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Gene: BECN1 |
Gene summary for BECN1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | BECN1 | Gene ID | 8678 |
| Gene name | beclin 1 | |
| Gene Alias | ATG6 | |
| Cytomap | 17q21.31 | |
| Gene Type | protein-coding | GO ID | GO:0000045 | UniProtAcc | A0A024R1X5 |
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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 |
| 8678 | BECN1 | LZE4T | Human | Esophagus | ESCC | 2.03e-08 | 2.94e-01 | 0.0811 |
| 8678 | BECN1 | LZE7T | Human | Esophagus | ESCC | 3.24e-10 | 5.86e-01 | 0.0667 |
| 8678 | BECN1 | LZE8T | Human | Esophagus | ESCC | 1.75e-09 | 2.27e-01 | 0.067 |
| 8678 | BECN1 | LZE20T | Human | Esophagus | ESCC | 1.98e-03 | 1.63e-01 | 0.0662 |
| 8678 | BECN1 | LZE24T | Human | Esophagus | ESCC | 2.30e-30 | 9.65e-01 | 0.0596 |
| 8678 | BECN1 | LZE21T | Human | Esophagus | ESCC | 6.12e-04 | 2.61e-01 | 0.0655 |
| 8678 | BECN1 | LZE6T | Human | Esophagus | ESCC | 3.59e-05 | 3.03e-01 | 0.0845 |
| 8678 | BECN1 | P1T-E | Human | Esophagus | ESCC | 4.93e-04 | 5.49e-01 | 0.0875 |
| 8678 | BECN1 | P2T-E | Human | Esophagus | ESCC | 1.21e-29 | 4.20e-01 | 0.1177 |
| 8678 | BECN1 | P4T-E | Human | Esophagus | ESCC | 6.14e-35 | 8.99e-01 | 0.1323 |
| 8678 | BECN1 | P5T-E | Human | Esophagus | ESCC | 5.00e-20 | 6.06e-01 | 0.1327 |
| 8678 | BECN1 | P8T-E | Human | Esophagus | ESCC | 6.74e-48 | 1.11e+00 | 0.0889 |
| 8678 | BECN1 | P9T-E | Human | Esophagus | ESCC | 1.43e-08 | 2.25e-01 | 0.1131 |
| 8678 | BECN1 | P10T-E | Human | Esophagus | ESCC | 1.89e-23 | 2.03e-01 | 0.116 |
| 8678 | BECN1 | P11T-E | Human | Esophagus | ESCC | 1.74e-15 | 5.69e-01 | 0.1426 |
| 8678 | BECN1 | P12T-E | Human | Esophagus | ESCC | 1.29e-33 | 5.65e-01 | 0.1122 |
| 8678 | BECN1 | P15T-E | Human | Esophagus | ESCC | 5.09e-24 | 6.88e-01 | 0.1149 |
| 8678 | BECN1 | P16T-E | Human | Esophagus | ESCC | 3.45e-18 | 4.26e-01 | 0.1153 |
| 8678 | BECN1 | P17T-E | Human | Esophagus | ESCC | 6.97e-05 | 2.81e-01 | 0.1278 |
| 8678 | BECN1 | P19T-E | Human | Esophagus | ESCC | 8.99e-08 | 5.33e-01 | 0.1662 |
| Page: 1 2 3 4 5 6 |
| 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 | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ |
| ∗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:0097193111 | Esophagus | ESCC | intrinsic apoptotic signaling pathway | 222/8552 | 288/18723 | 5.87e-28 | 2.02e-25 | 222 |
| GO:014001414 | Esophagus | ESCC | mitotic nuclear division | 218/8552 | 287/18723 | 6.17e-26 | 1.78e-23 | 218 |
| GO:2001233111 | Esophagus | ESCC | regulation of apoptotic signaling pathway | 256/8552 | 356/18723 | 4.11e-24 | 1.04e-21 | 256 |
| GO:001623617 | Esophagus | ESCC | macroautophagy | 216/8552 | 291/18723 | 1.94e-23 | 4.57e-21 | 216 |
| GO:0022411111 | Esophagus | ESCC | cellular component disassembly | 305/8552 | 443/18723 | 1.94e-23 | 4.57e-21 | 305 |
| GO:0009896111 | Esophagus | ESCC | positive regulation of catabolic process | 332/8552 | 492/18723 | 4.36e-23 | 9.22e-21 | 332 |
| GO:005165617 | Esophagus | ESCC | establishment of organelle localization | 273/8552 | 390/18723 | 9.13e-23 | 1.81e-20 | 273 |
| GO:000007011 | Esophagus | ESCC | mitotic sister chromatid segregation | 138/8552 | 168/18723 | 1.37e-22 | 2.63e-20 | 138 |
| GO:0006979111 | Esophagus | ESCC | response to oxidative stress | 303/8552 | 446/18723 | 7.15e-22 | 1.30e-19 | 303 |
| GO:0031331111 | Esophagus | ESCC | positive regulation of cellular catabolic process | 292/8552 | 427/18723 | 8.67e-22 | 1.53e-19 | 292 |
| GO:00008194 | Esophagus | ESCC | sister chromatid segregation | 157/8552 | 202/18723 | 8.41e-21 | 1.33e-18 | 157 |
| GO:003304416 | Esophagus | ESCC | regulation of chromosome organization | 145/8552 | 187/18723 | 3.80e-19 | 4.31e-17 | 145 |
| GO:0062197111 | Esophagus | ESCC | cellular response to chemical stress | 234/8552 | 337/18723 | 5.37e-19 | 5.97e-17 | 234 |
| GO:000705911 | Esophagus | ESCC | chromosome segregation | 238/8552 | 346/18723 | 1.72e-18 | 1.82e-16 | 238 |
| GO:001050617 | Esophagus | ESCC | regulation of autophagy | 220/8552 | 317/18723 | 6.72e-18 | 6.36e-16 | 220 |
| GO:2001242111 | Esophagus | ESCC | regulation of intrinsic apoptotic signaling pathway | 128/8552 | 164/18723 | 1.75e-17 | 1.50e-15 | 128 |
| GO:0034599111 | Esophagus | ESCC | cellular response to oxidative stress | 197/8552 | 288/18723 | 3.76e-15 | 2.15e-13 | 197 |
| GO:0071496111 | Esophagus | ESCC | cellular response to external stimulus | 215/8552 | 320/18723 | 4.29e-15 | 2.43e-13 | 215 |
| GO:000703417 | Esophagus | ESCC | vacuolar transport | 119/8552 | 157/18723 | 1.16e-14 | 6.30e-13 | 119 |
| GO:000961518 | Esophagus | ESCC | response to virus | 238/8552 | 367/18723 | 6.65e-14 | 3.32e-12 | 238 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa05014210 | Esophagus | ESCC | Amyotrophic lateral sclerosis | 266/4205 | 364/8465 | 1.31e-20 | 2.20e-18 | 1.13e-18 | 266 |
| hsa05016210 | Esophagus | ESCC | Huntington disease | 226/4205 | 306/8465 | 1.38e-18 | 8.72e-17 | 4.46e-17 | 226 |
| hsa05022210 | Esophagus | ESCC | Pathways of neurodegeneration - multiple diseases | 318/4205 | 476/8465 | 6.10e-15 | 2.04e-13 | 1.05e-13 | 318 |
| hsa05010210 | Esophagus | ESCC | Alzheimer disease | 263/4205 | 384/8465 | 1.80e-14 | 5.47e-13 | 2.80e-13 | 263 |
| hsa05131211 | Esophagus | ESCC | Shigellosis | 176/4205 | 247/8465 | 2.27e-12 | 4.01e-11 | 2.05e-11 | 176 |
| hsa05167211 | Esophagus | ESCC | Kaposi sarcoma-associated herpesvirus infection | 136/4205 | 194/8465 | 4.28e-09 | 4.22e-08 | 2.16e-08 | 136 |
| hsa0414010 | Esophagus | ESCC | Autophagy - animal | 101/4205 | 141/8465 | 7.60e-08 | 6.21e-07 | 3.18e-07 | 101 |
| hsa04137210 | Esophagus | ESCC | Mitophagy - animal | 54/4205 | 72/8465 | 9.33e-06 | 4.96e-05 | 2.54e-05 | 54 |
| hsa0501728 | Esophagus | ESCC | Spinocerebellar ataxia | 94/4205 | 143/8465 | 6.77e-05 | 2.90e-04 | 1.48e-04 | 94 |
| hsa042156 | Esophagus | ESCC | Apoptosis - multiple species | 25/4205 | 32/8465 | 9.13e-04 | 2.92e-03 | 1.49e-03 | 25 |
| hsa041362 | Esophagus | ESCC | Autophagy - other | 23/4205 | 32/8465 | 8.99e-03 | 2.14e-02 | 1.09e-02 | 23 |
| hsa0501438 | Esophagus | ESCC | Amyotrophic lateral sclerosis | 266/4205 | 364/8465 | 1.31e-20 | 2.20e-18 | 1.13e-18 | 266 |
| hsa0501638 | Esophagus | ESCC | Huntington disease | 226/4205 | 306/8465 | 1.38e-18 | 8.72e-17 | 4.46e-17 | 226 |
| hsa0502238 | Esophagus | ESCC | Pathways of neurodegeneration - multiple diseases | 318/4205 | 476/8465 | 6.10e-15 | 2.04e-13 | 1.05e-13 | 318 |
| hsa0501038 | Esophagus | ESCC | Alzheimer disease | 263/4205 | 384/8465 | 1.80e-14 | 5.47e-13 | 2.80e-13 | 263 |
| hsa05131310 | Esophagus | ESCC | Shigellosis | 176/4205 | 247/8465 | 2.27e-12 | 4.01e-11 | 2.05e-11 | 176 |
| hsa0516738 | Esophagus | ESCC | Kaposi sarcoma-associated herpesvirus infection | 136/4205 | 194/8465 | 4.28e-09 | 4.22e-08 | 2.16e-08 | 136 |
| hsa0414015 | Esophagus | ESCC | Autophagy - animal | 101/4205 | 141/8465 | 7.60e-08 | 6.21e-07 | 3.18e-07 | 101 |
| hsa0413738 | Esophagus | ESCC | Mitophagy - animal | 54/4205 | 72/8465 | 9.33e-06 | 4.96e-05 | 2.54e-05 | 54 |
| hsa0501736 | Esophagus | ESCC | Spinocerebellar ataxia | 94/4205 | 143/8465 | 6.77e-05 | 2.90e-04 | 1.48e-04 | 94 |
| Page: 1 2 3 4 5 6 7 |
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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 |
| ∗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 |
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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 |
| BECN1 | SNV | Missense_Mutation | novel | c.1264G>A | p.Glu422Lys | p.E422K | Q14457 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-D8-A27G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| BECN1 | SNV | Missense_Mutation | rs748062728 | c.107G>A | p.Arg36His | p.R36H | Q14457 | protein_coding | tolerated(0.07) | benign(0.179) | TCGA-S3-AA17-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | anastrozole | SD |
| BECN1 | insertion | Nonsense_Mutation | novel | c.53_54insACCGAGGCGGGCAGATCACCTGAGGTCAGGAGTTCGAGA | p.Cys18delinsTer | p.C18delins* | Q14457 | protein_coding | TCGA-A8-A07R-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Ancillary | zoledronic | SD | ||
| BECN1 | deletion | Frame_Shift_Del | novel | c.750delN | p.Glu251LysfsTer14 | p.E251Kfs*14 | Q14457 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| BECN1 | SNV | Missense_Mutation | novel | c.735N>A | p.Asp245Glu | p.D245E | Q14457 | protein_coding | tolerated(0.16) | possibly_damaging(0.657) | TCGA-C5-A8YQ-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | PD |
| BECN1 | SNV | Missense_Mutation | novel | c.211N>A | p.Glu71Lys | p.E71K | Q14457 | protein_coding | deleterious(0.04) | possibly_damaging(0.495) | TCGA-HM-A4S6-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Chemotherapy | cisplatin | CR |
| BECN1 | SNV | Missense_Mutation | c.1150G>C | p.Glu384Gln | p.E384Q | Q14457 | protein_coding | deleterious(0.03) | probably_damaging(0.995) | TCGA-IR-A3LK-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | PD | |
| BECN1 | SNV | Missense_Mutation | novel | c.38N>G | p.Gln13Arg | p.Q13R | Q14457 | protein_coding | tolerated(0.56) | benign(0.003) | TCGA-AA-3848-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD |
| BECN1 | SNV | Missense_Mutation | rs759566966 | c.341G>A | p.Arg114Gln | p.R114Q | Q14457 | protein_coding | tolerated(0.69) | benign(0.003) | TCGA-CM-4744-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| BECN1 | insertion | Frame_Shift_Ins | novel | c.254_255insC | p.Ala86SerfsTer20 | p.A86Sfs*20 | Q14457 | protein_coding | TCGA-AG-A02N-01 | Colorectum | rectum adenocarcinoma | Male | >=65 | I/II | Chemotherapy | folinic | CR |
| Page: 1 2 3 4 |
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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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