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Gene: PALM3 |
Gene summary for PALM3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PALM3 | Gene ID | 342979 |
| Gene name | paralemmin 3 | |
| Gene Alias | PALM3 | |
| Cytomap | 19p13.12 | |
| Gene Type | protein-coding | GO ID | GO:0001959 | UniProtAcc | A6NDB9 |
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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 |
| 342979 | PALM3 | male-WTA | Human | Thyroid | PTC | 6.38e-17 | 2.47e-01 | 0.1037 |
| 342979 | PALM3 | PTC01 | Human | Thyroid | PTC | 2.31e-12 | 2.24e-01 | 0.1899 |
| 342979 | PALM3 | PTC03 | Human | Thyroid | PTC | 3.32e-08 | 2.89e-01 | 0.1784 |
| 342979 | PALM3 | PTC05 | Human | Thyroid | PTC | 2.70e-19 | 6.59e-01 | 0.2065 |
| 342979 | PALM3 | PTC06 | Human | Thyroid | PTC | 6.32e-23 | 5.40e-01 | 0.2057 |
| 342979 | PALM3 | PTC07 | Human | Thyroid | PTC | 1.13e-11 | 2.24e-01 | 0.2044 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 |
| Cervix | N_HPV |  |
| Endometrium | AEH |  |
| Endometrium | EEC |  |
| Prostate | BPH |  |
| Prostate | Tumor |  |
| ∗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:00607597 | Thyroid | PTC | regulation of response to cytokine stimulus | 70/5968 | 162/18723 | 1.54e-03 | 8.58e-03 | 70 |
| GO:00019596 | Thyroid | PTC | regulation of cytokine-mediated signaling pathway | 64/5968 | 150/18723 | 3.43e-03 | 1.66e-02 | 64 |
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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 |
| PALM3 | SNV | Missense_Mutation | rs61749577 | c.1912N>G | p.Pro638Ala | p.P638A | A6NDB9 | protein_coding | tolerated(0.06) | benign(0.147) | TCGA-AC-A3QQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PALM3 | SNV | Missense_Mutation | novel | c.1975N>A | p.Ala659Thr | p.A659T | A6NDB9 | protein_coding | tolerated(0.09) | probably_damaging(0.969) | TCGA-D8-A1XZ-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | tamoxiphen+anastrozolum | SD |
| PALM3 | SNV | Missense_Mutation | novel | c.1713N>T | p.Glu571Asp | p.E571D | A6NDB9 | protein_coding | deleterious(0.01) | possibly_damaging(0.556) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| PALM3 | SNV | Missense_Mutation | c.694G>A | p.Ala232Thr | p.A232T | A6NDB9 | protein_coding | deleterious(0.05) | possibly_damaging(0.879) | TCGA-EK-A2RK-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PALM3 | SNV | Missense_Mutation | c.470C>G | p.Ser157Cys | p.S157C | A6NDB9 | protein_coding | deleterious(0) | probably_damaging(0.947) | TCGA-JW-A5VL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| PALM3 | SNV | Missense_Mutation | c.267N>G | p.Phe89Leu | p.F89L | A6NDB9 | protein_coding | tolerated(0.08) | probably_damaging(0.994) | TCGA-JW-A852-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | PD | |
| PALM3 | SNV | Missense_Mutation | novel | c.1693A>G | p.Asn565Asp | p.N565D | A6NDB9 | protein_coding | tolerated_low_confidence(0.07) | benign(0) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| PALM3 | SNV | Missense_Mutation | c.1963N>A | p.Glu655Lys | p.E655K | A6NDB9 | protein_coding | deleterious(0) | probably_damaging(0.978) | TCGA-G4-6320-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | oxaliplatin | SD | |
| PALM3 | SNV | Missense_Mutation | novel | c.617A>C | p.Glu206Ala | p.E206A | A6NDB9 | protein_coding | tolerated(0.11) | benign(0.059) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| PALM3 | deletion | Frame_Shift_Del | c.841delN | p.Val281TrpfsTer12 | p.V281Wfs*12 | A6NDB9 | protein_coding | TCGA-A6-6780-01 | Colorectum | colon adenocarcinoma | 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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