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Gene: LEF1 |
Gene summary for LEF1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LEF1 | Gene ID | 51176 |
| Gene name | lymphoid enhancer binding factor 1 | |
| Gene Alias | LEF-1 | |
| Cytomap | 4q25 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | Q659G9 |
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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 |
| 51176 | LEF1 | LZE7T | Human | Esophagus | ESCC | 3.99e-05 | 1.79e-01 | 0.0667 |
| 51176 | LEF1 | P2T-E | Human | Esophagus | ESCC | 1.08e-21 | 4.94e-01 | 0.1177 |
| 51176 | LEF1 | P4T-E | Human | Esophagus | ESCC | 2.03e-18 | 4.82e-01 | 0.1323 |
| 51176 | LEF1 | P9T-E | Human | Esophagus | ESCC | 9.84e-07 | 2.32e-01 | 0.1131 |
| 51176 | LEF1 | P10T-E | Human | Esophagus | ESCC | 3.43e-16 | 4.18e-01 | 0.116 |
| 51176 | LEF1 | P12T-E | Human | Esophagus | ESCC | 4.80e-02 | 1.21e-01 | 0.1122 |
| 51176 | LEF1 | P15T-E | Human | Esophagus | ESCC | 5.02e-12 | 1.95e-01 | 0.1149 |
| 51176 | LEF1 | P16T-E | Human | Esophagus | ESCC | 3.63e-28 | 5.39e-01 | 0.1153 |
| 51176 | LEF1 | P23T-E | Human | Esophagus | ESCC | 6.85e-11 | 3.79e-01 | 0.108 |
| 51176 | LEF1 | P26T-E | Human | Esophagus | ESCC | 8.98e-20 | 3.52e-01 | 0.1276 |
| 51176 | LEF1 | P27T-E | Human | Esophagus | ESCC | 2.75e-29 | 6.33e-01 | 0.1055 |
| 51176 | LEF1 | P28T-E | Human | Esophagus | ESCC | 4.46e-04 | 1.53e-01 | 0.1149 |
| 51176 | LEF1 | P30T-E | Human | Esophagus | ESCC | 6.92e-04 | 2.79e-01 | 0.137 |
| 51176 | LEF1 | P32T-E | Human | Esophagus | ESCC | 1.89e-07 | 1.88e-01 | 0.1666 |
| 51176 | LEF1 | P39T-E | Human | Esophagus | ESCC | 2.79e-04 | 1.50e-01 | 0.0894 |
| 51176 | LEF1 | P42T-E | Human | Esophagus | ESCC | 1.78e-14 | 3.63e-01 | 0.1175 |
| 51176 | LEF1 | P48T-E | Human | Esophagus | ESCC | 4.05e-03 | 2.09e-01 | 0.0959 |
| 51176 | LEF1 | P52T-E | Human | Esophagus | ESCC | 1.57e-07 | 4.37e-01 | 0.1555 |
| 51176 | LEF1 | P54T-E | Human | Esophagus | ESCC | 5.94e-05 | 1.71e-01 | 0.0975 |
| 51176 | LEF1 | P56T-E | Human | Esophagus | ESCC | 5.36e-07 | 1.05e+00 | 0.1613 |
| Page: 1 2 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 |
| ∗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:0001890110 | Esophagus | ESCC | placenta development | 98/8552 | 144/18723 | 4.46e-08 | 8.11e-07 | 98 |
| GO:004578527 | Esophagus | ESCC | positive regulation of cell adhesion | 255/8552 | 437/18723 | 5.07e-08 | 9.11e-07 | 255 |
| GO:001908312 | Esophagus | ESCC | viral transcription | 41/8552 | 50/18723 | 1.35e-07 | 2.17e-06 | 41 |
| GO:0061458110 | Esophagus | ESCC | reproductive system development | 247/8552 | 427/18723 | 2.24e-07 | 3.42e-06 | 247 |
| GO:004860818 | Esophagus | ESCC | reproductive structure development | 245/8552 | 424/18723 | 2.82e-07 | 4.14e-06 | 245 |
| GO:003011117 | Esophagus | ESCC | regulation of Wnt signaling pathway | 194/8552 | 328/18723 | 5.39e-07 | 7.14e-06 | 194 |
| GO:006007016 | Esophagus | ESCC | canonical Wnt signaling pathway | 180/8552 | 303/18723 | 9.15e-07 | 1.17e-05 | 180 |
| GO:000164918 | Esophagus | ESCC | osteoblast differentiation | 140/8552 | 229/18723 | 1.63e-06 | 1.95e-05 | 140 |
| GO:000257317 | Esophagus | ESCC | myeloid leukocyte differentiation | 128/8552 | 208/18723 | 2.75e-06 | 3.15e-05 | 128 |
| GO:000150317 | Esophagus | ESCC | ossification | 232/8552 | 408/18723 | 3.00e-06 | 3.40e-05 | 232 |
| GO:00107184 | Esophagus | ESCC | positive regulation of epithelial to mesenchymal transition | 40/8552 | 52/18723 | 4.25e-06 | 4.56e-05 | 40 |
| GO:00073698 | Esophagus | ESCC | gastrulation | 115/8552 | 185/18723 | 4.35e-06 | 4.64e-05 | 115 |
| GO:006056210 | Esophagus | ESCC | epithelial tube morphogenesis | 187/8552 | 325/18723 | 9.95e-06 | 9.44e-05 | 187 |
| GO:000189219 | Esophagus | ESCC | embryonic placenta development | 57/8552 | 82/18723 | 1.06e-05 | 1.01e-04 | 57 |
| GO:00605417 | Esophagus | ESCC | respiratory system development | 123/8552 | 203/18723 | 1.26e-05 | 1.15e-04 | 123 |
| GO:00603242 | Esophagus | ESCC | face development | 34/8552 | 44/18723 | 1.90e-05 | 1.67e-04 | 34 |
| GO:00420636 | Esophagus | ESCC | gliogenesis | 172/8552 | 301/18723 | 3.75e-05 | 3.04e-04 | 172 |
| GO:005185115 | Esophagus | ESCC | modulation by host of symbiont process | 43/8552 | 60/18723 | 4.00e-05 | 3.22e-04 | 43 |
| GO:003017716 | Esophagus | ESCC | positive regulation of Wnt signaling pathway | 87/8552 | 140/18723 | 6.18e-05 | 4.73e-04 | 87 |
| GO:00439662 | Esophagus | ESCC | histone H3 acetylation | 43/8552 | 61/18723 | 7.57e-05 | 5.67e-04 | 43 |
| Page: 1 2 3 4 5 6 7 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa05132211 | Esophagus | ESCC | Salmonella infection | 191/4205 | 249/8465 | 6.51e-19 | 5.45e-17 | 2.79e-17 | 191 |
| hsa0521020 | Esophagus | ESCC | Colorectal cancer | 69/4205 | 86/8465 | 4.06e-09 | 4.13e-08 | 2.11e-08 | 69 |
| hsa05167211 | Esophagus | ESCC | Kaposi sarcoma-associated herpesvirus infection | 136/4205 | 194/8465 | 4.28e-09 | 4.22e-08 | 2.16e-08 | 136 |
| hsa0521516 | Esophagus | ESCC | Prostate cancer | 72/4205 | 97/8465 | 6.12e-07 | 4.10e-06 | 2.10e-06 | 72 |
| hsa0452030 | Esophagus | ESCC | Adherens junction | 69/4205 | 93/8465 | 1.08e-06 | 6.83e-06 | 3.50e-06 | 69 |
| hsa0521628 | Esophagus | ESCC | Thyroid cancer | 32/4205 | 37/8465 | 2.98e-06 | 1.72e-05 | 8.81e-06 | 32 |
| hsa0521320 | Esophagus | ESCC | Endometrial cancer | 45/4205 | 58/8465 | 1.14e-05 | 5.98e-05 | 3.06e-05 | 45 |
| hsa0522518 | Esophagus | ESCC | Hepatocellular carcinoma | 109/4205 | 168/8465 | 4.27e-05 | 1.88e-04 | 9.64e-05 | 109 |
| hsa052215 | Esophagus | ESCC | Acute myeloid leukemia | 49/4205 | 67/8465 | 7.43e-05 | 3.07e-04 | 1.57e-04 | 49 |
| hsa0439018 | Esophagus | ESCC | Hippo signaling pathway | 92/4205 | 157/8465 | 1.46e-02 | 3.31e-02 | 1.69e-02 | 92 |
| hsa05132310 | Esophagus | ESCC | Salmonella infection | 191/4205 | 249/8465 | 6.51e-19 | 5.45e-17 | 2.79e-17 | 191 |
| hsa05210110 | Esophagus | ESCC | Colorectal cancer | 69/4205 | 86/8465 | 4.06e-09 | 4.13e-08 | 2.11e-08 | 69 |
| hsa0516738 | Esophagus | ESCC | Kaposi sarcoma-associated herpesvirus infection | 136/4205 | 194/8465 | 4.28e-09 | 4.22e-08 | 2.16e-08 | 136 |
| hsa0521517 | Esophagus | ESCC | Prostate cancer | 72/4205 | 97/8465 | 6.12e-07 | 4.10e-06 | 2.10e-06 | 72 |
| hsa04520114 | Esophagus | ESCC | Adherens junction | 69/4205 | 93/8465 | 1.08e-06 | 6.83e-06 | 3.50e-06 | 69 |
| hsa0521638 | Esophagus | ESCC | Thyroid cancer | 32/4205 | 37/8465 | 2.98e-06 | 1.72e-05 | 8.81e-06 | 32 |
| hsa05213110 | Esophagus | ESCC | Endometrial cancer | 45/4205 | 58/8465 | 1.14e-05 | 5.98e-05 | 3.06e-05 | 45 |
| hsa0522519 | Esophagus | ESCC | Hepatocellular carcinoma | 109/4205 | 168/8465 | 4.27e-05 | 1.88e-04 | 9.64e-05 | 109 |
| hsa0522113 | Esophagus | ESCC | Acute myeloid leukemia | 49/4205 | 67/8465 | 7.43e-05 | 3.07e-04 | 1.57e-04 | 49 |
| hsa0439019 | Esophagus | ESCC | Hippo signaling pathway | 92/4205 | 157/8465 | 1.46e-02 | 3.31e-02 | 1.69e-02 | 92 |
| Page: 1 2 |
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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 |
| LEF1 | MLUM | Breast | DCIS | KCNE4,ZNF385D,RHOBTB3, etc. | 6.41e-01 |  |
| LEF1 | TFH | Breast | DCIS | MAL,TCF7,LDHB, etc. | 8.56e-02 | |
| LEF1 | CD4TN | Breast | DCIS | MAL,TCF7,LDHB, etc. | 2.85e-01 | |
| LEF1 | TH17 | Breast | DCIS | MAL,TCF7,LDHB, etc. | 4.54e-02 | |
| LEF1 | CD8TEXINT | Breast | Healthy | MAL,TCF7,LDHB, etc. | 1.36e-01 |  |
| LEF1 | CD4TN | Breast | IDC | MAL,TCF7,LDHB, etc. | 1.21e-01 |  |
| LEF1 | TFH | Breast | IDC | MAL,TCF7,LDHB, etc. | 1.43e-01 | |
| LEF1 | TH17 | Breast | IDC | MAL,TCF7,LDHB, etc. | 4.90e-02 | |
| LEF1 | CD8TCM | Breast | Precancer | MAL,TCF7,LDHB, etc. | 5.86e-01 |  |
| LEF1 | TFH | Cervix | CC | TCF7,TRABD2A,MAL, etc. | 5.58e-02 |  |
| ∗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 2 3 4 5 |
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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 |
| LEF1 | SNV | Missense_Mutation | c.194C>T | p.Pro65Leu | p.P65L | Q9UJU2 | protein_coding | deleterious(0.01) | possibly_damaging(0.511) | TCGA-AR-A2LH-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD | |
| LEF1 | insertion | Nonsense_Mutation | novel | c.449_450insTGAGTTTGAGAGGGAGGACCAGTCTTGGTCGTGGTGAATTTGAAGT | p.Val151GlufsTer12 | p.V151Efs*12 | Q9UJU2 | protein_coding | TCGA-A2-A0CU-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| LEF1 | SNV | Missense_Mutation | rs377048071 | c.706G>A | p.Asp236Asn | p.D236N | Q9UJU2 | protein_coding | tolerated(1) | benign(0.018) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| LEF1 | SNV | Missense_Mutation | novel | c.145G>A | p.Asp49Asn | p.D49N | Q9UJU2 | protein_coding | tolerated(0.05) | probably_damaging(1) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| LEF1 | SNV | Missense_Mutation | c.826N>A | p.Asp276Asn | p.D276N | Q9UJU2 | protein_coding | tolerated(0.19) | benign(0.009) | TCGA-EA-A3Y4-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| LEF1 | SNV | Missense_Mutation | rs146861754 | c.745G>A | p.Gly249Ser | p.G249S | Q9UJU2 | protein_coding | tolerated(0.45) | benign(0.079) | TCGA-AA-3811-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD |
| LEF1 | SNV | Missense_Mutation | c.362N>G | p.Asn121Ser | p.N121S | Q9UJU2 | protein_coding | tolerated(0.54) | benign(0.017) | TCGA-AA-3815-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| LEF1 | SNV | Missense_Mutation | novel | c.788N>C | p.Ile263Thr | p.I263T | Q9UJU2 | protein_coding | deleterious(0) | probably_damaging(0.954) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| LEF1 | SNV | Missense_Mutation | c.914N>T | p.Ala305Val | p.A305V | Q9UJU2 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AA-3994-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | capecitabine | CR | |
| LEF1 | SNV | Missense_Mutation | novel | c.916N>C | p.Phe306Leu | p.F306L | Q9UJU2 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| Page: 1 2 3 4 5 6 7 |
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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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