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Gene: SHC3 |
Gene summary for SHC3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SHC3 | Gene ID | 53358 |
| Gene name | SHC adaptor protein 3 | |
| Gene Alias | N-Shc | |
| Cytomap | 9q22.1 | |
| Gene Type | protein-coding | GO ID | GO:0007154 | UniProtAcc | Q92529 |
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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 |
| 53358 | SHC3 | RNA-P25T1-P25T1-1 | Human | Lung | AIS | 6.02e-10 | 5.69e-01 | -0.2116 |
| 53358 | SHC3 | RNA-P25T1-P25T1-2 | Human | Lung | AIS | 3.01e-06 | 7.82e-01 | -0.1941 |
| 53358 | SHC3 | RNA-P25T1-P25T1-3 | Human | Lung | AIS | 1.55e-06 | 6.97e-01 | -0.2107 |
| 53358 | SHC3 | RNA-P25T1-P25T1-4 | Human | Lung | AIS | 1.04e-14 | 7.33e-01 | -0.2119 |
| 53358 | SHC3 | RNA-P6T1-P6T1-4 | Human | Lung | MIAC | 5.20e-04 | 7.61e-01 | -0.0263 |
| Page: 1 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma |
| ∗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:005125826 | Esophagus | HGIN | protein polymerization | 66/2587 | 297/18723 | 4.96e-05 | 1.19e-03 | 66 |
| GO:003004120 | Esophagus | HGIN | actin filament polymerization | 40/2587 | 191/18723 | 4.29e-03 | 3.82e-02 | 40 |
| GO:0051258111 | Esophagus | ESCC | protein polymerization | 183/8552 | 297/18723 | 1.94e-08 | 3.75e-07 | 183 |
| GO:000701527 | Esophagus | ESCC | actin filament organization | 259/8552 | 442/18723 | 2.37e-08 | 4.50e-07 | 259 |
| GO:000815420 | Esophagus | ESCC | actin polymerization or depolymerization | 130/8552 | 218/18723 | 2.19e-05 | 1.88e-04 | 130 |
| GO:0030041110 | Esophagus | ESCC | actin filament polymerization | 114/8552 | 191/18723 | 6.46e-05 | 4.92e-04 | 114 |
| GO:005125822 | Liver | HCC | protein polymerization | 182/7958 | 297/18723 | 4.17e-11 | 1.58e-09 | 182 |
| GO:000701522 | Liver | HCC | actin filament organization | 252/7958 | 442/18723 | 3.83e-10 | 1.25e-08 | 252 |
| GO:000815422 | Liver | HCC | actin polymerization or depolymerization | 130/7958 | 218/18723 | 2.31e-07 | 4.14e-06 | 130 |
| GO:003004122 | Liver | HCC | actin filament polymerization | 116/7958 | 191/18723 | 2.66e-07 | 4.68e-06 | 116 |
| GO:000717312 | Lung | AIS | epidermal growth factor receptor signaling pathway | 29/1849 | 108/18723 | 3.99e-07 | 3.23e-05 | 29 |
| GO:003812712 | Lung | AIS | ERBB signaling pathway | 30/1849 | 121/18723 | 1.60e-06 | 9.91e-05 | 30 |
| GO:000717322 | Lung | MIAC | epidermal growth factor receptor signaling pathway | 20/967 | 108/18723 | 5.82e-07 | 9.33e-05 | 20 |
| GO:003812722 | Lung | MIAC | ERBB signaling pathway | 20/967 | 121/18723 | 3.70e-06 | 3.88e-04 | 20 |
| GO:0007015112 | Thyroid | PTC | actin filament organization | 225/5968 | 442/18723 | 3.76e-17 | 3.44e-15 | 225 |
| GO:0051258113 | Thyroid | PTC | protein polymerization | 154/5968 | 297/18723 | 5.35e-13 | 2.66e-11 | 154 |
| GO:000815426 | Thyroid | PTC | actin polymerization or depolymerization | 117/5968 | 218/18723 | 1.85e-11 | 7.21e-10 | 117 |
| GO:003004125 | Thyroid | PTC | actin filament polymerization | 99/5968 | 191/18723 | 7.40e-09 | 1.85e-07 | 99 |
| GO:0007015210 | Thyroid | ATC | actin filament organization | 227/6293 | 442/18723 | 5.96e-15 | 3.85e-13 | 227 |
| GO:005125829 | Thyroid | ATC | protein polymerization | 159/6293 | 297/18723 | 9.33e-13 | 3.96e-11 | 159 |
| Page: 1 2 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0451022 | Lung | AIS | Focal adhesion | 57/961 | 203/8465 | 3.17e-11 | 3.43e-09 | 2.19e-09 | 57 |
| hsa0510023 | Lung | AIS | Bacterial invasion of epithelial cells | 25/961 | 77/8465 | 6.03e-07 | 2.44e-05 | 1.56e-05 | 25 |
| hsa0152122 | Lung | AIS | EGFR tyrosine kinase inhibitor resistance | 20/961 | 79/8465 | 3.92e-04 | 3.85e-03 | 2.47e-03 | 20 |
| hsa0401221 | Lung | AIS | ErbB signaling pathway | 21/961 | 85/8465 | 4.06e-04 | 3.87e-03 | 2.47e-03 | 21 |
| hsa015222 | Lung | AIS | Endocrine resistance | 22/961 | 98/8465 | 1.21e-03 | 9.02e-03 | 5.77e-03 | 22 |
| hsa0472221 | Lung | AIS | Neurotrophin signaling pathway | 25/961 | 119/8465 | 1.59e-03 | 1.05e-02 | 6.72e-03 | 25 |
| hsa0521421 | Lung | AIS | Glioma | 17/961 | 75/8465 | 3.76e-03 | 2.00e-02 | 1.28e-02 | 17 |
| hsa0522521 | Lung | AIS | Hepatocellular carcinoma | 31/961 | 168/8465 | 4.11e-03 | 2.15e-02 | 1.38e-02 | 31 |
| hsa0522022 | Lung | AIS | Chronic myeloid leukemia | 17/961 | 76/8465 | 4.34e-03 | 2.23e-02 | 1.43e-02 | 17 |
| hsa0492621 | Lung | AIS | Relaxin signaling pathway | 25/961 | 129/8465 | 4.95e-03 | 2.47e-02 | 1.58e-02 | 25 |
| hsa0493521 | Lung | AIS | Growth hormone synthesis, secretion and action | 23/961 | 120/8465 | 7.85e-03 | 3.58e-02 | 2.29e-02 | 23 |
| hsa0491522 | Lung | AIS | Estrogen signaling pathway | 25/961 | 138/8465 | 1.18e-02 | 4.83e-02 | 3.09e-02 | 25 |
| hsa0451032 | Lung | AIS | Focal adhesion | 57/961 | 203/8465 | 3.17e-11 | 3.43e-09 | 2.19e-09 | 57 |
| hsa0510033 | Lung | AIS | Bacterial invasion of epithelial cells | 25/961 | 77/8465 | 6.03e-07 | 2.44e-05 | 1.56e-05 | 25 |
| hsa0152132 | Lung | AIS | EGFR tyrosine kinase inhibitor resistance | 20/961 | 79/8465 | 3.92e-04 | 3.85e-03 | 2.47e-03 | 20 |
| hsa0401231 | Lung | AIS | ErbB signaling pathway | 21/961 | 85/8465 | 4.06e-04 | 3.87e-03 | 2.47e-03 | 21 |
| hsa0152211 | Lung | AIS | Endocrine resistance | 22/961 | 98/8465 | 1.21e-03 | 9.02e-03 | 5.77e-03 | 22 |
| hsa0472231 | Lung | AIS | Neurotrophin signaling pathway | 25/961 | 119/8465 | 1.59e-03 | 1.05e-02 | 6.72e-03 | 25 |
| hsa052143 | Lung | AIS | Glioma | 17/961 | 75/8465 | 3.76e-03 | 2.00e-02 | 1.28e-02 | 17 |
| hsa0522531 | Lung | AIS | Hepatocellular carcinoma | 31/961 | 168/8465 | 4.11e-03 | 2.15e-02 | 1.38e-02 | 31 |
| 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 |
| ∗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 |
| SHC3 | SNV | Missense_Mutation | c.1157N>A | p.Gly386Glu | p.G386E | Q92529 | protein_coding | tolerated(0.11) | benign(0.037) | TCGA-A8-A075-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | epirubicin | CR | |
| SHC3 | SNV | Missense_Mutation | novel | c.669G>A | p.Met223Ile | p.M223I | Q92529 | protein_coding | deleterious(0.04) | benign(0.067) | TCGA-A8-A08H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SHC3 | SNV | Missense_Mutation | rs771029388 | c.962N>T | p.Arg321Leu | p.R321L | Q92529 | protein_coding | deleterious(0) | probably_damaging(0.953) | TCGA-B6-A0I1-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| SHC3 | SNV | Missense_Mutation | rs138519014 | c.991N>A | p.Glu331Lys | p.E331K | Q92529 | protein_coding | tolerated(0.08) | benign(0.027) | TCGA-JX-A3Q0-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD |
| SHC3 | SNV | Missense_Mutation | c.50N>T | p.Ser17Leu | p.S17L | Q92529 | protein_coding | deleterious(0) | benign(0.437) | TCGA-AY-A69D-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| SHC3 | SNV | Missense_Mutation | c.605N>T | p.Arg202Ile | p.R202I | Q92529 | protein_coding | deleterious(0.02) | benign(0.045) | TCGA-CA-6718-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | PD | |
| SHC3 | SNV | Missense_Mutation | rs17852381 | c.1661N>A | p.Arg554Gln | p.R554Q | Q92529 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-F4-6570-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SHC3 | SNV | Missense_Mutation | rs771029388 | c.962N>A | p.Arg321Gln | p.R321Q | Q92529 | protein_coding | deleterious(0) | probably_damaging(0.957) | TCGA-A5-A0G1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SHC3 | SNV | Missense_Mutation | novel | c.1159N>T | p.Asp387Tyr | p.D387Y | Q92529 | protein_coding | tolerated(0.73) | benign(0.254) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| SHC3 | SNV | Missense_Mutation | novel | c.1088N>T | p.Arg363Ile | p.R363I | Q92529 | protein_coding | deleterious(0.03) | benign(0.077) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 |
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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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