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Gene: PDLIM5 |
Gene summary for PDLIM5 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PDLIM5 | Gene ID | 10611 |
| Gene name | PDZ and LIM domain 5 | |
| Gene Alias | ENH | |
| Cytomap | 4q22.3 | |
| Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | Q96HC4 |
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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 |
| 10611 | PDLIM5 | GSM4909282 | Human | Breast | IDC | 6.96e-06 | -3.35e-01 | -0.0288 |
| 10611 | PDLIM5 | GSM4909285 | Human | Breast | IDC | 1.36e-11 | -4.31e-01 | 0.21 |
| 10611 | PDLIM5 | GSM4909286 | Human | Breast | IDC | 7.58e-05 | -2.91e-01 | 0.1081 |
| 10611 | PDLIM5 | GSM4909293 | Human | Breast | IDC | 1.51e-10 | -4.20e-01 | 0.1581 |
| 10611 | PDLIM5 | GSM4909294 | Human | Breast | IDC | 2.23e-16 | -4.69e-01 | 0.2022 |
| 10611 | PDLIM5 | GSM4909296 | Human | Breast | IDC | 8.65e-16 | -3.89e-01 | 0.1524 |
| 10611 | PDLIM5 | GSM4909297 | Human | Breast | IDC | 2.88e-12 | -4.11e-01 | 0.1517 |
| 10611 | PDLIM5 | GSM4909298 | Human | Breast | IDC | 1.23e-04 | 9.56e-02 | 0.1551 |
| 10611 | PDLIM5 | GSM4909304 | Human | Breast | IDC | 4.33e-02 | -2.89e-01 | 0.1636 |
| 10611 | PDLIM5 | GSM4909306 | Human | Breast | IDC | 6.30e-05 | -3.61e-01 | 0.1564 |
| 10611 | PDLIM5 | GSM4909311 | Human | Breast | IDC | 4.62e-24 | -4.38e-01 | 0.1534 |
| 10611 | PDLIM5 | GSM4909312 | Human | Breast | IDC | 3.34e-09 | -3.16e-01 | 0.1552 |
| 10611 | PDLIM5 | GSM4909315 | Human | Breast | IDC | 4.30e-10 | -4.20e-01 | 0.21 |
| 10611 | PDLIM5 | GSM4909319 | Human | Breast | IDC | 4.80e-27 | -4.47e-01 | 0.1563 |
| 10611 | PDLIM5 | GSM4909320 | Human | Breast | IDC | 9.16e-05 | -4.28e-01 | 0.1575 |
| 10611 | PDLIM5 | GSM4909321 | Human | Breast | IDC | 2.85e-25 | -5.30e-01 | 0.1559 |
| 10611 | PDLIM5 | ctrl6 | Human | Breast | Precancer | 5.08e-07 | 5.07e-01 | -0.0061 |
| 10611 | PDLIM5 | NCCBC14 | Human | Breast | DCIS | 2.88e-08 | -2.69e-01 | 0.2021 |
| 10611 | PDLIM5 | NCCBC2 | Human | Breast | DCIS | 8.01e-03 | 2.02e-01 | 0.1554 |
| 10611 | PDLIM5 | NCCBC3 | Human | Breast | DCIS | 1.53e-03 | -2.84e-01 | 0.1198 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 |
| 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 | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid 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 | ||
| 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:001097518 | Skin | SCCIS | regulation of neuron projection development | 44/919 | 445/18723 | 8.33e-06 | 3.03e-04 | 44 |
| GO:005080814 | Skin | SCCIS | synapse organization | 42/919 | 426/18723 | 1.43e-05 | 4.70e-04 | 42 |
| GO:001470616 | Skin | SCCIS | striated muscle tissue development | 38/919 | 384/18723 | 3.33e-05 | 8.88e-04 | 38 |
| GO:004269215 | Skin | SCCIS | muscle cell differentiation | 37/919 | 384/18723 | 7.38e-05 | 1.71e-03 | 37 |
| GO:006099615 | Skin | SCCIS | dendritic spine development | 15/919 | 99/18723 | 9.34e-05 | 2.10e-03 | 15 |
| GO:004858817 | Skin | SCCIS | developmental cell growth | 25/919 | 234/18723 | 2.23e-04 | 4.13e-03 | 25 |
| GO:190188816 | Skin | SCCIS | regulation of cell junction assembly | 22/919 | 204/18723 | 4.55e-04 | 7.28e-03 | 22 |
| GO:001489613 | Skin | SCCIS | muscle hypertrophy | 14/919 | 104/18723 | 5.54e-04 | 8.47e-03 | 14 |
| GO:010602714 | Skin | SCCIS | neuron projection organization | 13/919 | 93/18723 | 6.00e-04 | 9.01e-03 | 13 |
| GO:00487384 | Skin | SCCIS | cardiac muscle tissue development | 24/919 | 236/18723 | 6.06e-04 | 9.04e-03 | 24 |
| GO:00350513 | Skin | SCCIS | cardiocyte differentiation | 18/919 | 156/18723 | 6.58e-04 | 9.61e-03 | 18 |
| GO:001489712 | Skin | SCCIS | striated muscle hypertrophy | 13/919 | 102/18723 | 1.44e-03 | 1.63e-02 | 13 |
| GO:009706114 | Skin | SCCIS | dendritic spine organization | 11/919 | 84/18723 | 2.63e-03 | 2.48e-02 | 11 |
| GO:000330012 | Skin | SCCIS | cardiac muscle hypertrophy | 12/919 | 99/18723 | 3.31e-03 | 2.97e-02 | 12 |
| GO:0055007 | Skin | SCCIS | cardiac muscle cell differentiation | 14/919 | 125/18723 | 3.31e-03 | 2.97e-02 | 14 |
| GO:005114616 | Skin | SCCIS | striated muscle cell differentiation | 25/919 | 283/18723 | 3.38e-03 | 3.01e-02 | 25 |
| GO:009917313 | Skin | SCCIS | postsynapse organization | 17/919 | 168/18723 | 3.77e-03 | 3.27e-02 | 17 |
| GO:003526512 | Skin | SCCIS | organ growth | 17/919 | 178/18723 | 6.73e-03 | 4.96e-02 | 17 |
| GO:001604925 | Skin | cSCC | cell growth | 173/4864 | 482/18723 | 7.21e-07 | 1.34e-05 | 173 |
| GO:006099622 | Skin | cSCC | dendritic spine development | 40/4864 | 99/18723 | 1.18e-03 | 7.70e-03 | 40 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 |
| 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 |
| PDLIM5 | M2MAC | Oral cavity | EOLP | LCN2,RFXAP,PITX1, etc. | 8.18e-02 |  |
| PDLIM5 | PLA | Oral cavity | LP | LCN2,RFXAP,PITX1, etc. | 4.72e-01 |  |
| PDLIM5 | M2MAC | Oral cavity | NEOLP | LCN2,RFXAP,PITX1, etc. | 1.12e-01 |  |
| PDLIM5 | cDC | Oral cavity | OSCC | LCN2,RFXAP,PITX1, etc. | 5.10e-01 |  |
| ∗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 |
| PDLIM5 | SNV | Missense_Mutation | c.160G>C | p.Asp54His | p.D54H | Q96HC4 | protein_coding | deleterious(0) | probably_damaging(0.964) | TCGA-PE-A5DE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | CR | |
| PDLIM5 | SNV | Missense_Mutation | c.151N>G | p.Leu51Val | p.L51V | Q96HC4 | protein_coding | tolerated(0.57) | benign(0.017) | TCGA-C5-A1BK-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| PDLIM5 | SNV | Missense_Mutation | novel | c.1148C>T | p.Ser383Phe | p.S383F | Q96HC4 | protein_coding | deleterious(0.01) | benign(0.311) | TCGA-EA-A3HU-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| PDLIM5 | SNV | Missense_Mutation | novel | c.82N>A | p.Leu28Met | p.L28M | Q96HC4 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-VS-A9U7-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| PDLIM5 | SNV | Missense_Mutation | novel | c.1387G>A | p.Ala463Thr | p.A463T | Q96HC4 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-5M-AAT6-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | PD |
| PDLIM5 | SNV | Missense_Mutation | rs201891054 | c.427N>T | p.Arg143Cys | p.R143C | Q96HC4 | protein_coding | deleterious(0.03) | possibly_damaging(0.764) | TCGA-A6-6654-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Chemotherapy | oxaliplatin | SD |
| PDLIM5 | SNV | Missense_Mutation | novel | c.218N>A | p.Cys73Tyr | p.C73Y | Q96HC4 | protein_coding | deleterious(0) | probably_damaging(0.972) | TCGA-A6-A565-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unspecific | 5FU | PD |
| PDLIM5 | SNV | Missense_Mutation | novel | c.1076N>C | p.Leu359Pro | p.L359P | Q96HC4 | protein_coding | tolerated(0.29) | benign(0.001) | TCGA-AA-3845-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| PDLIM5 | SNV | Missense_Mutation | novel | c.1334N>A | p.Arg445Gln | p.R445Q | Q96HC4 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| PDLIM5 | SNV | Missense_Mutation | c.1090N>G | p.Ser364Ala | p.S364A | Q96HC4 | protein_coding | tolerated(0.16) | benign(0.003) | TCGA-CM-5861-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | PD |
| Page: 1 2 3 4 5 |
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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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