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Gene: PDLIM4 |
Gene summary for PDLIM4 |
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Gene information | Species | Human | Gene symbol | PDLIM4 | Gene ID | 8572 |
Gene name | PDZ and LIM domain 4 | |
Gene Alias | RIL | |
Cytomap | 5q31.1 | |
Gene Type | protein-coding | GO ID | GO:0006996 | UniProtAcc | A0A0S2Z4N4 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
8572 | PDLIM4 | brca10 | Human | Breast | Precancer | 6.54e-08 | 4.12e-01 | -0.0029 |
8572 | PDLIM4 | M1 | Human | Breast | IDC | 4.69e-07 | -3.78e-01 | 0.1577 |
8572 | PDLIM4 | NCCBC14 | Human | Breast | DCIS | 4.84e-07 | -3.23e-01 | 0.2021 |
8572 | PDLIM4 | NCCBC5 | Human | Breast | DCIS | 1.84e-07 | -3.18e-01 | 0.2046 |
8572 | PDLIM4 | P1 | Human | Breast | IDC | 4.63e-11 | -3.71e-01 | 0.1527 |
8572 | PDLIM4 | DCIS2 | Human | Breast | DCIS | 2.96e-59 | 5.40e-01 | 0.0085 |
8572 | PDLIM4 | AEH-subject1 | Human | Endometrium | AEH | 3.00e-09 | -3.07e-01 | -0.3059 |
8572 | PDLIM4 | AEH-subject2 | Human | Endometrium | AEH | 1.82e-03 | -2.59e-01 | -0.2525 |
8572 | PDLIM4 | AEH-subject3 | Human | Endometrium | AEH | 2.88e-04 | -1.85e-01 | -0.2576 |
8572 | PDLIM4 | AEH-subject4 | Human | Endometrium | AEH | 5.89e-07 | -3.41e-01 | -0.2657 |
8572 | PDLIM4 | AEH-subject5 | Human | Endometrium | AEH | 8.13e-20 | -4.52e-01 | -0.2953 |
8572 | PDLIM4 | EEC-subject1 | Human | Endometrium | EEC | 2.61e-10 | -3.15e-01 | -0.2682 |
8572 | PDLIM4 | EEC-subject2 | Human | Endometrium | EEC | 1.60e-14 | -3.49e-01 | -0.2607 |
8572 | PDLIM4 | EEC-subject3 | Human | Endometrium | EEC | 5.49e-24 | -4.11e-01 | -0.2525 |
8572 | PDLIM4 | EEC-subject4 | Human | Endometrium | EEC | 2.09e-11 | -3.86e-01 | -0.2571 |
8572 | PDLIM4 | EEC-subject5 | Human | Endometrium | EEC | 3.63e-04 | -2.53e-01 | -0.249 |
8572 | PDLIM4 | GSM5276934 | Human | Endometrium | EEC | 5.98e-11 | 3.95e-01 | -0.0913 |
8572 | PDLIM4 | GSM5276935 | Human | Endometrium | EEC | 1.12e-12 | -3.88e-01 | -0.123 |
8572 | PDLIM4 | GSM5276937 | Human | Endometrium | EEC | 6.66e-25 | 5.96e-01 | -0.0897 |
8572 | PDLIM4 | GSM6177620_NYU_UCEC1_lib1_lib1 | Human | Endometrium | EEC | 9.26e-24 | -4.39e-01 | -0.1869 |
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∗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 |
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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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GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:00315329 | Endometrium | AEH | actin cytoskeleton reorganization | 32/2100 | 107/18723 | 1.24e-07 | 5.80e-06 | 32 |
GO:003153214 | Endometrium | EEC | actin cytoskeleton reorganization | 33/2168 | 107/18723 | 7.46e-08 | 3.89e-06 | 33 |
GO:003153218 | Esophagus | ESCC | actin cytoskeleton reorganization | 72/8552 | 107/18723 | 5.03e-06 | 5.31e-05 | 72 |
GO:003153212 | Liver | HCC | actin cytoskeleton reorganization | 59/7958 | 107/18723 | 5.57e-03 | 2.32e-02 | 59 |
GO:003153216 | Oral cavity | OSCC | actin cytoskeleton reorganization | 65/7305 | 107/18723 | 4.25e-06 | 4.93e-05 | 65 |
GO:003153217 | Oral cavity | LP | actin cytoskeleton reorganization | 38/4623 | 107/18723 | 7.93e-03 | 4.36e-02 | 38 |
GO:003153223 | Oral cavity | EOLP | actin cytoskeleton reorganization | 34/2218 | 107/18723 | 3.66e-08 | 1.41e-06 | 34 |
GO:003153210 | Prostate | BPH | actin cytoskeleton reorganization | 40/3107 | 107/18723 | 1.82e-07 | 4.04e-06 | 40 |
GO:003153215 | Prostate | Tumor | actin cytoskeleton reorganization | 38/3246 | 107/18723 | 4.76e-06 | 7.44e-05 | 38 |
GO:003153224 | Skin | cSCC | actin cytoskeleton reorganization | 42/4864 | 107/18723 | 1.76e-03 | 1.07e-02 | 42 |
GO:003153220 | Thyroid | PTC | actin cytoskeleton reorganization | 60/5968 | 107/18723 | 1.91e-07 | 3.51e-06 | 60 |
GO:0031532111 | Thyroid | ATC | actin cytoskeleton reorganization | 62/6293 | 107/18723 | 2.01e-07 | 3.17e-06 | 62 |
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Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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Cell-cell communication analysis |
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Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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Single-cell gene regulatory network inference analysis |
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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 |
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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 |
PDLIM4 | SNV | Missense_Mutation | c.932N>T | p.Lys311Met | p.K311M | P50479 | protein_coding | deleterious(0.03) | probably_damaging(0.942) | TCGA-A2-A04P-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | taxol | PD | |
PDLIM4 | SNV | Missense_Mutation | c.829N>A | p.Glu277Lys | p.E277K | P50479 | protein_coding | deleterious(0.02) | possibly_damaging(0.793) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR | |
PDLIM4 | insertion | Frame_Shift_Ins | novel | c.498_499insC | p.Ser169GlnfsTer3 | p.S169Qfs*3 | P50479 | protein_coding | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR | ||
PDLIM4 | SNV | Missense_Mutation | c.713N>T | p.Thr238Met | p.T238M | P50479 | protein_coding | deleterious(0) | benign(0.174) | TCGA-A5-A2K5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
PDLIM4 | SNV | Missense_Mutation | rs202040278 | c.853G>A | p.Gly285Ser | p.G285S | P50479 | protein_coding | tolerated(0.05) | probably_damaging(0.945) | TCGA-AJ-A3EK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR |
PDLIM4 | SNV | Missense_Mutation | rs778997358 | c.601G>A | p.Val201Met | p.V201M | P50479 | protein_coding | tolerated(0.09) | benign(0.014) | TCGA-AJ-A3OL-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatin | PD |
PDLIM4 | SNV | Missense_Mutation | novel | c.626N>A | p.Gly209Asp | p.G209D | P50479 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AP-A1DK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
PDLIM4 | SNV | Missense_Mutation | novel | c.97N>T | p.His33Tyr | p.H33Y | P50479 | protein_coding | deleterious(0.01) | benign(0.129) | TCGA-DI-A1BU-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | paclitaxel | SD |
PDLIM4 | SNV | Missense_Mutation | novel | c.931N>G | p.Lys311Glu | p.K311E | P50479 | protein_coding | deleterious(0.01) | benign(0.366) | TCGA-DI-A1BU-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | paclitaxel | SD |
PDLIM4 | SNV | Missense_Mutation | novel | c.381N>C | p.Glu127Asp | p.E127D | P50479 | protein_coding | tolerated(0.77) | benign(0) | TCGA-EY-A3L3-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Chemotherapy | taxol | CR |
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Related drugs of malignant transformation related genes |
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(DGIdb 4.0) |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
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