|
Gene: SMARCC2 |
Gene summary for SMARCC2 |
Gene summary. |
Gene information | Species | Human | Gene symbol | SMARCC2 | Gene ID | 6601 |
Gene name | SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 2 | |
Gene Alias | BAF170 | |
Cytomap | 12q13.2 | |
Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | Q8TAQ2 |
Top |
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 |
6601 | SMARCC2 | LZE2T | Human | Esophagus | ESCC | 2.51e-10 | 7.68e-01 | 0.082 |
6601 | SMARCC2 | LZE4T | Human | Esophagus | ESCC | 6.15e-10 | 4.51e-01 | 0.0811 |
6601 | SMARCC2 | LZE5T | Human | Esophagus | ESCC | 4.17e-04 | 3.78e-01 | 0.0514 |
6601 | SMARCC2 | LZE7T | Human | Esophagus | ESCC | 1.12e-15 | 8.92e-01 | 0.0667 |
6601 | SMARCC2 | LZE8T | Human | Esophagus | ESCC | 5.18e-07 | 3.28e-01 | 0.067 |
6601 | SMARCC2 | LZE20T | Human | Esophagus | ESCC | 2.74e-10 | 3.03e-01 | 0.0662 |
6601 | SMARCC2 | LZE22T | Human | Esophagus | ESCC | 1.73e-08 | 5.86e-01 | 0.068 |
6601 | SMARCC2 | LZE24T | Human | Esophagus | ESCC | 2.45e-24 | 7.23e-01 | 0.0596 |
6601 | SMARCC2 | LZE21T | Human | Esophagus | ESCC | 3.41e-08 | 5.16e-01 | 0.0655 |
6601 | SMARCC2 | LZE6T | Human | Esophagus | ESCC | 6.50e-07 | 2.38e-01 | 0.0845 |
6601 | SMARCC2 | P1T-E | Human | Esophagus | ESCC | 1.26e-20 | 9.13e-01 | 0.0875 |
6601 | SMARCC2 | P2T-E | Human | Esophagus | ESCC | 5.28e-51 | 1.02e+00 | 0.1177 |
6601 | SMARCC2 | P4T-E | Human | Esophagus | ESCC | 1.72e-27 | 5.90e-01 | 0.1323 |
6601 | SMARCC2 | P5T-E | Human | Esophagus | ESCC | 2.06e-28 | 5.50e-01 | 0.1327 |
6601 | SMARCC2 | P8T-E | Human | Esophagus | ESCC | 5.83e-37 | 5.91e-01 | 0.0889 |
6601 | SMARCC2 | P9T-E | Human | Esophagus | ESCC | 6.27e-22 | 3.97e-01 | 0.1131 |
6601 | SMARCC2 | P10T-E | Human | Esophagus | ESCC | 1.97e-29 | 5.62e-01 | 0.116 |
6601 | SMARCC2 | P11T-E | Human | Esophagus | ESCC | 8.38e-12 | 5.09e-01 | 0.1426 |
6601 | SMARCC2 | P12T-E | Human | Esophagus | ESCC | 1.79e-39 | 7.28e-01 | 0.1122 |
6601 | SMARCC2 | P15T-E | Human | Esophagus | ESCC | 1.55e-27 | 6.84e-01 | 0.1149 |
Page: 1 2 3 4 5 6 7 |
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. |
Top |
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:00063375 | Oral cavity | OSCC | nucleosome disassembly | 13/7305 | 18/18723 | 4.45e-03 | 1.79e-02 | 13 |
GO:002241117 | Prostate | BPH | cellular component disassembly | 121/3107 | 443/18723 | 6.34e-09 | 2.25e-07 | 121 |
GO:00329849 | Prostate | BPH | protein-containing complex disassembly | 65/3107 | 224/18723 | 2.19e-06 | 3.60e-05 | 65 |
GO:00063259 | Prostate | BPH | chromatin organization | 101/3107 | 409/18723 | 1.52e-05 | 1.94e-04 | 101 |
GO:00329867 | Prostate | BPH | protein-DNA complex disassembly | 10/3107 | 20/18723 | 5.73e-04 | 3.98e-03 | 10 |
GO:00063382 | Prostate | BPH | chromatin remodeling | 62/3107 | 255/18723 | 9.47e-04 | 5.97e-03 | 62 |
GO:00063374 | Prostate | BPH | nucleosome disassembly | 8/3107 | 18/18723 | 5.17e-03 | 2.43e-02 | 8 |
GO:00314985 | Prostate | BPH | chromatin disassembly | 8/3107 | 20/18723 | 1.09e-02 | 4.50e-02 | 8 |
GO:002241118 | Prostate | Tumor | cellular component disassembly | 121/3246 | 443/18723 | 8.10e-08 | 2.23e-06 | 121 |
GO:000632514 | Prostate | Tumor | chromatin organization | 104/3246 | 409/18723 | 2.02e-05 | 2.62e-04 | 104 |
GO:003298413 | Prostate | Tumor | protein-containing complex disassembly | 61/3246 | 224/18723 | 1.36e-04 | 1.26e-03 | 61 |
GO:003298614 | Prostate | Tumor | protein-DNA complex disassembly | 10/3246 | 20/18723 | 8.21e-04 | 5.54e-03 | 10 |
GO:000633811 | Prostate | Tumor | chromatin remodeling | 63/3246 | 255/18723 | 1.73e-03 | 1.02e-02 | 63 |
GO:000633712 | Prostate | Tumor | nucleosome disassembly | 8/3246 | 18/18723 | 6.81e-03 | 3.09e-02 | 8 |
GO:0022411112 | Skin | cSCC | cellular component disassembly | 201/4864 | 443/18723 | 4.09e-19 | 5.69e-17 | 201 |
GO:003298418 | Skin | cSCC | protein-containing complex disassembly | 98/4864 | 224/18723 | 5.31e-09 | 1.77e-07 | 98 |
GO:000632519 | Skin | cSCC | chromatin organization | 147/4864 | 409/18723 | 4.41e-06 | 6.52e-05 | 147 |
GO:003298617 | Skin | cSCC | protein-DNA complex disassembly | 15/4864 | 20/18723 | 6.31e-06 | 8.91e-05 | 15 |
GO:000633714 | Skin | cSCC | nucleosome disassembly | 13/4864 | 18/18723 | 5.27e-05 | 5.35e-04 | 13 |
GO:000633812 | Skin | cSCC | chromatin remodeling | 94/4864 | 255/18723 | 7.58e-05 | 7.26e-04 | 94 |
Page: 1 2 3 |
Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa04714211 | Esophagus | ESCC | Thermogenesis | 163/4205 | 232/8465 | 9.22e-11 | 1.14e-09 | 5.86e-10 | 163 |
hsa0522518 | Esophagus | ESCC | Hepatocellular carcinoma | 109/4205 | 168/8465 | 4.27e-05 | 1.88e-04 | 9.64e-05 | 109 |
hsa04714310 | Esophagus | ESCC | Thermogenesis | 163/4205 | 232/8465 | 9.22e-11 | 1.14e-09 | 5.86e-10 | 163 |
hsa0522519 | Esophagus | ESCC | Hepatocellular carcinoma | 109/4205 | 168/8465 | 4.27e-05 | 1.88e-04 | 9.64e-05 | 109 |
hsa0471414 | Liver | Cirrhotic | Thermogenesis | 121/2530 | 232/8465 | 5.70e-13 | 1.36e-11 | 8.36e-12 | 121 |
hsa0471415 | Liver | Cirrhotic | Thermogenesis | 121/2530 | 232/8465 | 5.70e-13 | 1.36e-11 | 8.36e-12 | 121 |
hsa0471422 | Liver | HCC | Thermogenesis | 170/4020 | 232/8465 | 5.36e-16 | 2.25e-14 | 1.25e-14 | 170 |
hsa052258 | Liver | HCC | Hepatocellular carcinoma | 106/4020 | 168/8465 | 2.87e-05 | 1.85e-04 | 1.03e-04 | 106 |
hsa0471432 | Liver | HCC | Thermogenesis | 170/4020 | 232/8465 | 5.36e-16 | 2.25e-14 | 1.25e-14 | 170 |
hsa0522511 | Liver | HCC | Hepatocellular carcinoma | 106/4020 | 168/8465 | 2.87e-05 | 1.85e-04 | 1.03e-04 | 106 |
hsa0471430 | Oral cavity | OSCC | Thermogenesis | 138/3704 | 232/8465 | 7.67e-07 | 4.35e-06 | 2.22e-06 | 138 |
hsa0522516 | Oral cavity | OSCC | Hepatocellular carcinoma | 97/3704 | 168/8465 | 1.63e-04 | 5.52e-04 | 2.81e-04 | 97 |
hsa04714113 | Oral cavity | OSCC | Thermogenesis | 138/3704 | 232/8465 | 7.67e-07 | 4.35e-06 | 2.22e-06 | 138 |
hsa0522517 | Oral cavity | OSCC | Hepatocellular carcinoma | 97/3704 | 168/8465 | 1.63e-04 | 5.52e-04 | 2.81e-04 | 97 |
hsa0471428 | Prostate | BPH | Thermogenesis | 110/1718 | 232/8465 | 5.16e-21 | 1.42e-19 | 8.78e-20 | 110 |
hsa0522514 | Prostate | BPH | Hepatocellular carcinoma | 51/1718 | 168/8465 | 1.17e-03 | 5.22e-03 | 3.23e-03 | 51 |
hsa04714112 | Prostate | BPH | Thermogenesis | 110/1718 | 232/8465 | 5.16e-21 | 1.42e-19 | 8.78e-20 | 110 |
hsa0522515 | Prostate | BPH | Hepatocellular carcinoma | 51/1718 | 168/8465 | 1.17e-03 | 5.22e-03 | 3.23e-03 | 51 |
hsa0471429 | Prostate | Tumor | Thermogenesis | 110/1791 | 232/8465 | 1.56e-19 | 3.96e-18 | 2.46e-18 | 110 |
hsa0522522 | Prostate | Tumor | Hepatocellular carcinoma | 53/1791 | 168/8465 | 9.65e-04 | 4.44e-03 | 2.75e-03 | 53 |
Page: 1 2 |
Top |
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 |
Top |
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 |
∗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 |
Top |
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 |
SMARCC2 | SNV | Missense_Mutation | novel | c.1873N>C | p.Ala625Pro | p.A625P | protein_coding | deleterious(0.02) | possibly_damaging(0.729) | TCGA-A8-A096-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
SMARCC2 | SNV | Missense_Mutation | rs200224449 | c.902N>A | p.Arg301His | p.R301H | protein_coding | tolerated(0.17) | probably_damaging(0.927) | TCGA-A8-A0A7-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
SMARCC2 | SNV | Missense_Mutation | rs761098190 | c.3494N>C | p.Asn1165Thr | p.N1165T | protein_coding | deleterious_low_confidence(0.05) | benign(0.015) | TCGA-AQ-A1H3-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | SD | |
SMARCC2 | SNV | Missense_Mutation | rs761098190 | c.3494N>C | p.Asn1165Thr | p.N1165T | protein_coding | deleterious_low_confidence(0.05) | benign(0.015) | TCGA-AR-A1AP-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | SD | |
SMARCC2 | SNV | Missense_Mutation | c.1624N>C | p.Val542Leu | p.V542L | protein_coding | tolerated(0.22) | probably_damaging(0.971) | TCGA-C8-A12K-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
SMARCC2 | SNV | Missense_Mutation | c.3392G>A | p.Gly1131Asp | p.G1131D | protein_coding | deleterious_low_confidence(0.01) | benign(0.219) | TCGA-C8-A12U-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
SMARCC2 | SNV | Missense_Mutation | c.2845N>A | p.Glu949Lys | p.E949K | protein_coding | deleterious(0) | probably_damaging(0.956) | TCGA-C8-A1HM-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | doxorubicin | CR | ||
SMARCC2 | SNV | Missense_Mutation | c.2426G>T | p.Gly809Val | p.G809V | protein_coding | tolerated(0.06) | possibly_damaging(0.696) | TCGA-C8-A26Y-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
SMARCC2 | SNV | Missense_Mutation | c.1606G>A | p.Asp536Asn | p.D536N | protein_coding | deleterious(0) | probably_damaging(0.99) | TCGA-C8-A26Y-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
SMARCC2 | SNV | Missense_Mutation | c.253N>G | p.Lys85Glu | p.K85E | protein_coding | deleterious(0.03) | probably_damaging(0.987) | TCGA-E9-A1NA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD |
Page: 1 2 3 4 5 6 7 8 9 10 11 12 |
Top |
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 |