19 | 4.86e-01 | 0.1551 |
5763 | PTMS | GSM4909304 | Human | Breast | IDC | 2.39e-49 | 7.88e-01 | 0.1636 |
5763 | PTMS | GSM4909306 | Human | Breast | IDC | 4.14e-04 | 3.12e-01 | 0.1564 |
5763 | PTMS | GSM4909307 | Human | Breast | IDC | 1.13e-02 | -3.29e-01 | 0.1569 |
5763 | PTMS | GSM4909311 | Human | Breast | IDC | 5.52e-35 | -3.86e-01 | 0.1534 |
5763 | PTMS | GSM4909312 | Human | Breast | IDC | 7.64e-13 | -2.40e-01 | 0.1552 |
5763 | PTMS | GSM4909316 | Human | Breast | IDC | 4.96e-03 | -4.04e-01 | 0.21 |
5763 | PTMS | GSM4909317 | Human | Breast | IDC | 5.04e-06 | 3.00e-01 | 0.1355 |
5763 | PTMS | GSM4909318 | Human | Breast | IDC | 6.97e-13 | 5.75e-01 | 0.2031 |
5763 | PTMS | GSM4909319 | Human | Breast | IDC | 2.24e-54 | 2.02e-01 | 0.1563 |
5763 | PTMS | GSM4909320 | Human | Breast | IDC | 4.92e-09 | 1.11e-01 | 0.1575 |
5763 | PTMS | GSM4909321 | Human | Breast | IDC | 8.52e-15 | 3.48e-02 | 0.1559 |
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Transcriptomic changes along malignancy continuum. |
∗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: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 |
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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 |
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 |
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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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