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Gene: PTDSS1 |
Gene summary for PTDSS1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PTDSS1 | Gene ID | 9791 |
| Gene name | phosphatidylserine synthase 1 | |
| Gene Alias | LMHD | |
| Cytomap | 8q22.1 | |
| Gene Type | protein-coding | GO ID | GO:0006575 | UniProtAcc | P48651 |
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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 |
| 9791 | PTDSS1 | LZE2T | Human | Esophagus | ESCC | 2.08e-09 | 1.47e+00 | 0.082 |
| 9791 | PTDSS1 | LZE4T | Human | Esophagus | ESCC | 3.60e-32 | 1.47e+00 | 0.0811 |
| 9791 | PTDSS1 | LZE7T | Human | Esophagus | ESCC | 1.11e-08 | 6.50e-01 | 0.0667 |
| 9791 | PTDSS1 | LZE20T | Human | Esophagus | ESCC | 3.80e-05 | 3.27e-01 | 0.0662 |
| 9791 | PTDSS1 | LZE24T | Human | Esophagus | ESCC | 8.34e-27 | 8.05e-01 | 0.0596 |
| 9791 | PTDSS1 | LZE21T | Human | Esophagus | ESCC | 2.37e-09 | 6.16e-01 | 0.0655 |
| 9791 | PTDSS1 | LZE6T | Human | Esophagus | ESCC | 4.98e-05 | 2.03e-01 | 0.0845 |
| 9791 | PTDSS1 | P2T-E | Human | Esophagus | ESCC | 2.36e-31 | 5.83e-01 | 0.1177 |
| 9791 | PTDSS1 | P4T-E | Human | Esophagus | ESCC | 1.14e-22 | 8.30e-01 | 0.1323 |
| 9791 | PTDSS1 | P5T-E | Human | Esophagus | ESCC | 5.39e-23 | 7.29e-01 | 0.1327 |
| 9791 | PTDSS1 | P8T-E | Human | Esophagus | ESCC | 1.50e-19 | 1.66e-01 | 0.0889 |
| 9791 | PTDSS1 | P9T-E | Human | Esophagus | ESCC | 3.55e-32 | 9.85e-01 | 0.1131 |
| 9791 | PTDSS1 | P10T-E | Human | Esophagus | ESCC | 6.16e-43 | 8.14e-01 | 0.116 |
| 9791 | PTDSS1 | P11T-E | Human | Esophagus | ESCC | 4.05e-16 | 8.93e-01 | 0.1426 |
| 9791 | PTDSS1 | P12T-E | Human | Esophagus | ESCC | 2.59e-36 | 8.76e-01 | 0.1122 |
| 9791 | PTDSS1 | P15T-E | Human | Esophagus | ESCC | 7.14e-39 | 9.33e-01 | 0.1149 |
| 9791 | PTDSS1 | P16T-E | Human | Esophagus | ESCC | 3.16e-51 | 1.06e+00 | 0.1153 |
| 9791 | PTDSS1 | P17T-E | Human | Esophagus | ESCC | 2.60e-02 | 3.02e-01 | 0.1278 |
| 9791 | PTDSS1 | P19T-E | Human | Esophagus | ESCC | 6.89e-07 | 6.92e-01 | 0.1662 |
| 9791 | PTDSS1 | P20T-E | Human | Esophagus | ESCC | 1.45e-15 | 3.69e-01 | 0.1124 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 | ||
| 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:00086544 | Esophagus | ESCC | phospholipid biosynthetic process | 162/8552 | 253/18723 | 2.59e-09 | 5.73e-08 | 162 |
| GO:00464744 | Esophagus | ESCC | glycerophospholipid biosynthetic process | 135/8552 | 211/18723 | 5.75e-08 | 1.02e-06 | 135 |
| GO:00450175 | Esophagus | ESCC | glycerolipid biosynthetic process | 154/8552 | 252/18723 | 5.20e-07 | 6.96e-06 | 154 |
| GO:00066446 | Esophagus | ESCC | phospholipid metabolic process | 218/8552 | 383/18723 | 5.37e-06 | 5.59e-05 | 218 |
| GO:00066505 | Esophagus | ESCC | glycerophospholipid metabolic process | 174/8552 | 306/18723 | 4.92e-05 | 3.85e-04 | 174 |
| GO:00065757 | Esophagus | ESCC | cellular modified amino acid metabolic process | 112/8552 | 188/18723 | 8.31e-05 | 6.06e-04 | 112 |
| GO:00423986 | Esophagus | ESCC | cellular modified amino acid biosynthetic process | 34/8552 | 46/18723 | 9.39e-05 | 6.70e-04 | 34 |
| GO:00464864 | Esophagus | ESCC | glycerolipid metabolic process | 211/8552 | 392/18723 | 6.51e-04 | 3.46e-03 | 211 |
| GO:000657521 | Liver | HCC | cellular modified amino acid metabolic process | 119/7958 | 188/18723 | 6.47e-09 | 1.67e-07 | 119 |
| GO:00086542 | Liver | HCC | phospholipid biosynthetic process | 150/7958 | 253/18723 | 4.77e-08 | 1.03e-06 | 150 |
| GO:00066444 | Liver | HCC | phospholipid metabolic process | 214/7958 | 383/18723 | 7.25e-08 | 1.48e-06 | 214 |
| GO:004648611 | Liver | HCC | glycerolipid metabolic process | 215/7958 | 392/18723 | 4.54e-07 | 7.49e-06 | 215 |
| GO:004501711 | Liver | HCC | glycerolipid biosynthetic process | 143/7958 | 252/18723 | 3.27e-06 | 4.31e-05 | 143 |
| GO:00066504 | Liver | HCC | glycerophospholipid metabolic process | 168/7958 | 306/18723 | 7.27e-06 | 8.62e-05 | 168 |
| GO:004647411 | Liver | HCC | glycerophospholipid biosynthetic process | 121/7958 | 211/18723 | 9.12e-06 | 1.06e-04 | 121 |
| GO:004239821 | Liver | HCC | cellular modified amino acid biosynthetic process | 34/7958 | 46/18723 | 1.53e-05 | 1.67e-04 | 34 |
| GO:00086543 | Oral cavity | OSCC | phospholipid biosynthetic process | 130/7305 | 253/18723 | 3.96e-05 | 3.46e-04 | 130 |
| GO:00423985 | Oral cavity | OSCC | cellular modified amino acid biosynthetic process | 31/7305 | 46/18723 | 9.03e-05 | 6.88e-04 | 31 |
| GO:00464743 | Oral cavity | OSCC | glycerophospholipid biosynthetic process | 102/7305 | 211/18723 | 3.50e-03 | 1.48e-02 | 102 |
| GO:00066445 | Oral cavity | OSCC | phospholipid metabolic process | 175/7305 | 383/18723 | 4.21e-03 | 1.71e-02 | 175 |
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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 |
| PTDSS1 | SNV | Missense_Mutation | novel | c.210G>T | p.Trp70Cys | p.W70C | P48651 | protein_coding | deleterious(0.03) | benign(0.014) | TCGA-A8-A07R-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Ancillary | zoledronic | SD |
| PTDSS1 | SNV | Missense_Mutation | c.1012N>C | p.Tyr338His | p.Y338H | P48651 | protein_coding | deleterious(0) | probably_damaging(0.93) | TCGA-D8-A1XK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine+cyclophosphamide | SD | |
| PTDSS1 | SNV | Missense_Mutation | c.65N>A | p.Arg22Gln | p.R22Q | P48651 | protein_coding | tolerated(0.48) | benign(0.109) | TCGA-E9-A1N9-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| PTDSS1 | insertion | Frame_Shift_Ins | novel | c.891_892insAATATAAAAAACAAGAAACAGATTGCAGAACCTGTTA | p.Gln298AsnfsTer16 | p.Q298Nfs*16 | P48651 | protein_coding | TCGA-B6-A0IC-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| PTDSS1 | SNV | Missense_Mutation | novel | c.622N>T | p.Pro208Ser | p.P208S | P48651 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-EA-A3Y4-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| PTDSS1 | SNV | Missense_Mutation | novel | c.8C>A | p.Ser3Tyr | p.S3Y | P48651 | protein_coding | deleterious_low_confidence(0.02) | benign(0.102) | TCGA-VS-A8EK-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | PD |
| PTDSS1 | SNV | Missense_Mutation | c.41N>G | p.Asp14Gly | p.D14G | P48651 | protein_coding | deleterious(0.03) | benign(0.072) | TCGA-AA-3715-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
| PTDSS1 | SNV | Missense_Mutation | novel | c.14N>C | p.Val5Ala | p.V5A | P48651 | protein_coding | tolerated_low_confidence(0.92) | benign(0) | TCGA-AA-3947-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PTDSS1 | SNV | Missense_Mutation | novel | c.1061N>A | p.Cys354Tyr | p.C354Y | P48651 | protein_coding | deleterious(0) | probably_damaging(0.992) | TCGA-AA-3949-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| PTDSS1 | SNV | Missense_Mutation | c.281N>G | p.Thr94Ser | p.T94S | P48651 | protein_coding | deleterious(0.01) | possibly_damaging(0.71) | TCGA-AD-A5EJ-01 | Colorectum | colon adenocarcinoma | 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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