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Gene: SMARCD2 |
Gene summary for SMARCD2 |
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Gene information | Species | Human | Gene symbol | SMARCD2 | Gene ID | 6603 |
Gene name | SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2 | |
Gene Alias | BAF60B | |
Cytomap | 17q23.3 | |
Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | Q92925 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
6603 | SMARCD2 | P130T-E | Human | Esophagus | ESCC | 3.32e-26 | 5.29e-01 | 0.1676 |
6603 | SMARCD2 | HCC1_Meng | Human | Liver | HCC | 1.16e-50 | 2.91e-02 | 0.0246 |
6603 | SMARCD2 | HCC2_Meng | Human | Liver | HCC | 1.26e-24 | 1.37e-01 | 0.0107 |
6603 | SMARCD2 | HCC2 | Human | Liver | HCC | 7.54e-05 | 2.23e+00 | 0.5341 |
6603 | SMARCD2 | Pt13.b | Human | Liver | HCC | 1.35e-02 | 4.87e-02 | 0.0251 |
6603 | SMARCD2 | Pt14.b | Human | Liver | HCC | 2.28e-02 | 1.76e-01 | 0.018 |
6603 | SMARCD2 | S014 | Human | Liver | HCC | 1.43e-07 | 3.90e-01 | 0.2254 |
6603 | SMARCD2 | S015 | Human | Liver | HCC | 4.34e-03 | 3.02e-01 | 0.2375 |
6603 | SMARCD2 | S016 | Human | Liver | HCC | 5.42e-07 | 2.77e-01 | 0.2243 |
6603 | SMARCD2 | S027 | Human | Liver | HCC | 3.83e-10 | 6.89e-01 | 0.2446 |
6603 | SMARCD2 | S028 | Human | Liver | HCC | 5.87e-18 | 6.95e-01 | 0.2503 |
6603 | SMARCD2 | S029 | Human | Liver | HCC | 7.22e-13 | 6.32e-01 | 0.2581 |
6603 | SMARCD2 | C04 | Human | Oral cavity | OSCC | 3.70e-08 | 5.51e-01 | 0.2633 |
6603 | SMARCD2 | C21 | Human | Oral cavity | OSCC | 2.57e-06 | 3.25e-01 | 0.2678 |
6603 | SMARCD2 | C30 | Human | Oral cavity | OSCC | 1.36e-38 | 1.52e+00 | 0.3055 |
6603 | SMARCD2 | C38 | Human | Oral cavity | OSCC | 9.54e-09 | 1.22e+00 | 0.172 |
6603 | SMARCD2 | C43 | Human | Oral cavity | OSCC | 2.25e-11 | 4.50e-01 | 0.1704 |
6603 | SMARCD2 | C46 | Human | Oral cavity | OSCC | 2.00e-20 | 6.91e-01 | 0.1673 |
6603 | SMARCD2 | C51 | Human | Oral cavity | OSCC | 2.33e-03 | 5.65e-01 | 0.2674 |
6603 | SMARCD2 | C57 | Human | Oral cavity | OSCC | 3.48e-02 | 2.31e-01 | 0.1679 |
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∗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 |
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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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GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:0022411 | Colorectum | AD | cellular component disassembly | 147/3918 | 443/18723 | 8.53e-10 | 6.76e-08 | 147 |
GO:0032984 | Colorectum | AD | protein-containing complex disassembly | 81/3918 | 224/18723 | 9.41e-08 | 4.65e-06 | 81 |
GO:0006325 | Colorectum | AD | chromatin organization | 119/3918 | 409/18723 | 4.85e-05 | 8.33e-04 | 119 |
GO:0032986 | Colorectum | AD | protein-DNA complex disassembly | 12/3918 | 20/18723 | 1.60e-04 | 2.21e-03 | 12 |
GO:0031498 | Colorectum | AD | chromatin disassembly | 11/3918 | 20/18723 | 8.39e-04 | 8.21e-03 | 11 |
GO:0006337 | Colorectum | AD | nucleosome disassembly | 10/3918 | 18/18723 | 1.31e-03 | 1.15e-02 | 10 |
GO:0006338 | Colorectum | AD | chromatin remodeling | 70/3918 | 255/18723 | 7.44e-03 | 4.53e-02 | 70 |
GO:00224111 | Colorectum | SER | cellular component disassembly | 114/2897 | 443/18723 | 1.17e-08 | 9.59e-07 | 114 |
GO:00329841 | Colorectum | SER | protein-containing complex disassembly | 61/2897 | 224/18723 | 4.17e-06 | 1.60e-04 | 61 |
GO:00063251 | Colorectum | SER | chromatin organization | 89/2897 | 409/18723 | 4.15e-04 | 6.17e-03 | 89 |
GO:00314981 | Colorectum | SER | chromatin disassembly | 8/2897 | 20/18723 | 7.14e-03 | 4.99e-02 | 8 |
GO:00329861 | Colorectum | SER | protein-DNA complex disassembly | 8/2897 | 20/18723 | 7.14e-03 | 4.99e-02 | 8 |
GO:00224112 | Colorectum | MSS | cellular component disassembly | 130/3467 | 443/18723 | 1.44e-08 | 8.46e-07 | 130 |
GO:00329842 | Colorectum | MSS | protein-containing complex disassembly | 69/3467 | 224/18723 | 5.61e-06 | 1.50e-04 | 69 |
GO:00329862 | Colorectum | MSS | protein-DNA complex disassembly | 12/3467 | 20/18723 | 4.55e-05 | 8.35e-04 | 12 |
GO:00063252 | Colorectum | MSS | chromatin organization | 107/3467 | 409/18723 | 7.22e-05 | 1.21e-03 | 107 |
GO:00314982 | Colorectum | MSS | chromatin disassembly | 11/3467 | 20/18723 | 2.77e-04 | 3.67e-03 | 11 |
GO:00063371 | Colorectum | MSS | nucleosome disassembly | 10/3467 | 18/18723 | 4.76e-04 | 5.58e-03 | 10 |
GO:0022411111 | Esophagus | ESCC | cellular component disassembly | 305/8552 | 443/18723 | 1.94e-23 | 4.57e-21 | 305 |
GO:003298416 | Esophagus | ESCC | protein-containing complex disassembly | 151/8552 | 224/18723 | 3.45e-11 | 1.15e-09 | 151 |
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Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa04714 | Colorectum | AD | Thermogenesis | 120/2092 | 232/8465 | 2.76e-19 | 1.16e-17 | 7.37e-18 | 120 |
hsa05225 | Colorectum | AD | Hepatocellular carcinoma | 59/2092 | 168/8465 | 1.50e-03 | 8.69e-03 | 5.54e-03 | 59 |
hsa047141 | Colorectum | AD | Thermogenesis | 120/2092 | 232/8465 | 2.76e-19 | 1.16e-17 | 7.37e-18 | 120 |
hsa052251 | Colorectum | AD | Hepatocellular carcinoma | 59/2092 | 168/8465 | 1.50e-03 | 8.69e-03 | 5.54e-03 | 59 |
hsa047142 | Colorectum | SER | Thermogenesis | 106/1580 | 232/8465 | 1.15e-21 | 6.34e-20 | 4.61e-20 | 106 |
hsa047143 | Colorectum | SER | Thermogenesis | 106/1580 | 232/8465 | 1.15e-21 | 6.34e-20 | 4.61e-20 | 106 |
hsa047144 | Colorectum | MSS | Thermogenesis | 113/1875 | 232/8465 | 1.52e-19 | 4.62e-18 | 2.83e-18 | 113 |
hsa052252 | Colorectum | MSS | Hepatocellular carcinoma | 56/1875 | 168/8465 | 5.04e-04 | 3.45e-03 | 2.11e-03 | 56 |
hsa047145 | Colorectum | MSS | Thermogenesis | 113/1875 | 232/8465 | 1.52e-19 | 4.62e-18 | 2.83e-18 | 113 |
hsa052253 | Colorectum | MSS | Hepatocellular carcinoma | 56/1875 | 168/8465 | 5.04e-04 | 3.45e-03 | 2.11e-03 | 56 |
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 |
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 |
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Cell-cell communication analysis |
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Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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Single-cell gene regulatory network inference analysis |
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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 |
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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 |
SMARCD2 | SNV | Missense_Mutation | c.1268T>A | p.Phe423Tyr | p.F423Y | Q92925 | protein_coding | tolerated(0.05) | probably_damaging(0.991) | TCGA-A8-A09Q-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | anastrozole | SD | |
SMARCD2 | insertion | Frame_Shift_Ins | novel | c.1320_1321insTTCCTAGCCTTTCTAAACCAAAGTTCTTTGCCATTCCTACAAGCCCA | p.His441PhefsTer26 | p.H441Ffs*26 | Q92925 | protein_coding | TCGA-B6-A0IN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | ||
SMARCD2 | SNV | Missense_Mutation | c.417G>C | p.Lys139Asn | p.K139N | Q92925 | protein_coding | deleterious(0) | possibly_damaging(0.764) | TCGA-IR-A3LH-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
SMARCD2 | SNV | Missense_Mutation | rs757140754 | c.1417C>T | p.Arg473Cys | p.R473C | Q92925 | protein_coding | tolerated(0.06) | benign(0.003) | TCGA-A6-6780-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
SMARCD2 | SNV | Missense_Mutation | c.1009N>T | p.Leu337Phe | p.L337F | Q92925 | protein_coding | deleterious(0.03) | probably_damaging(0.926) | TCGA-AD-6895-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD | |
SMARCD2 | SNV | Missense_Mutation | rs750388563 | c.1300N>A | p.Ala434Thr | p.A434T | Q92925 | protein_coding | tolerated(0.22) | benign(0.022) | TCGA-AY-4071-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
SMARCD2 | SNV | Missense_Mutation | rs866391405 | c.1100N>A | p.Arg367Gln | p.R367Q | Q92925 | protein_coding | tolerated(0.06) | probably_damaging(0.995) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
SMARCD2 | SNV | Missense_Mutation | rs749078019 | c.314N>A | p.Pro105His | p.P105H | Q92925 | protein_coding | deleterious(0) | possibly_damaging(0.838) | TCGA-AZ-6601-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
SMARCD2 | SNV | Missense_Mutation | c.1507G>A | p.Ala503Thr | p.A503T | Q92925 | protein_coding | tolerated(0.58) | benign(0.114) | TCGA-CA-6718-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | PD | |
SMARCD2 | SNV | Missense_Mutation | rs759533186 | c.1186N>A | p.Asp396Asn | p.D396N | Q92925 | protein_coding | deleterious(0.04) | probably_damaging(0.964) | TCGA-EI-6917-01 | Colorectum | rectum adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5fluorouracil+oxaciplatina+l-folinian | SD |
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Related drugs of malignant transformation related genes |
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(DGIdb 4.0) |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
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