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Gene: SHANK2 |
Gene summary for SHANK2 |
Gene summary. |
Gene information | Species | Human | Gene symbol | SHANK2 | Gene ID | 22941 |
Gene name | SH3 and multiple ankyrin repeat domains 2 | |
Gene Alias | AUTS17 | |
Cytomap | 11q13.3-q13.4 | |
Gene Type | protein-coding | GO ID | GO:0003008 | UniProtAcc | Q9UPX8 |
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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 |
22941 | SHANK2 | HTA11_6818_2000001011 | Human | Colorectum | AD | 4.37e-02 | 4.85e-01 | 0.0112 |
22941 | SHANK2 | HTA11_6818_2000001021 | Human | Colorectum | AD | 9.18e-04 | 6.04e-01 | 0.0588 |
22941 | SHANK2 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 7.51e-16 | -5.09e-01 | 0.294 |
22941 | SHANK2 | A001-C-207 | Human | Colorectum | FAP | 1.80e-03 | -1.39e-01 | 0.1278 |
22941 | SHANK2 | A015-C-203 | Human | Colorectum | FAP | 1.96e-33 | -3.84e-01 | -0.1294 |
22941 | SHANK2 | A015-C-204 | Human | Colorectum | FAP | 7.67e-05 | -2.47e-01 | -0.0228 |
22941 | SHANK2 | A014-C-040 | Human | Colorectum | FAP | 3.61e-04 | -9.17e-02 | -0.1184 |
22941 | SHANK2 | A002-C-201 | Human | Colorectum | FAP | 1.47e-12 | -1.98e-01 | 0.0324 |
22941 | SHANK2 | A002-C-203 | Human | Colorectum | FAP | 1.11e-04 | 1.54e-02 | 0.2786 |
22941 | SHANK2 | A001-C-119 | Human | Colorectum | FAP | 3.98e-09 | -3.80e-01 | -0.1557 |
22941 | SHANK2 | A001-C-108 | Human | Colorectum | FAP | 3.73e-21 | -1.84e-01 | -0.0272 |
22941 | SHANK2 | A002-C-205 | Human | Colorectum | FAP | 3.09e-24 | -2.56e-01 | -0.1236 |
22941 | SHANK2 | A001-C-104 | Human | Colorectum | FAP | 2.67e-04 | -6.23e-02 | 0.0184 |
22941 | SHANK2 | A015-C-006 | Human | Colorectum | FAP | 4.96e-19 | -2.73e-01 | -0.0994 |
22941 | SHANK2 | A015-C-106 | Human | Colorectum | FAP | 3.20e-14 | -1.81e-01 | -0.0511 |
22941 | SHANK2 | A002-C-114 | Human | Colorectum | FAP | 2.32e-22 | -3.80e-01 | -0.1561 |
22941 | SHANK2 | A015-C-104 | Human | Colorectum | FAP | 9.30e-40 | -5.12e-01 | -0.1899 |
22941 | SHANK2 | A001-C-014 | Human | Colorectum | FAP | 8.13e-21 | -3.26e-01 | 0.0135 |
22941 | SHANK2 | A002-C-016 | Human | Colorectum | FAP | 1.37e-26 | -3.79e-01 | 0.0521 |
22941 | SHANK2 | A015-C-002 | Human | Colorectum | FAP | 3.76e-14 | -3.86e-01 | -0.0763 |
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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:0034329 | Colorectum | AD | cell junction assembly | 136/3918 | 420/18723 | 2.02e-08 | 1.15e-06 | 136 |
GO:0050808 | Colorectum | AD | synapse organization | 112/3918 | 426/18723 | 4.25e-03 | 2.92e-02 | 112 |
GO:00343292 | Colorectum | MSS | cell junction assembly | 120/3467 | 420/18723 | 2.51e-07 | 1.07e-05 | 120 |
GO:00508082 | Colorectum | MSS | synapse organization | 101/3467 | 426/18723 | 3.96e-03 | 2.89e-02 | 101 |
GO:00343293 | Colorectum | FAP | cell junction assembly | 105/2622 | 420/18723 | 1.03e-09 | 2.18e-07 | 105 |
GO:00508083 | Colorectum | FAP | synapse organization | 91/2622 | 426/18723 | 1.90e-05 | 4.74e-04 | 91 |
GO:00343294 | Colorectum | CRC | cell junction assembly | 83/2078 | 420/18723 | 1.08e-07 | 1.29e-05 | 83 |
GO:00508084 | Colorectum | CRC | synapse organization | 71/2078 | 426/18723 | 3.02e-04 | 4.76e-03 | 71 |
GO:0050804 | Colorectum | CRC | modulation of chemical synaptic transmission | 70/2078 | 439/18723 | 1.15e-03 | 1.33e-02 | 70 |
GO:0099177 | Colorectum | CRC | regulation of trans-synaptic signaling | 70/2078 | 440/18723 | 1.23e-03 | 1.38e-02 | 70 |
GO:00343299 | Endometrium | AEH | cell junction assembly | 78/2100 | 420/18723 | 4.80e-06 | 1.24e-04 | 78 |
GO:00508086 | Endometrium | AEH | synapse organization | 67/2100 | 426/18723 | 2.67e-03 | 1.94e-02 | 67 |
GO:003432914 | Endometrium | EEC | cell junction assembly | 79/2168 | 420/18723 | 8.37e-06 | 1.85e-04 | 79 |
GO:005080812 | Endometrium | EEC | synapse organization | 68/2168 | 426/18723 | 3.73e-03 | 2.49e-02 | 68 |
GO:003432918 | Esophagus | ESCC | cell junction assembly | 227/8552 | 420/18723 | 3.06e-04 | 1.83e-03 | 227 |
GO:00353297 | Esophagus | ESCC | hippo signaling | 26/8552 | 40/18723 | 1.08e-02 | 3.66e-02 | 26 |
GO:00343296 | Liver | NAFLD | cell junction assembly | 66/1882 | 420/18723 | 1.64e-04 | 3.00e-03 | 66 |
GO:0035329 | Liver | NAFLD | hippo signaling | 10/1882 | 40/18723 | 5.20e-03 | 4.05e-02 | 10 |
GO:0035331 | Liver | NAFLD | negative regulation of hippo signaling | 5/1882 | 13/18723 | 6.58e-03 | 4.69e-02 | 5 |
GO:00353311 | Liver | Cirrhotic | negative regulation of hippo signaling | 8/4634 | 13/18723 | 5.27e-03 | 2.70e-02 | 8 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa04724 | Colorectum | CRC | Glutamatergic synapse | 24/1091 | 115/8465 | 1.07e-02 | 4.74e-02 | 3.21e-02 | 24 |
hsa047241 | Colorectum | CRC | Glutamatergic synapse | 24/1091 | 115/8465 | 1.07e-02 | 4.74e-02 | 3.21e-02 | 24 |
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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 |
SHANK2 | SNV | Missense_Mutation | novel | c.3344N>T | p.Gly1115Val | p.G1115V | protein_coding | tolerated_low_confidence(0.13) | benign(0.096) | TCGA-21-1083-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
SHANK2 | SNV | Missense_Mutation | novel | c.2636N>T | p.Ser879Ile | p.S879I | protein_coding | tolerated(0.06) | benign(0.12) | TCGA-22-4599-01 | Lung | lung squamous cell carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
SHANK2 | SNV | Missense_Mutation | rs782616036 | c.2233N>A | p.Glu745Lys | p.E745K | protein_coding | tolerated(0.13) | benign(0.092) | TCGA-33-4566-01 | Lung | lung squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
SHANK2 | SNV | Missense_Mutation | novel | c.665C>T | p.Ser222Leu | p.S222L | protein_coding | tolerated(0.2) | benign(0.087) | TCGA-37-4130-01 | Lung | lung squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
SHANK2 | SNV | Missense_Mutation | novel | c.3594N>C | p.Trp1198Cys | p.W1198C | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-37-A5EN-01 | Lung | lung squamous cell carcinoma | Male | <65 | III/IV | Unknown | Unknown | SD | |
SHANK2 | SNV | Missense_Mutation | c.1900N>A | p.Ala634Thr | p.A634T | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-56-7222-01 | Lung | lung squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | cisplatin | PD | ||
SHANK2 | SNV | Missense_Mutation | c.3341N>T | p.Ser1114Leu | p.S1114L | protein_coding | tolerated(0.11) | possibly_damaging(0.46) | TCGA-66-2773-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | ||
SHANK2 | SNV | Missense_Mutation | novel | c.776A>T | p.Gln259Leu | p.Q259L | protein_coding | deleterious(0.01) | possibly_damaging(0.624) | TCGA-66-2785-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
SHANK2 | SNV | Missense_Mutation | novel | c.1207G>C | p.Glu403Gln | p.E403Q | protein_coding | deleterious(0.04) | probably_damaging(0.999) | TCGA-77-7141-01 | Lung | lung squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
SHANK2 | SNV | Missense_Mutation | novel | c.281N>T | p.Gly94Val | p.G94V | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-77-A5GH-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
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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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