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Gene: SMARCD1 |
Gene summary for SMARCD1 |
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Gene information | Species | Human | Gene symbol | SMARCD1 | Gene ID | 6602 |
Gene name | SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1 | |
Gene Alias | BAF60A | |
Cytomap | 12q13.12 | |
Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | Q96GM5 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
6602 | SMARCD1 | HTA11_411_2000001011 | Human | Colorectum | SER | 2.67e-02 | 4.72e-01 | -0.2602 |
6602 | SMARCD1 | HTA11_1391_2000001011 | Human | Colorectum | AD | 4.38e-05 | 2.32e-01 | -0.059 |
6602 | SMARCD1 | HTA11_2992_2000001011 | Human | Colorectum | SER | 1.77e-03 | 3.13e-01 | -0.1706 |
6602 | SMARCD1 | HTA11_866_3004761011 | Human | Colorectum | AD | 8.88e-05 | 2.28e-01 | 0.096 |
6602 | SMARCD1 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 4.78e-03 | 2.54e-01 | 0.281 |
6602 | SMARCD1 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 5.87e-17 | 5.44e-01 | 0.3859 |
6602 | SMARCD1 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 1.45e-02 | 2.57e-01 | 0.2585 |
6602 | SMARCD1 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 1.25e-02 | 2.50e-01 | 0.3005 |
6602 | SMARCD1 | LZE4T | Human | Esophagus | ESCC | 9.60e-03 | 1.43e-01 | 0.0811 |
6602 | SMARCD1 | LZE7T | Human | Esophagus | ESCC | 3.45e-06 | 3.45e-01 | 0.0667 |
6602 | SMARCD1 | LZE24T | Human | Esophagus | ESCC | 7.89e-12 | 3.34e-01 | 0.0596 |
6602 | SMARCD1 | P1T-E | Human | Esophagus | ESCC | 3.90e-05 | 4.56e-01 | 0.0875 |
6602 | SMARCD1 | P2T-E | Human | Esophagus | ESCC | 1.44e-45 | 9.14e-01 | 0.1177 |
6602 | SMARCD1 | P4T-E | Human | Esophagus | ESCC | 5.21e-22 | 4.90e-01 | 0.1323 |
6602 | SMARCD1 | P5T-E | Human | Esophagus | ESCC | 4.15e-08 | 1.55e-01 | 0.1327 |
6602 | SMARCD1 | P8T-E | Human | Esophagus | ESCC | 9.72e-23 | 4.26e-01 | 0.0889 |
6602 | SMARCD1 | P9T-E | Human | Esophagus | ESCC | 5.20e-04 | 1.58e-01 | 0.1131 |
6602 | SMARCD1 | P10T-E | Human | Esophagus | ESCC | 1.32e-32 | 6.16e-01 | 0.116 |
6602 | SMARCD1 | P11T-E | Human | Esophagus | ESCC | 2.65e-07 | 3.71e-01 | 0.1426 |
6602 | SMARCD1 | P12T-E | Human | Esophagus | ESCC | 2.38e-23 | 4.15e-01 | 0.1122 |
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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:0006354 | Colorectum | AD | DNA-templated transcription, elongation | 31/3918 | 91/18723 | 2.46e-03 | 1.90e-02 | 31 |
GO:0006368 | Colorectum | AD | transcription elongation from RNA polymerase II promoter | 24/3918 | 69/18723 | 5.35e-03 | 3.52e-02 | 24 |
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 |
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Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa05225 | Colorectum | AD | Hepatocellular carcinoma | 59/2092 | 168/8465 | 1.50e-03 | 8.69e-03 | 5.54e-03 | 59 |
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 |
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 |
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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 |
SMARCD1 | SNV | Missense_Mutation | novel | c.1286A>C | p.Glu429Ala | p.E429A | Q96GM5 | protein_coding | deleterious(0.02) | benign(0.023) | TCGA-EO-A22R-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
SMARCD1 | SNV | Missense_Mutation | c.699N>A | p.Phe233Leu | p.F233L | Q96GM5 | protein_coding | deleterious(0.02) | possibly_damaging(0.817) | TCGA-EO-A22U-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
SMARCD1 | SNV | Missense_Mutation | novel | c.690G>T | p.Lys230Asn | p.K230N | Q96GM5 | protein_coding | deleterious(0) | probably_damaging(0.964) | TCGA-EY-A1GI-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
SMARCD1 | SNV | Missense_Mutation | rs147034181 | c.413G>A | p.Arg138His | p.R138H | Q96GM5 | protein_coding | deleterious(0.03) | probably_damaging(0.943) | TCGA-FI-A2D5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatinum | PD |
SMARCD1 | SNV | Missense_Mutation | novel | c.808N>A | p.Phe270Ile | p.F270I | Q96GM5 | protein_coding | tolerated(0.06) | possibly_damaging(0.749) | TCGA-KP-A3VZ-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
SMARCD1 | deletion | Frame_Shift_Del | novel | c.249delG | p.Asn84ThrfsTer79 | p.N84Tfs*79 | Q96GM5 | protein_coding | TCGA-AP-A1DP-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Chemotherapy | paclitaxel | PD | ||
SMARCD1 | deletion | Frame_Shift_Del | novel | c.249delG | p.Asn84ThrfsTer79 | p.N84Tfs*79 | Q96GM5 | protein_coding | TCGA-AX-A1C4-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
SMARCD1 | SNV | Missense_Mutation | novel | c.1540N>G | p.Asn514Asp | p.N514D | Q96GM5 | protein_coding | tolerated(0.17) | benign(0.334) | TCGA-DD-AACK-01 | Liver | liver hepatocellular carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
SMARCD1 | SNV | Missense_Mutation | novel | c.298N>A | p.Arg100Ser | p.R100S | Q96GM5 | protein_coding | tolerated(0.06) | benign(0.185) | TCGA-53-7626-01 | Lung | lung adenocarcinoma | Female | >=65 | I/II | Unspecific | Cisplatin | PD |
SMARCD1 | SNV | Missense_Mutation | rs764685953 | c.203N>T | p.Arg68Leu | p.R68L | Q96GM5 | protein_coding | tolerated_low_confidence(0.05) | benign(0.11) | TCGA-55-6970-01 | Lung | lung adenocarcinoma | Female | >=65 | III/IV | Chemotherapy | cisplatin | PD |
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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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