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Gene: PDLIM2 |
Gene summary for PDLIM2 |
Gene summary. |
Gene information | Species | Human | Gene symbol | PDLIM2 | Gene ID | 64236 |
Gene name | PDZ and LIM domain 2 | |
Gene Alias | MYSTIQUE | |
Cytomap | 8p21.3 | |
Gene Type | protein-coding | GO ID | GO:0006996 | UniProtAcc | Q96JY6 |
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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 |
64236 | PDLIM2 | HTA11_2487_2000001011 | Human | Colorectum | SER | 1.60e-12 | 4.02e-01 | -0.1808 |
64236 | PDLIM2 | HTA11_347_2000001011 | Human | Colorectum | AD | 3.45e-06 | 1.78e-01 | -0.1954 |
64236 | PDLIM2 | HTA11_2112_2000001011 | Human | Colorectum | SER | 1.50e-04 | 5.07e-01 | -0.2196 |
64236 | PDLIM2 | HTA11_696_2000001011 | Human | Colorectum | AD | 9.56e-07 | 1.59e-01 | -0.1464 |
64236 | PDLIM2 | HTA11_1391_2000001011 | Human | Colorectum | AD | 5.08e-04 | 1.43e-01 | -0.059 |
64236 | PDLIM2 | HTA11_2992_2000001011 | Human | Colorectum | SER | 1.72e-05 | 3.79e-01 | -0.1706 |
64236 | PDLIM2 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 2.92e-03 | 1.99e-01 | 0.2585 |
64236 | PDLIM2 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 9.04e-05 | 1.21e-01 | 0.3005 |
64236 | PDLIM2 | LZE4T | Human | Esophagus | ESCC | 9.50e-16 | 4.19e-01 | 0.0811 |
64236 | PDLIM2 | LZE24T | Human | Esophagus | ESCC | 2.26e-11 | 4.63e-01 | 0.0596 |
64236 | PDLIM2 | LZE21T | Human | Esophagus | ESCC | 7.54e-07 | 2.12e-01 | 0.0655 |
64236 | PDLIM2 | P2T-E | Human | Esophagus | ESCC | 7.68e-10 | 1.00e-01 | 0.1177 |
64236 | PDLIM2 | P4T-E | Human | Esophagus | ESCC | 1.44e-17 | 4.92e-01 | 0.1323 |
64236 | PDLIM2 | P5T-E | Human | Esophagus | ESCC | 1.17e-10 | 2.96e-01 | 0.1327 |
64236 | PDLIM2 | P8T-E | Human | Esophagus | ESCC | 7.78e-09 | 2.91e-01 | 0.0889 |
64236 | PDLIM2 | P9T-E | Human | Esophagus | ESCC | 1.92e-06 | 2.08e-01 | 0.1131 |
64236 | PDLIM2 | P10T-E | Human | Esophagus | ESCC | 8.51e-57 | 1.10e+00 | 0.116 |
64236 | PDLIM2 | P11T-E | Human | Esophagus | ESCC | 1.33e-06 | 1.64e-01 | 0.1426 |
64236 | PDLIM2 | P12T-E | Human | Esophagus | ESCC | 1.59e-27 | 6.32e-01 | 0.1122 |
64236 | PDLIM2 | P15T-E | Human | Esophagus | ESCC | 3.08e-10 | 3.22e-01 | 0.1149 |
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Transcriptomic changes along malignancy continuum. |
∗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). |
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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
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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 |
PDLIM2 | insertion | In_Frame_Ins | novel | c.1122_1123insTTCTTGACTTTTGACTTTTTGTTTCTAGCAGCTTCT | p.Ser374_Pro375insPheLeuThrPheAspPheLeuPheLeuAlaAlaSer | p.S374_P375insFLTFDFLFLAAS | Q96JY6 | protein_coding | TCGA-A8-A09D-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | CR | ||
PDLIM2 | deletion | Frame_Shift_Del | novel | c.1566delC | p.Ala523ProfsTer46 | p.A523Pfs*46 | Q96JY6 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | ||
PDLIM2 | SNV | Missense_Mutation | rs748585448 | c.979N>T | p.Arg327Trp | p.R327W | Q96JY6 | protein_coding | deleterious(0.02) | probably_damaging(0.99) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
PDLIM2 | SNV | Missense_Mutation | novel | c.1032N>G | p.Asp344Glu | p.D344E | Q96JY6 | protein_coding | tolerated(0.5) | benign(0.023) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
PDLIM2 | SNV | Missense_Mutation | rs201708972 | c.1207N>T | p.Arg403Cys | p.R403C | Q96JY6 | protein_coding | deleterious(0.02) | benign(0.007) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
PDLIM2 | SNV | Missense_Mutation | rs779427808 | c.1448N>A | p.Arg483Gln | p.R483Q | Q96JY6 | protein_coding | tolerated(0.07) | benign(0.23) | TCGA-C5-A7UH-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Chemotherapy | cisplatin | SD |
PDLIM2 | SNV | Missense_Mutation | rs762318482 | c.1666C>T | p.Arg556Cys | p.R556C | Q96JY6 | protein_coding | deleterious(0.01) | probably_damaging(0.999) | TCGA-A6-6781-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | oxaliplatin | SD |
PDLIM2 | SNV | Missense_Mutation | novel | c.869A>G | p.Asp290Gly | p.D290G | Q96JY6 | protein_coding | tolerated(0.25) | benign(0.026) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR |
PDLIM2 | SNV | Missense_Mutation | c.1151N>T | p.Ser384Ile | p.S384I | Q96JY6 | protein_coding | deleterious(0.01) | probably_damaging(0.979) | TCGA-CM-4743-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Chemotherapy | capecitabine | SD | |
PDLIM2 | SNV | Missense_Mutation | c.1728N>G | p.Phe576Leu | p.F576L | Q96JY6 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AG-A01W-01 | Colorectum | rectum adenocarcinoma | Female | >=65 | I/II | Chemotherapy | 5-fluorouracil | CR |
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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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