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Gene: CLDN4 |
Gene summary for CLDN4 |
Gene summary. |
Gene information | Species | Human | Gene symbol | CLDN4 | Gene ID | 1364 |
Gene name | claudin 4 | |
Gene Alias | CPE-R | |
Cytomap | 7q11.23 | |
Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | O14493 |
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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 |
1364 | CLDN4 | GSM4909280 | Human | Breast | Precancer | 3.36e-04 | 3.43e-01 | 0.0305 |
1364 | CLDN4 | GSM4909281 | Human | Breast | IDC | 1.63e-14 | -4.12e-01 | 0.21 |
1364 | CLDN4 | GSM4909282 | Human | Breast | IDC | 2.01e-13 | 4.11e-01 | -0.0288 |
1364 | CLDN4 | GSM4909285 | Human | Breast | IDC | 5.90e-09 | -2.32e-01 | 0.21 |
1364 | CLDN4 | GSM4909286 | Human | Breast | IDC | 1.55e-23 | -5.52e-01 | 0.1081 |
1364 | CLDN4 | GSM4909288 | Human | Breast | IDC | 7.42e-03 | -4.43e-01 | 0.0988 |
1364 | CLDN4 | GSM4909290 | Human | Breast | IDC | 1.28e-20 | -7.92e-01 | 0.2096 |
1364 | CLDN4 | GSM4909294 | Human | Breast | IDC | 2.42e-17 | -5.94e-01 | 0.2022 |
1364 | CLDN4 | GSM4909297 | Human | Breast | IDC | 6.95e-14 | -4.57e-01 | 0.1517 |
1364 | CLDN4 | GSM4909298 | Human | Breast | IDC | 7.84e-08 | -3.63e-01 | 0.1551 |
1364 | CLDN4 | GSM4909300 | Human | Breast | IDC | 3.38e-07 | 4.00e-01 | 0.0334 |
1364 | CLDN4 | GSM4909302 | Human | Breast | IDC | 7.19e-06 | -4.40e-01 | 0.1545 |
1364 | CLDN4 | GSM4909304 | Human | Breast | IDC | 1.12e-14 | -4.36e-01 | 0.1636 |
1364 | CLDN4 | GSM4909305 | Human | Breast | IDC | 7.25e-07 | 3.33e-01 | 0.0436 |
1364 | CLDN4 | GSM4909307 | Human | Breast | IDC | 1.04e-06 | -4.16e-01 | 0.1569 |
1364 | CLDN4 | GSM4909308 | Human | Breast | IDC | 2.92e-19 | -5.81e-01 | 0.158 |
1364 | CLDN4 | GSM4909311 | Human | Breast | IDC | 6.44e-37 | -6.24e-01 | 0.1534 |
1364 | CLDN4 | GSM4909313 | Human | Breast | IDC | 6.80e-06 | 1.84e-01 | 0.0391 |
1364 | CLDN4 | GSM4909315 | Human | Breast | IDC | 2.60e-36 | -9.18e-01 | 0.21 |
1364 | CLDN4 | GSM4909316 | Human | Breast | IDC | 2.27e-15 | -1.02e+00 | 0.21 |
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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 |
GO:004854522 | Liver | HCC | response to steroid hormone | 206/7958 | 339/18723 | 6.81e-12 | 2.92e-10 | 206 |
GO:002260422 | Liver | HCC | regulation of cell morphogenesis | 188/7958 | 309/18723 | 4.84e-11 | 1.82e-09 | 188 |
GO:190165422 | Liver | HCC | response to ketone | 119/7958 | 194/18723 | 8.65e-08 | 1.72e-06 | 119 |
GO:005254722 | Liver | HCC | regulation of peptidase activity | 247/7958 | 461/18723 | 8.28e-07 | 1.27e-05 | 247 |
GO:004206022 | Liver | HCC | wound healing | 219/7958 | 422/18723 | 5.34e-05 | 5.04e-04 | 219 |
GO:000762321 | Liver | HCC | circadian rhythm | 117/7958 | 210/18723 | 7.29e-05 | 6.54e-04 | 117 |
GO:001095212 | Liver | HCC | positive regulation of peptidase activity | 110/7958 | 197/18723 | 1.04e-04 | 8.98e-04 | 110 |
GO:006104122 | Liver | HCC | regulation of wound healing | 78/7958 | 134/18723 | 1.73e-04 | 1.36e-03 | 78 |
GO:190303421 | Liver | HCC | regulation of response to wounding | 94/7958 | 167/18723 | 2.19e-04 | 1.66e-03 | 94 |
GO:004851121 | Liver | HCC | rhythmic process | 156/7958 | 298/18723 | 3.54e-04 | 2.46e-03 | 156 |
GO:009030321 | Liver | HCC | positive regulation of wound healing | 38/7958 | 59/18723 | 5.61e-04 | 3.61e-03 | 38 |
GO:004521622 | Liver | HCC | cell-cell junction organization | 107/7958 | 200/18723 | 1.06e-03 | 6.11e-03 | 107 |
GO:005087822 | Liver | HCC | regulation of body fluid levels | 191/7958 | 379/18723 | 1.06e-03 | 6.11e-03 | 191 |
GO:190303621 | Liver | HCC | positive regulation of response to wounding | 44/7958 | 72/18723 | 1.10e-03 | 6.32e-03 | 44 |
GO:00325701 | Liver | HCC | response to progesterone | 25/7958 | 37/18723 | 1.82e-03 | 9.38e-03 | 25 |
GO:004329712 | Liver | HCC | apical junction assembly | 45/7958 | 78/18723 | 4.83e-03 | 2.03e-02 | 45 |
GO:00075651 | Liver | HCC | female pregnancy | 99/7958 | 193/18723 | 8.24e-03 | 3.23e-02 | 99 |
GO:01201935 | Liver | HCC | tight junction organization | 45/7958 | 80/18723 | 9.02e-03 | 3.48e-02 | 45 |
GO:01201925 | Liver | HCC | tight junction assembly | 42/7958 | 74/18723 | 9.32e-03 | 3.57e-02 | 42 |
GO:000704312 | Liver | HCC | cell-cell junction assembly | 76/7958 | 146/18723 | 1.23e-02 | 4.47e-02 | 76 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0513018 | Breast | Precancer | Pathogenic Escherichia coli infection | 38/684 | 197/8465 | 3.12e-07 | 5.81e-06 | 4.45e-06 | 38 |
hsa0453018 | Breast | Precancer | Tight junction | 31/684 | 169/8465 | 1.13e-05 | 1.26e-04 | 9.64e-05 | 31 |
hsa0513019 | Breast | Precancer | Pathogenic Escherichia coli infection | 38/684 | 197/8465 | 3.12e-07 | 5.81e-06 | 4.45e-06 | 38 |
hsa0453019 | Breast | Precancer | Tight junction | 31/684 | 169/8465 | 1.13e-05 | 1.26e-04 | 9.64e-05 | 31 |
hsa0453024 | Breast | IDC | Tight junction | 38/867 | 169/8465 | 2.07e-06 | 3.20e-05 | 2.39e-05 | 38 |
hsa0513024 | Breast | IDC | Pathogenic Escherichia coli infection | 42/867 | 197/8465 | 2.66e-06 | 3.92e-05 | 2.94e-05 | 42 |
hsa0467024 | Breast | IDC | Leukocyte transendothelial migration | 21/867 | 114/8465 | 5.41e-03 | 3.13e-02 | 2.34e-02 | 21 |
hsa0453034 | Breast | IDC | Tight junction | 38/867 | 169/8465 | 2.07e-06 | 3.20e-05 | 2.39e-05 | 38 |
hsa0513034 | Breast | IDC | Pathogenic Escherichia coli infection | 42/867 | 197/8465 | 2.66e-06 | 3.92e-05 | 2.94e-05 | 42 |
hsa0467034 | Breast | IDC | Leukocyte transendothelial migration | 21/867 | 114/8465 | 5.41e-03 | 3.13e-02 | 2.34e-02 | 21 |
hsa0513043 | Breast | DCIS | Pathogenic Escherichia coli infection | 42/846 | 197/8465 | 1.40e-06 | 2.15e-05 | 1.59e-05 | 42 |
hsa0453044 | Breast | DCIS | Tight junction | 37/846 | 169/8465 | 3.07e-06 | 4.20e-05 | 3.09e-05 | 37 |
hsa0513053 | Breast | DCIS | Pathogenic Escherichia coli infection | 42/846 | 197/8465 | 1.40e-06 | 2.15e-05 | 1.59e-05 | 42 |
hsa0453054 | Breast | DCIS | Tight junction | 37/846 | 169/8465 | 3.07e-06 | 4.20e-05 | 3.09e-05 | 37 |
hsa0513020 | Cervix | CC | Pathogenic Escherichia coli infection | 63/1267 | 197/8465 | 9.28e-10 | 2.00e-08 | 1.19e-08 | 63 |
hsa0453020 | Cervix | CC | Tight junction | 49/1267 | 169/8465 | 1.87e-06 | 1.78e-05 | 1.05e-05 | 49 |
hsa0467020 | Cervix | CC | Leukocyte transendothelial migration | 36/1267 | 114/8465 | 5.22e-06 | 4.83e-05 | 2.86e-05 | 36 |
hsa045147 | Cervix | CC | Cell adhesion molecules | 36/1267 | 157/8465 | 4.94e-03 | 1.67e-02 | 9.86e-03 | 36 |
hsa05130110 | Cervix | CC | Pathogenic Escherichia coli infection | 63/1267 | 197/8465 | 9.28e-10 | 2.00e-08 | 1.19e-08 | 63 |
hsa04530110 | Cervix | CC | Tight junction | 49/1267 | 169/8465 | 1.87e-06 | 1.78e-05 | 1.05e-05 | 49 |
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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 |
CLDN4 | SNV | Missense_Mutation | c.428N>C | p.Ile143Thr | p.I143T | O14493 | protein_coding | deleterious(0.03) | benign(0.137) | TCGA-BH-A18G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
CLDN4 | SNV | Missense_Mutation | c.322C>A | p.Leu108Met | p.L108M | O14493 | protein_coding | tolerated(0.12) | benign(0.015) | TCGA-AZ-6601-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
CLDN4 | deletion | Frame_Shift_Del | c.532delN | p.Leu180CysfsTer115 | p.L180Cfs*115 | O14493 | protein_coding | TCGA-AD-A5EJ-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |||
CLDN4 | deletion | Frame_Shift_Del | c.532delN | p.Leu180CysfsTer115 | p.L180Cfs*115 | O14493 | protein_coding | TCGA-CK-6746-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |||
CLDN4 | SNV | Missense_Mutation | novel | c.259N>G | p.Ser87Gly | p.S87G | O14493 | protein_coding | deleterious(0.04) | benign(0.026) | TCGA-AP-A1DK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
CLDN4 | SNV | Missense_Mutation | novel | c.133N>G | p.Thr45Ala | p.T45A | O14493 | protein_coding | deleterious(0.03) | benign(0.015) | TCGA-E6-A1M0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatin | SD |
CLDN4 | SNV | Missense_Mutation | rs782337604 | c.497N>C | p.Val166Ala | p.V166A | O14493 | protein_coding | deleterious(0) | benign(0.278) | TCGA-EC-A1QX-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Chemotherapy | cyclophosphamide | PD |
CLDN4 | SNV | Missense_Mutation | novel | c.370N>A | p.Val124Met | p.V124M | O14493 | protein_coding | tolerated(0.16) | benign(0.038) | TCGA-EO-A22U-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
CLDN4 | SNV | Missense_Mutation | novel | c.327N>T | p.Glu109Asp | p.E109D | O14493 | protein_coding | tolerated(0.27) | benign(0.007) | TCGA-EO-A22X-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unspecific | Carboplatin | Complete Response |
CLDN4 | SNV | Missense_Mutation | rs200176069 | c.488C>T | p.Ser163Leu | p.S163L | O14493 | protein_coding | deleterious(0.03) | possibly_damaging(0.686) | TCGA-EY-A4KR-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatin | PD |
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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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