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Gene: PHLDA1 |
Gene summary for PHLDA1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PHLDA1 | Gene ID | 22822 |
| Gene name | pleckstrin homology like domain family A member 1 | |
| Gene Alias | DT1P1B11 | |
| Cytomap | 12q21.2 | |
| Gene Type | protein-coding | GO ID | GO:0006807 | UniProtAcc | Q8WV24 |
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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 |
| 22822 | PHLDA1 | GSM4909281 | Human | Breast | IDC | 3.80e-10 | -5.43e-01 | 0.21 |
| 22822 | PHLDA1 | GSM4909282 | Human | Breast | IDC | 4.36e-14 | -5.80e-01 | -0.0288 |
| 22822 | PHLDA1 | GSM4909285 | Human | Breast | IDC | 2.40e-11 | -5.09e-01 | 0.21 |
| 22822 | PHLDA1 | GSM4909286 | Human | Breast | IDC | 8.28e-28 | -6.96e-01 | 0.1081 |
| 22822 | PHLDA1 | GSM4909287 | Human | Breast | IDC | 2.49e-10 | -4.84e-01 | 0.2057 |
| 22822 | PHLDA1 | GSM4909291 | Human | Breast | IDC | 9.31e-15 | -6.52e-01 | 0.1753 |
| 22822 | PHLDA1 | GSM4909292 | Human | Breast | IDC | 2.15e-04 | -7.09e-01 | 0.1236 |
| 22822 | PHLDA1 | GSM4909293 | Human | Breast | IDC | 6.93e-27 | -6.87e-01 | 0.1581 |
| 22822 | PHLDA1 | GSM4909294 | Human | Breast | IDC | 4.09e-28 | -6.51e-01 | 0.2022 |
| 22822 | PHLDA1 | GSM4909296 | Human | Breast | IDC | 1.13e-19 | -6.13e-01 | 0.1524 |
| 22822 | PHLDA1 | GSM4909297 | Human | Breast | IDC | 5.53e-10 | -4.08e-01 | 0.1517 |
| 22822 | PHLDA1 | GSM4909298 | Human | Breast | IDC | 1.49e-04 | -3.63e-01 | 0.1551 |
| 22822 | PHLDA1 | GSM4909301 | Human | Breast | IDC | 3.96e-29 | -6.98e-01 | 0.1577 |
| 22822 | PHLDA1 | GSM4909302 | Human | Breast | IDC | 1.62e-18 | -5.90e-01 | 0.1545 |
| 22822 | PHLDA1 | GSM4909303 | Human | Breast | IDC | 2.08e-02 | -5.00e-01 | 0.0438 |
| 22822 | PHLDA1 | GSM4909304 | Human | Breast | IDC | 5.02e-25 | -6.84e-01 | 0.1636 |
| 22822 | PHLDA1 | GSM4909306 | Human | Breast | IDC | 7.53e-09 | -5.44e-01 | 0.1564 |
| 22822 | PHLDA1 | GSM4909307 | Human | Breast | IDC | 2.67e-09 | -5.27e-01 | 0.1569 |
| 22822 | PHLDA1 | GSM4909308 | Human | Breast | IDC | 2.45e-11 | -5.22e-01 | 0.158 |
| 22822 | PHLDA1 | GSM4909309 | Human | Breast | IDC | 4.06e-09 | -4.89e-01 | 0.0483 |
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| 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 | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| GC |  | CAG: Chronic atrophic gastritis |
| CAG with IM: Chronic atrophic gastritis with intestinal metaplasia | ||
| CSG: Chronic superficial gastritis | ||
| GC: Gastric cancer | ||
| SIM: Severe intestinal metaplasia | ||
| WIM: Wild intestinal metaplasia | ||
| 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:00091002 | Esophagus | ESCC | glycoprotein metabolic process | 226/8552 | 387/18723 | 2.64e-07 | 3.94e-06 | 226 |
| GO:00091012 | Esophagus | ESCC | glycoprotein biosynthetic process | 181/8552 | 317/18723 | 2.54e-05 | 2.15e-04 | 181 |
| GO:0009100 | Liver | HCC | glycoprotein metabolic process | 193/7958 | 387/18723 | 1.89e-03 | 9.62e-03 | 193 |
| GO:00091001 | Oral cavity | OSCC | glycoprotein metabolic process | 185/7305 | 387/18723 | 2.37e-04 | 1.54e-03 | 185 |
| GO:00091011 | Oral cavity | OSCC | glycoprotein biosynthetic process | 151/7305 | 317/18723 | 1.01e-03 | 5.26e-03 | 151 |
| GO:00091013 | Thyroid | PTC | glycoprotein biosynthetic process | 123/5968 | 317/18723 | 5.05e-03 | 2.33e-02 | 123 |
| GO:00091003 | Thyroid | PTC | glycoprotein metabolic process | 147/5968 | 387/18723 | 5.87e-03 | 2.64e-02 | 147 |
| GO:000910011 | Thyroid | ATC | glycoprotein metabolic process | 153/6293 | 387/18723 | 7.90e-03 | 3.06e-02 | 153 |
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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 |
| PHLDA1 | insertion | Frame_Shift_Ins | novel | c.509_510insA | p.Cys171ValfsTer246 | p.C171Vfs*246 | Q8WV24 | protein_coding | TCGA-D5-6927-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | ||
| PHLDA1 | deletion | Frame_Shift_Del | c.1088_1091delACTC | p.His363ArgfsTer93 | p.H363Rfs*93 | Q8WV24 | protein_coding | TCGA-F4-6856-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Ancillary | leucovorin | CR | |||
| PHLDA1 | insertion | Frame_Shift_Ins | novel | c.753_754insAC | p.Phe252ThrfsTer5 | p.F252Tfs*5 | Q8WV24 | protein_coding | TCGA-AH-6903-01 | Colorectum | rectum adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5-fu | CR | ||
| PHLDA1 | SNV | Missense_Mutation | c.1028N>A | p.Pro343His | p.P343H | Q8WV24 | protein_coding | deleterious_low_confidence(0.01) | probably_damaging(0.998) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD | |
| PHLDA1 | SNV | Missense_Mutation | novel | c.800N>T | p.Pro267Leu | p.P267L | Q8WV24 | protein_coding | deleterious_low_confidence(0.04) | benign(0.127) | TCGA-AP-A1DK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PHLDA1 | SNV | Missense_Mutation | c.799N>G | p.Pro267Ala | p.P267A | Q8WV24 | protein_coding | tolerated_low_confidence(0.18) | benign(0.12) | TCGA-D1-A0ZS-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| PHLDA1 | SNV | Missense_Mutation | c.974N>A | p.Pro325His | p.P325H | Q8WV24 | protein_coding | deleterious_low_confidence(0) | possibly_damaging(0.694) | TCGA-D1-A103-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PHLDA1 | SNV | Missense_Mutation | novel | c.1015N>T | p.Pro339Ser | p.P339S | Q8WV24 | protein_coding | deleterious_low_confidence(0.02) | benign(0.009) | TCGA-EO-A3KX-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PHLDA1 | SNV | Missense_Mutation | novel | c.1187G>A | p.Ser396Asn | p.S396N | Q8WV24 | protein_coding | deleterious_low_confidence(0) | possibly_damaging(0.559) | TCGA-FI-A2D0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PHLDA1 | SNV | Missense_Mutation | c.172G>A | p.Asp58Asn | p.D58N | Q8WV24 | protein_coding | tolerated_low_confidence(0.06) | benign(0.001) | TCGA-G3-A3CK-01 | Liver | liver hepatocellular carcinoma | Male | <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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