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Gene: PDCD4 |
Gene summary for PDCD4 |
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Gene information | Species | Human | Gene symbol | PDCD4 | Gene ID | 27250 |
Gene name | programmed cell death 4 | |
Gene Alias | H731 | |
Cytomap | 10q25.2 | |
Gene Type | protein-coding | GO ID | GO:0000165 | UniProtAcc | B4DKX4 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
27250 | PDCD4 | GSM4909293 | Human | Breast | IDC | 5.25e-16 | 4.16e-01 | 0.1581 |
27250 | PDCD4 | GSM4909294 | Human | Breast | IDC | 1.60e-02 | 1.41e-01 | 0.2022 |
27250 | PDCD4 | GSM4909296 | Human | Breast | IDC | 7.85e-04 | -1.72e-01 | 0.1524 |
27250 | PDCD4 | GSM4909297 | Human | Breast | IDC | 5.25e-15 | -1.33e-01 | 0.1517 |
27250 | PDCD4 | GSM4909299 | Human | Breast | IDC | 1.12e-02 | 2.58e-01 | 0.035 |
27250 | PDCD4 | GSM4909303 | Human | Breast | IDC | 2.67e-09 | 6.36e-01 | 0.0438 |
27250 | PDCD4 | GSM4909305 | Human | Breast | IDC | 3.31e-07 | 4.07e-01 | 0.0436 |
27250 | PDCD4 | GSM4909306 | Human | Breast | IDC | 2.70e-18 | 4.65e-01 | 0.1564 |
27250 | PDCD4 | GSM4909311 | Human | Breast | IDC | 1.12e-18 | -2.53e-01 | 0.1534 |
27250 | PDCD4 | GSM4909312 | Human | Breast | IDC | 2.14e-08 | 6.63e-02 | 0.1552 |
27250 | PDCD4 | GSM4909317 | Human | Breast | IDC | 4.22e-09 | 4.05e-01 | 0.1355 |
27250 | PDCD4 | GSM4909318 | Human | Breast | IDC | 6.46e-04 | 3.07e-01 | 0.2031 |
27250 | PDCD4 | GSM4909319 | Human | Breast | IDC | 3.65e-32 | -2.44e-01 | 0.1563 |
27250 | PDCD4 | GSM4909320 | Human | Breast | IDC | 1.48e-05 | -4.41e-01 | 0.1575 |
27250 | PDCD4 | GSM4909321 | Human | Breast | IDC | 1.89e-12 | -3.71e-01 | 0.1559 |
27250 | PDCD4 | brca10 | Human | Breast | Precancer | 1.25e-09 | -4.40e-01 | -0.0029 |
27250 | PDCD4 | NCCBC11 | Human | Breast | DCIS | 7.02e-25 | 9.95e-01 | 0.1232 |
27250 | PDCD4 | NCCBC14 | Human | Breast | DCIS | 5.84e-16 | 4.02e-01 | 0.2021 |
27250 | PDCD4 | NCCBC3 | Human | Breast | DCIS | 3.11e-05 | 2.18e-01 | 0.1198 |
27250 | PDCD4 | NCCBC5 | Human | Breast | DCIS | 8.63e-06 | 7.17e-02 | 0.2046 |
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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:00075688 | Breast | Precancer | aging | 41/1080 | 339/18723 | 5.95e-06 | 1.71e-04 | 41 |
GO:00022378 | Breast | Precancer | response to molecule of bacterial origin | 43/1080 | 363/18723 | 6.05e-06 | 1.72e-04 | 43 |
GO:00507293 | Breast | Precancer | positive regulation of inflammatory response | 23/1080 | 142/18723 | 6.51e-06 | 1.81e-04 | 23 |
GO:00324968 | Breast | Precancer | response to lipopolysaccharide | 41/1080 | 343/18723 | 7.94e-06 | 2.17e-04 | 41 |
GO:0050727 | Breast | Precancer | regulation of inflammatory response | 44/1080 | 386/18723 | 1.26e-05 | 3.22e-04 | 44 |
GO:00321034 | Breast | Precancer | positive regulation of response to external stimulus | 46/1080 | 427/18723 | 3.41e-05 | 7.40e-04 | 46 |
GO:00313493 | Breast | Precancer | positive regulation of defense response | 33/1080 | 278/18723 | 6.79e-05 | 1.36e-03 | 33 |
GO:00712227 | Breast | Precancer | cellular response to lipopolysaccharide | 25/1080 | 209/18723 | 4.41e-04 | 5.85e-03 | 25 |
GO:00712167 | Breast | Precancer | cellular response to biotic stimulus | 28/1080 | 246/18723 | 4.67e-04 | 6.14e-03 | 28 |
GO:19040193 | Breast | Precancer | epithelial cell apoptotic process | 17/1080 | 121/18723 | 5.76e-04 | 7.28e-03 | 17 |
GO:00712197 | Breast | Precancer | cellular response to molecule of bacterial origin | 25/1080 | 221/18723 | 1.00e-03 | 1.12e-02 | 25 |
GO:19040351 | Breast | Precancer | regulation of epithelial cell apoptotic process | 14/1080 | 96/18723 | 1.18e-03 | 1.28e-02 | 14 |
GO:00075694 | Breast | Precancer | cell aging | 17/1080 | 132/18723 | 1.55e-03 | 1.59e-02 | 17 |
GO:00018373 | Breast | Precancer | epithelial to mesenchymal transition | 19/1080 | 157/18723 | 1.78e-03 | 1.75e-02 | 19 |
GO:00513489 | Breast | Precancer | negative regulation of transferase activity | 27/1080 | 268/18723 | 3.49e-03 | 2.90e-02 | 27 |
GO:000756813 | Breast | IDC | aging | 52/1434 | 339/18723 | 1.14e-06 | 5.10e-05 | 52 |
GO:003249612 | Breast | IDC | response to lipopolysaccharide | 47/1434 | 343/18723 | 7.13e-05 | 1.43e-03 | 47 |
GO:000223712 | Breast | IDC | response to molecule of bacterial origin | 49/1434 | 363/18723 | 7.40e-05 | 1.47e-03 | 49 |
GO:005134814 | Breast | IDC | negative regulation of transferase activity | 39/1434 | 268/18723 | 7.89e-05 | 1.56e-03 | 39 |
GO:00313491 | Breast | IDC | positive regulation of defense response | 39/1434 | 278/18723 | 1.74e-04 | 2.95e-03 | 39 |
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Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0520514 | Breast | Precancer | Proteoglycans in cancer | 30/684 | 205/8465 | 1.00e-03 | 7.18e-03 | 5.50e-03 | 30 |
hsa0520515 | Breast | Precancer | Proteoglycans in cancer | 30/684 | 205/8465 | 1.00e-03 | 7.18e-03 | 5.50e-03 | 30 |
hsa0520523 | Breast | IDC | Proteoglycans in cancer | 42/867 | 205/8465 | 7.69e-06 | 9.99e-05 | 7.48e-05 | 42 |
hsa0520533 | Breast | IDC | Proteoglycans in cancer | 42/867 | 205/8465 | 7.69e-06 | 9.99e-05 | 7.48e-05 | 42 |
hsa0520542 | Breast | DCIS | Proteoglycans in cancer | 39/846 | 205/8465 | 5.36e-05 | 5.58e-04 | 4.11e-04 | 39 |
hsa0520552 | Breast | DCIS | Proteoglycans in cancer | 39/846 | 205/8465 | 5.36e-05 | 5.58e-04 | 4.11e-04 | 39 |
hsa05205 | Colorectum | AD | Proteoglycans in cancer | 70/2092 | 205/8465 | 1.37e-03 | 8.46e-03 | 5.39e-03 | 70 |
hsa052051 | Colorectum | AD | Proteoglycans in cancer | 70/2092 | 205/8465 | 1.37e-03 | 8.46e-03 | 5.39e-03 | 70 |
hsa052052 | Colorectum | SER | Proteoglycans in cancer | 58/1580 | 205/8465 | 4.37e-04 | 3.82e-03 | 2.77e-03 | 58 |
hsa052053 | Colorectum | SER | Proteoglycans in cancer | 58/1580 | 205/8465 | 4.37e-04 | 3.82e-03 | 2.77e-03 | 58 |
hsa052054 | Colorectum | MSS | Proteoglycans in cancer | 65/1875 | 205/8465 | 8.66e-04 | 5.38e-03 | 3.29e-03 | 65 |
hsa052055 | Colorectum | MSS | Proteoglycans in cancer | 65/1875 | 205/8465 | 8.66e-04 | 5.38e-03 | 3.29e-03 | 65 |
hsa052056 | Colorectum | FAP | Proteoglycans in cancer | 57/1404 | 205/8465 | 3.05e-05 | 3.29e-04 | 2.00e-04 | 57 |
hsa052057 | Colorectum | FAP | Proteoglycans in cancer | 57/1404 | 205/8465 | 3.05e-05 | 3.29e-04 | 2.00e-04 | 57 |
hsa052058 | Colorectum | CRC | Proteoglycans in cancer | 47/1091 | 205/8465 | 4.43e-05 | 8.70e-04 | 5.90e-04 | 47 |
hsa052059 | Colorectum | CRC | Proteoglycans in cancer | 47/1091 | 205/8465 | 4.43e-05 | 8.70e-04 | 5.90e-04 | 47 |
hsa0520518 | Endometrium | AEH | Proteoglycans in cancer | 53/1197 | 205/8465 | 5.43e-06 | 6.53e-05 | 4.78e-05 | 53 |
hsa0520519 | Endometrium | AEH | Proteoglycans in cancer | 53/1197 | 205/8465 | 5.43e-06 | 6.53e-05 | 4.78e-05 | 53 |
hsa0520524 | Endometrium | EEC | Proteoglycans in cancer | 52/1237 | 205/8465 | 3.01e-05 | 3.19e-04 | 2.38e-04 | 52 |
hsa0520534 | Endometrium | EEC | Proteoglycans in cancer | 52/1237 | 205/8465 | 3.01e-05 | 3.19e-04 | 2.38e-04 | 52 |
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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 |
PDCD4 | insertion | Frame_Shift_Ins | novel | c.965_966insCCATGCCTGGCTAATTATT | p.Gln322HisfsTer14 | p.Q322Hfs*14 | Q53EL6 | protein_coding | TCGA-B5-A11F-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Hormone Therapy | megace | SD | ||
PDCD4 | SNV | Missense_Mutation | c.330N>T | p.Arg110Ser | p.R110S | Q53EL6 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-64-5778-01 | Lung | lung adenocarcinoma | Male | <65 | I/II | Targeted Molecular therapy | tarceva | PD | |
PDCD4 | SNV | Missense_Mutation | novel | c.1295A>T | p.Glu432Val | p.E432V | Q53EL6 | protein_coding | tolerated(0.15) | benign(0.026) | TCGA-69-7764-01 | Lung | lung adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
PDCD4 | SNV | Missense_Mutation | c.1231G>A | p.Glu411Lys | p.E411K | Q53EL6 | protein_coding | deleterious(0.05) | benign(0.196) | TCGA-56-A5DR-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
PDCD4 | SNV | Missense_Mutation | novel | c.768N>T | p.Arg256Ser | p.R256S | Q53EL6 | protein_coding | tolerated(0.06) | benign(0.018) | TCGA-CR-7402-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Chemotherapy | carboplatin | SD |
PDCD4 | SNV | Missense_Mutation | c.604N>A | p.Val202Met | p.V202M | Q53EL6 | protein_coding | tolerated(0.14) | benign(0.056) | TCGA-BR-6852-01 | Stomach | stomach adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
PDCD4 | SNV | Missense_Mutation | novel | c.28N>G | p.Asn10Asp | p.N10D | Q53EL6 | protein_coding | deleterious_low_confidence(0.05) | benign(0.107) | TCGA-BR-8680-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Chemotherapy | oxaliplatin | CR |
PDCD4 | SNV | Missense_Mutation | c.169G>A | p.Ala57Thr | p.A57T | Q53EL6 | protein_coding | tolerated(0.19) | probably_damaging(0.996) | TCGA-F1-A448-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | capecitabine | CR | |
PDCD4 | SNV | Missense_Mutation | c.172N>G | p.Lys58Glu | p.K58E | Q53EL6 | protein_coding | deleterious(0.01) | benign(0.43) | TCGA-FP-A4BE-01 | Stomach | stomach adenocarcinoma | Male | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | |
PDCD4 | SNV | Missense_Mutation | c.724A>G | p.Lys242Glu | p.K242E | Q53EL6 | protein_coding | tolerated(0.66) | benign(0.074) | TCGA-HU-A4GN-01 | Stomach | stomach adenocarcinoma | Male | <65 | I/II | Chemotherapy | mitomycin | PD |
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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 |
27250 | PDCD4 | KINASE, DRUGGABLE GENOME | PACLITAXEL | PACLITAXEL | 25928036 |
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