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Gene: ALS2 |
Gene summary for ALS2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | ALS2 | Gene ID | 57679 |
| Gene name | alsin Rho guanine nucleotide exchange factor ALS2 | |
| Gene Alias | ALS2CR6 | |
| Cytomap | 2q33.1 | |
| Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | Q96Q42 |
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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 |
| 57679 | ALS2 | LZE24T | Human | Esophagus | ESCC | 3.72e-06 | 7.55e-02 | 0.0596 |
| 57679 | ALS2 | P2T-E | Human | Esophagus | ESCC | 2.51e-05 | 1.06e-01 | 0.1177 |
| 57679 | ALS2 | P4T-E | Human | Esophagus | ESCC | 1.11e-09 | 1.31e-01 | 0.1323 |
| 57679 | ALS2 | P8T-E | Human | Esophagus | ESCC | 6.09e-16 | 1.03e-01 | 0.0889 |
| 57679 | ALS2 | P9T-E | Human | Esophagus | ESCC | 2.66e-03 | 6.23e-02 | 0.1131 |
| 57679 | ALS2 | P10T-E | Human | Esophagus | ESCC | 4.26e-08 | 1.51e-01 | 0.116 |
| 57679 | ALS2 | P12T-E | Human | Esophagus | ESCC | 4.39e-11 | 1.97e-01 | 0.1122 |
| 57679 | ALS2 | P15T-E | Human | Esophagus | ESCC | 8.18e-08 | 1.78e-01 | 0.1149 |
| 57679 | ALS2 | P16T-E | Human | Esophagus | ESCC | 2.23e-07 | 1.18e-01 | 0.1153 |
| 57679 | ALS2 | P21T-E | Human | Esophagus | ESCC | 2.14e-07 | 1.26e-01 | 0.1617 |
| 57679 | ALS2 | P22T-E | Human | Esophagus | ESCC | 3.99e-06 | 8.78e-02 | 0.1236 |
| 57679 | ALS2 | P24T-E | Human | Esophagus | ESCC | 3.38e-11 | 7.69e-02 | 0.1287 |
| 57679 | ALS2 | P26T-E | Human | Esophagus | ESCC | 4.84e-12 | 1.12e-01 | 0.1276 |
| 57679 | ALS2 | P27T-E | Human | Esophagus | ESCC | 1.79e-06 | 7.09e-02 | 0.1055 |
| 57679 | ALS2 | P28T-E | Human | Esophagus | ESCC | 2.10e-12 | 1.11e-01 | 0.1149 |
| 57679 | ALS2 | P30T-E | Human | Esophagus | ESCC | 2.97e-04 | 2.03e-01 | 0.137 |
| 57679 | ALS2 | P31T-E | Human | Esophagus | ESCC | 1.16e-07 | 6.93e-02 | 0.1251 |
| 57679 | ALS2 | P32T-E | Human | Esophagus | ESCC | 1.73e-10 | 1.39e-01 | 0.1666 |
| 57679 | ALS2 | P36T-E | Human | Esophagus | ESCC | 2.52e-03 | 9.60e-02 | 0.1187 |
| 57679 | ALS2 | P37T-E | Human | Esophagus | ESCC | 1.07e-06 | 1.32e-01 | 0.1371 |
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| 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 |
| ∗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:0006979111 | Esophagus | ESCC | response to oxidative stress | 303/8552 | 446/18723 | 7.15e-22 | 1.30e-19 | 303 |
| GO:001605014 | Esophagus | ESCC | vesicle organization | 211/8552 | 300/18723 | 2.85e-18 | 2.87e-16 | 211 |
| GO:001619715 | Esophagus | ESCC | endosomal transport | 168/8552 | 230/18723 | 2.28e-17 | 1.93e-15 | 168 |
| GO:000170119 | Esophagus | ESCC | in utero embryonic development | 243/8552 | 367/18723 | 1.00e-15 | 6.86e-14 | 243 |
| GO:000703417 | Esophagus | ESCC | vacuolar transport | 119/8552 | 157/18723 | 1.16e-14 | 6.30e-13 | 119 |
| GO:007190016 | Esophagus | ESCC | regulation of protein serine/threonine kinase activity | 227/8552 | 359/18723 | 1.12e-11 | 4.10e-10 | 227 |
| GO:00070419 | Esophagus | ESCC | lysosomal transport | 83/8552 | 114/18723 | 3.52e-09 | 7.41e-08 | 83 |
| GO:003253520 | Esophagus | ESCC | regulation of cellular component size | 227/8552 | 383/18723 | 4.77e-08 | 8.60e-07 | 227 |
| GO:000703214 | Esophagus | ESCC | endosome organization | 61/8552 | 82/18723 | 1.13e-07 | 1.85e-06 | 61 |
| GO:000726510 | Esophagus | ESCC | Ras protein signal transduction | 201/8552 | 337/18723 | 1.44e-07 | 2.30e-06 | 201 |
| GO:00719029 | Esophagus | ESCC | positive regulation of protein serine/threonine kinase activity | 124/8552 | 200/18723 | 2.27e-06 | 2.61e-05 | 124 |
| GO:004586018 | Esophagus | ESCC | positive regulation of protein kinase activity | 219/8552 | 386/18723 | 6.91e-06 | 6.97e-05 | 219 |
| GO:003367420 | Esophagus | ESCC | positive regulation of kinase activity | 260/8552 | 467/18723 | 7.26e-06 | 7.22e-05 | 260 |
| GO:004311218 | Esophagus | ESCC | receptor metabolic process | 104/8552 | 166/18723 | 7.44e-06 | 7.37e-05 | 104 |
| GO:00166019 | Esophagus | ESCC | Rac protein signal transduction | 33/8552 | 42/18723 | 1.35e-05 | 1.23e-04 | 33 |
| GO:006156415 | Esophagus | ESCC | axon development | 251/8552 | 467/18723 | 2.41e-04 | 1.49e-03 | 251 |
| GO:00018813 | Esophagus | ESCC | receptor recycling | 25/8552 | 33/18723 | 4.30e-04 | 2.43e-03 | 25 |
| GO:0035020 | Esophagus | ESCC | regulation of Rac protein signal transduction | 17/8552 | 21/18723 | 1.03e-03 | 5.19e-03 | 17 |
| GO:00465789 | Esophagus | ESCC | regulation of Ras protein signal transduction | 106/8552 | 189/18723 | 2.49e-03 | 1.08e-02 | 106 |
| GO:000740915 | Esophagus | ESCC | axonogenesis | 219/8552 | 418/18723 | 3.14e-03 | 1.31e-02 | 219 |
| Page: 1 2 |
| 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 |
| hsa05022210 | Esophagus | ESCC | Pathways of neurodegeneration - multiple diseases | 318/4205 | 476/8465 | 6.10e-15 | 2.04e-13 | 1.05e-13 | 318 |
| hsa0501438 | Esophagus | ESCC | Amyotrophic lateral sclerosis | 266/4205 | 364/8465 | 1.31e-20 | 2.20e-18 | 1.13e-18 | 266 |
| hsa0502238 | Esophagus | ESCC | Pathways of neurodegeneration - multiple diseases | 318/4205 | 476/8465 | 6.10e-15 | 2.04e-13 | 1.05e-13 | 318 |
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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 |
| ALS2 | SNV | Missense_Mutation | c.1234N>A | p.Glu412Lys | p.E412K | Q96Q42 | protein_coding | tolerated(0.18) | possibly_damaging(0.718) | TCGA-A7-A26E-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | cytoxan | SD | |
| ALS2 | SNV | Missense_Mutation | c.2334N>G | p.Phe778Leu | p.F778L | Q96Q42 | protein_coding | tolerated(0.08) | probably_damaging(0.984) | TCGA-A8-A07B-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| ALS2 | SNV | Missense_Mutation | novel | c.3020C>A | p.Ala1007Asp | p.A1007D | Q96Q42 | protein_coding | deleterious(0) | possibly_damaging(0.54) | TCGA-A8-A08R-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| ALS2 | SNV | Missense_Mutation | c.1964N>C | p.Gly655Ala | p.G655A | Q96Q42 | protein_coding | tolerated(0.5) | benign(0.013) | TCGA-BH-A1FU-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| ALS2 | SNV | Missense_Mutation | c.4522N>A | p.Val1508Ile | p.V1508I | Q96Q42 | protein_coding | tolerated(0.37) | benign(0.145) | TCGA-GM-A2DH-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxol | CR | |
| ALS2 | insertion | Frame_Shift_Ins | novel | c.1529_1530insTGAGGCAGGTGGAT | p.Pro511GlufsTer19 | p.P511Efs*19 | Q96Q42 | protein_coding | TCGA-A8-A07R-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Ancillary | zoledronic | SD | ||
| ALS2 | insertion | Nonsense_Mutation | novel | c.3259_3260insTCTCCTTCTATTCCCACAGTTTAAGCCAATGATTAAGC | p.Tyr1087PhefsTer11 | p.Y1087Ffs*11 | Q96Q42 | protein_coding | TCGA-AO-A0JB-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | SD | ||
| ALS2 | insertion | Nonsense_Mutation | novel | c.936_937insTACTTATAAA | p.Thr313TyrfsTer3 | p.T313Yfs*3 | Q96Q42 | protein_coding | TCGA-AR-A0U0-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| ALS2 | SNV | Missense_Mutation | rs765296378 | c.2734C>T | p.Arg912Cys | p.R912C | Q96Q42 | protein_coding | tolerated(0.1) | probably_damaging(1) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| ALS2 | SNV | Missense_Mutation | c.1039G>A | p.Glu347Lys | p.E347K | Q96Q42 | protein_coding | tolerated(0.09) | benign(0.015) | TCGA-LP-A4AW-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 |
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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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