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Gene: PLSCR1 |
Gene summary for PLSCR1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PLSCR1 | Gene ID | 5359 |
| Gene name | phospholipid scramblase 1 | |
| Gene Alias | MMTRA1B | |
| Cytomap | 3q24 | |
| Gene Type | protein-coding | GO ID | GO:0001775 | UniProtAcc | O15162 |
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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 |
| 5359 | PLSCR1 | CA_HPV_1 | Human | Cervix | CC | 1.12e-05 | 3.42e-01 | 0.0264 |
| 5359 | PLSCR1 | CA_HPV_2 | Human | Cervix | CC | 2.97e-07 | 3.55e-01 | 0.0391 |
| 5359 | PLSCR1 | HSIL_HPV_2 | Human | Cervix | HSIL_HPV | 2.24e-04 | 2.52e-01 | 0.0208 |
| 5359 | PLSCR1 | CCI_2 | Human | Cervix | CC | 1.67e-14 | 2.08e+00 | 0.5249 |
| 5359 | PLSCR1 | CCI_3 | Human | Cervix | CC | 5.22e-03 | 6.56e-01 | 0.516 |
| 5359 | PLSCR1 | Tumor | Human | Cervix | CC | 3.75e-37 | 7.32e-01 | 0.1241 |
| 5359 | PLSCR1 | sample3 | Human | Cervix | CC | 1.51e-48 | 8.09e-01 | 0.1387 |
| 5359 | PLSCR1 | H2 | Human | Cervix | HSIL_HPV | 9.92e-05 | 2.74e-01 | 0.0632 |
| 5359 | PLSCR1 | T3 | Human | Cervix | CC | 3.37e-46 | 8.09e-01 | 0.1389 |
| 5359 | PLSCR1 | HTA11_3410_2000001011 | Human | Colorectum | AD | 4.33e-11 | -5.09e-01 | 0.0155 |
| 5359 | PLSCR1 | HTA11_696_2000001011 | Human | Colorectum | AD | 1.30e-05 | -4.14e-01 | -0.1464 |
| 5359 | PLSCR1 | HTA11_866_2000001011 | Human | Colorectum | AD | 3.20e-02 | -3.08e-01 | -0.1001 |
| 5359 | PLSCR1 | HTA11_10711_2000001011 | Human | Colorectum | AD | 3.12e-03 | -4.89e-01 | 0.0338 |
| 5359 | PLSCR1 | HTA11_7696_3000711011 | Human | Colorectum | AD | 1.50e-05 | -3.64e-01 | 0.0674 |
| 5359 | PLSCR1 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 5.30e-11 | -4.83e-01 | 0.3005 |
| 5359 | PLSCR1 | F007 | Human | Colorectum | FAP | 1.35e-06 | -5.09e-01 | 0.1176 |
| 5359 | PLSCR1 | A001-C-207 | Human | Colorectum | FAP | 3.54e-02 | -2.79e-01 | 0.1278 |
| 5359 | PLSCR1 | A015-C-203 | Human | Colorectum | FAP | 9.96e-21 | -3.69e-01 | -0.1294 |
| 5359 | PLSCR1 | A015-C-204 | Human | Colorectum | FAP | 7.17e-06 | -3.95e-01 | -0.0228 |
| 5359 | PLSCR1 | A014-C-040 | Human | Colorectum | FAP | 1.98e-03 | -5.14e-01 | -0.1184 |
| Page: 1 2 3 4 5 6 7 8 9 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 | ||
| 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 | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| 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:00508173 | Liver | Cyst | coagulation | 16/496 | 222/18723 | 2.97e-04 | 9.67e-03 | 16 |
| GO:00065753 | Liver | Cyst | cellular modified amino acid metabolic process | 13/496 | 188/18723 | 1.55e-03 | 3.61e-02 | 13 |
| GO:00160328 | Lung | IAC | viral process | 94/2061 | 415/18723 | 5.11e-12 | 4.27e-09 | 94 |
| GO:00190588 | Lung | IAC | viral life cycle | 77/2061 | 317/18723 | 1.23e-11 | 4.83e-09 | 77 |
| GO:00521268 | Lung | IAC | movement in host environment | 48/2061 | 175/18723 | 1.30e-09 | 2.21e-07 | 48 |
| GO:00517018 | Lung | IAC | biological process involved in interaction with host | 52/2061 | 203/18723 | 3.74e-09 | 5.84e-07 | 52 |
| GO:00467188 | Lung | IAC | viral entry into host cell | 41/2061 | 144/18723 | 6.27e-09 | 9.08e-07 | 41 |
| GO:00444098 | Lung | IAC | entry into host | 42/2061 | 151/18723 | 8.80e-09 | 1.19e-06 | 42 |
| GO:00444038 | Lung | IAC | biological process involved in symbiotic interaction | 63/2061 | 290/18723 | 8.57e-08 | 8.34e-06 | 63 |
| GO:00420608 | Lung | IAC | wound healing | 76/2061 | 422/18723 | 1.01e-05 | 3.23e-04 | 76 |
| GO:00507928 | Lung | IAC | regulation of viral process | 37/2061 | 164/18723 | 1.56e-05 | 4.51e-04 | 37 |
| GO:00190798 | Lung | IAC | viral genome replication | 30/2061 | 131/18723 | 7.15e-05 | 1.51e-03 | 30 |
| GO:00457875 | Lung | IAC | positive regulation of cell cycle | 56/2061 | 313/18723 | 1.69e-04 | 3.01e-03 | 56 |
| GO:19039008 | Lung | IAC | regulation of viral life cycle | 31/2061 | 148/18723 | 3.07e-04 | 4.89e-03 | 31 |
| GO:00096156 | Lung | IAC | response to virus | 61/2061 | 367/18723 | 6.75e-04 | 9.12e-03 | 61 |
| GO:00100388 | Lung | IAC | response to metal ion | 61/2061 | 373/18723 | 1.02e-03 | 1.22e-02 | 61 |
| GO:00900684 | Lung | IAC | positive regulation of cell cycle process | 42/2061 | 236/18723 | 1.15e-03 | 1.35e-02 | 42 |
| GO:00159142 | Lung | IAC | phospholipid transport | 20/2061 | 96/18723 | 3.58e-03 | 3.00e-02 | 20 |
| GO:00321033 | Lung | IAC | positive regulation of response to external stimulus | 65/2061 | 427/18723 | 4.28e-03 | 3.41e-02 | 65 |
| GO:00027643 | Lung | IAC | immune response-regulating signaling pathway | 70/2061 | 468/18723 | 4.79e-03 | 3.72e-02 | 70 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 |
| 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 |
| PLSCR1 | SNV | Missense_Mutation | novel | c.19C>A | p.Gln7Lys | p.Q7K | O15162 | protein_coding | deleterious_low_confidence(0.02) | possibly_damaging(0.522) | TCGA-LL-A50Y-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | CR |
| PLSCR1 | insertion | Frame_Shift_Ins | novel | c.597_598insTGGAAACTAGGATTTCCAC | p.Gly200TrpfsTer29 | p.G200Wfs*29 | O15162 | protein_coding | TCGA-BH-A0DP-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | arimidex | SD | ||
| PLSCR1 | SNV | Missense_Mutation | novel | c.506G>A | p.Gly169Asp | p.G169D | O15162 | protein_coding | tolerated(0.29) | probably_damaging(0.968) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| PLSCR1 | SNV | Missense_Mutation | novel | c.820N>T | p.Ala274Ser | p.A274S | O15162 | protein_coding | tolerated(0.12) | benign(0.276) | TCGA-JW-A69B-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| PLSCR1 | SNV | Missense_Mutation | rs377240309 | c.837C>G | p.Ile279Met | p.I279M | O15162 | protein_coding | deleterious(0.01) | possibly_damaging(0.714) | TCGA-VS-A953-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | PD |
| PLSCR1 | SNV | Missense_Mutation | c.761N>A | p.Cys254Tyr | p.C254Y | O15162 | protein_coding | tolerated(0.41) | benign(0) | TCGA-A6-2682-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | 5 | PD | |
| PLSCR1 | SNV | Missense_Mutation | rs769076735 | c.452N>A | p.Arg151Gln | p.R151Q | O15162 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-AA-3977-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| PLSCR1 | SNV | Missense_Mutation | novel | c.652N>G | p.Thr218Ala | p.T218A | O15162 | protein_coding | tolerated(0.08) | benign(0.381) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PLSCR1 | SNV | Missense_Mutation | novel | c.850N>T | p.Asp284Tyr | p.D284Y | O15162 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| PLSCR1 | SNV | Missense_Mutation | novel | c.392N>G | p.Ile131Ser | p.I131S | O15162 | protein_coding | deleterious(0) | probably_damaging(0.988) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| Page: 1 2 3 4 |
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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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