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Gene: PALD1 |
Gene summary for PALD1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PALD1 | Gene ID | 27143 |
| Gene name | phosphatase domain containing paladin 1 | |
| Gene Alias | KIAA1274 | |
| Cytomap | 10q22.1 | |
| Gene Type | protein-coding | GO ID | GO:0006464 | UniProtAcc | A0A024QZM5 |
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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 |
| 27143 | PALD1 | HTA11_866_3004761011 | Human | Colorectum | AD | 2.47e-04 | 1.19e-01 | 0.096 |
| 27143 | PALD1 | HTA11_4255_2000001011 | Human | Colorectum | SER | 3.40e-02 | 2.17e-01 | 0.0446 |
| 27143 | PALD1 | HTA11_8622_2000001021 | Human | Colorectum | SER | 4.45e-03 | 1.99e-01 | 0.0528 |
| 27143 | PALD1 | HTA11_6818_2000001021 | Human | Colorectum | AD | 1.37e-04 | 1.89e-01 | 0.0588 |
| 27143 | PALD1 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 5.28e-34 | 5.99e-01 | 0.294 |
| 27143 | PALD1 | HTA11_99999965062_69753 | Human | Colorectum | MSI-H | 3.42e-04 | 4.27e-01 | 0.3487 |
| 27143 | PALD1 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 1.93e-12 | 3.74e-01 | 0.281 |
| 27143 | PALD1 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 1.09e-36 | 7.81e-01 | 0.3859 |
| 27143 | PALD1 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 5.79e-04 | 1.93e-01 | 0.2585 |
| 27143 | PALD1 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 9.89e-26 | 5.08e-01 | 0.3005 |
| 27143 | PALD1 | A001-C-108 | Human | Colorectum | FAP | 5.45e-05 | 2.49e-01 | -0.0272 |
| 27143 | PALD1 | A001-C-104 | Human | Colorectum | FAP | 8.94e-11 | 3.68e-01 | 0.0184 |
| 27143 | PALD1 | A015-C-106 | Human | Colorectum | FAP | 4.07e-04 | 2.21e-01 | -0.0511 |
| 27143 | PALD1 | A001-C-014 | Human | Colorectum | FAP | 1.92e-04 | 2.22e-01 | 0.0135 |
| 27143 | PALD1 | F034 | Human | Colorectum | FAP | 3.85e-03 | 1.66e-01 | -0.0665 |
| 27143 | PALD1 | CRC-1-8810 | Human | Colorectum | CRC | 3.85e-03 | 2.10e-01 | 0.6257 |
| 27143 | PALD1 | CRC-3-11773 | Human | Colorectum | CRC | 3.83e-12 | 3.86e-01 | 0.2564 |
| Page: 1 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 |
| ∗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:0016311 | Colorectum | AD | dephosphorylation | 123/3918 | 417/18723 | 1.84e-05 | 3.82e-04 | 123 |
| GO:0006470 | Colorectum | AD | protein dephosphorylation | 88/3918 | 281/18723 | 2.56e-05 | 4.89e-04 | 88 |
| GO:00064701 | Colorectum | SER | protein dephosphorylation | 65/2897 | 281/18723 | 4.44e-04 | 6.51e-03 | 65 |
| GO:00163111 | Colorectum | SER | dephosphorylation | 86/2897 | 417/18723 | 2.73e-03 | 2.46e-02 | 86 |
| GO:00064702 | Colorectum | MSS | protein dephosphorylation | 73/3467 | 281/18723 | 1.15e-03 | 1.12e-02 | 73 |
| GO:00163112 | Colorectum | MSS | dephosphorylation | 101/3467 | 417/18723 | 1.98e-03 | 1.70e-02 | 101 |
| GO:00064703 | Colorectum | MSI-H | protein dephosphorylation | 34/1319 | 281/18723 | 1.43e-03 | 2.22e-02 | 34 |
| GO:00163113 | Colorectum | FAP | dephosphorylation | 95/2622 | 417/18723 | 7.07e-07 | 3.32e-05 | 95 |
| GO:00064704 | Colorectum | FAP | protein dephosphorylation | 69/2622 | 281/18723 | 1.47e-06 | 6.39e-05 | 69 |
| GO:0035335 | Colorectum | FAP | peptidyl-tyrosine dephosphorylation | 23/2622 | 97/18723 | 6.95e-03 | 4.26e-02 | 23 |
| GO:00163114 | Colorectum | CRC | dephosphorylation | 79/2078 | 417/18723 | 1.27e-06 | 7.21e-05 | 79 |
| GO:00064705 | Colorectum | CRC | protein dephosphorylation | 57/2078 | 281/18723 | 4.49e-06 | 1.87e-04 | 57 |
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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 |
| PALD1 | SNV | Missense_Mutation | rs143037794 | c.97G>A | p.Val33Ile | p.V33I | Q9ULE6 | protein_coding | tolerated(0.05) | benign(0.02) | TCGA-A8-A06R-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | 5-fluorouracil | CR |
| PALD1 | SNV | Missense_Mutation | novel | c.73G>A | p.Gly25Ser | p.G25S | Q9ULE6 | protein_coding | tolerated(0.21) | benign(0.091) | TCGA-AQ-A7U7-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Targeted Molecular therapy | rituximab | CR |
| PALD1 | SNV | Missense_Mutation | novel | c.1424C>A | p.Pro475Gln | p.P475Q | Q9ULE6 | protein_coding | deleterious(0) | possibly_damaging(0.81) | TCGA-B6-A400-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| PALD1 | SNV | Missense_Mutation | c.1372C>T | p.Pro458Ser | p.P458S | Q9ULE6 | protein_coding | tolerated(0.08) | possibly_damaging(0.578) | TCGA-BH-A0E7-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| PALD1 | SNV | Missense_Mutation | rs146249112 | c.2443N>A | p.Glu815Lys | p.E815K | Q9ULE6 | protein_coding | deleterious(0.01) | benign(0.216) | TCGA-BH-A42V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PALD1 | SNV | Missense_Mutation | c.1750C>T | p.His584Tyr | p.H584Y | Q9ULE6 | protein_coding | deleterious(0.01) | benign(0.006) | TCGA-GM-A2D9-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| PALD1 | SNV | Missense_Mutation | novel | c.58G>A | p.Gly20Ser | p.G20S | Q9ULE6 | protein_coding | tolerated(0.43) | benign(0.031) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| PALD1 | SNV | Missense_Mutation | novel | c.217G>A | p.Asp73Asn | p.D73N | Q9ULE6 | protein_coding | deleterious(0.01) | possibly_damaging(0.905) | TCGA-C5-A902-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
| PALD1 | SNV | Missense_Mutation | rs368916968 | c.1328N>T | p.Pro443Leu | p.P443L | Q9ULE6 | protein_coding | tolerated(0.06) | benign(0.02) | TCGA-DS-A0VK-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | carboplatin | PD |
| PALD1 | SNV | Missense_Mutation | novel | c.898G>C | p.Asp300His | p.D300H | Q9ULE6 | protein_coding | deleterious(0.01) | possibly_damaging(0.849) | TCGA-JW-A5VL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 9 |
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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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