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Gene: SMCR8 |
Gene summary for SMCR8 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SMCR8 | Gene ID | 140775 |
| Gene name | SMCR8-C9orf72 complex subunit | |
| Gene Alias | DENND8A | |
| Cytomap | 17p11.2 | |
| Gene Type | protein-coding | GO ID | GO:0000045 | UniProtAcc | Q8TEV9 |
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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 |
| 140775 | SMCR8 | HCC1_Meng | Human | Liver | HCC | 7.10e-28 | 4.04e-02 | 0.0246 |
| 140775 | SMCR8 | HCC2_Meng | Human | Liver | HCC | 3.93e-11 | 5.56e-02 | 0.0107 |
| 140775 | SMCR8 | HCC1 | Human | Liver | HCC | 1.47e-10 | 2.17e+00 | 0.5336 |
| 140775 | SMCR8 | HCC2 | Human | Liver | HCC | 2.35e-20 | 3.13e+00 | 0.5341 |
| 140775 | SMCR8 | HCC5 | Human | Liver | HCC | 1.06e-08 | 1.31e+00 | 0.4932 |
| 140775 | SMCR8 | S014 | Human | Liver | HCC | 7.13e-03 | 1.97e-01 | 0.2254 |
| 140775 | SMCR8 | S027 | Human | Liver | HCC | 2.88e-03 | 3.97e-01 | 0.2446 |
| 140775 | SMCR8 | S028 | Human | Liver | HCC | 1.31e-13 | 4.79e-01 | 0.2503 |
| 140775 | SMCR8 | S029 | Human | Liver | HCC | 5.99e-09 | 4.50e-01 | 0.2581 |
| Page: 1 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease |
| ∗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:000989622 | Liver | HCC | positive regulation of catabolic process | 335/7958 | 492/18723 | 3.83e-31 | 1.87e-28 | 335 |
| GO:003133122 | Liver | HCC | positive regulation of cellular catabolic process | 295/7958 | 427/18723 | 3.20e-29 | 1.45e-26 | 295 |
| GO:001623621 | Liver | HCC | macroautophagy | 204/7958 | 291/18723 | 8.66e-22 | 1.41e-19 | 204 |
| GO:002241112 | Liver | HCC | cellular component disassembly | 282/7958 | 443/18723 | 1.02e-19 | 1.38e-17 | 282 |
| GO:001050621 | Liver | HCC | regulation of autophagy | 210/7958 | 317/18723 | 7.59e-18 | 8.45e-16 | 210 |
| GO:001056322 | Liver | HCC | negative regulation of phosphorus metabolic process | 259/7958 | 442/18723 | 4.29e-12 | 1.92e-10 | 259 |
| GO:004593622 | Liver | HCC | negative regulation of phosphate metabolic process | 258/7958 | 441/18723 | 6.00e-12 | 2.60e-10 | 258 |
| GO:000989522 | Liver | HCC | negative regulation of catabolic process | 196/7958 | 320/18723 | 7.98e-12 | 3.35e-10 | 196 |
| GO:003133022 | Liver | HCC | negative regulation of cellular catabolic process | 164/7958 | 262/18723 | 3.52e-11 | 1.35e-09 | 164 |
| GO:004232622 | Liver | HCC | negative regulation of phosphorylation | 227/7958 | 385/18723 | 3.98e-11 | 1.52e-09 | 227 |
| GO:005134822 | Liver | HCC | negative regulation of transferase activity | 166/7958 | 268/18723 | 8.97e-11 | 3.18e-09 | 166 |
| GO:000703311 | Liver | HCC | vacuole organization | 119/7958 | 180/18723 | 1.22e-10 | 4.25e-09 | 119 |
| GO:001624111 | Liver | HCC | regulation of macroautophagy | 96/7958 | 141/18723 | 6.82e-10 | 2.14e-08 | 96 |
| GO:001063912 | Liver | HCC | negative regulation of organelle organization | 204/7958 | 348/18723 | 7.67e-10 | 2.37e-08 | 204 |
| GO:003298411 | Liver | HCC | protein-containing complex disassembly | 138/7958 | 224/18723 | 5.59e-09 | 1.46e-07 | 138 |
| GO:003367322 | Liver | HCC | negative regulation of kinase activity | 144/7958 | 237/18723 | 9.76e-09 | 2.45e-07 | 144 |
| GO:000193322 | Liver | HCC | negative regulation of protein phosphorylation | 196/7958 | 342/18723 | 1.95e-08 | 4.63e-07 | 196 |
| GO:19050371 | Liver | HCC | autophagosome organization | 70/7958 | 103/18723 | 1.52e-07 | 2.82e-06 | 70 |
| GO:00105082 | Liver | HCC | positive regulation of autophagy | 81/7958 | 124/18723 | 2.34e-07 | 4.17e-06 | 81 |
| GO:00000451 | Liver | HCC | autophagosome assembly | 67/7958 | 99/18723 | 3.56e-07 | 6.07e-06 | 67 |
| Page: 1 2 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0501422 | Liver | HCC | Amyotrophic lateral sclerosis | 252/4020 | 364/8465 | 8.85e-18 | 7.41e-16 | 4.12e-16 | 252 |
| hsa0502222 | Liver | HCC | Pathways of neurodegeneration - multiple diseases | 298/4020 | 476/8465 | 6.59e-12 | 1.30e-10 | 7.22e-11 | 298 |
| hsa0414021 | Liver | HCC | Autophagy - animal | 99/4020 | 141/8465 | 3.08e-08 | 4.70e-07 | 2.61e-07 | 99 |
| hsa0501432 | Liver | HCC | Amyotrophic lateral sclerosis | 252/4020 | 364/8465 | 8.85e-18 | 7.41e-16 | 4.12e-16 | 252 |
| hsa0502232 | Liver | HCC | Pathways of neurodegeneration - multiple diseases | 298/4020 | 476/8465 | 6.59e-12 | 1.30e-10 | 7.22e-11 | 298 |
| hsa0414031 | Liver | HCC | Autophagy - animal | 99/4020 | 141/8465 | 3.08e-08 | 4.70e-07 | 2.61e-07 | 99 |
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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 |
| SMCR8 | SNV | Missense_Mutation | novel | c.1547G>C | p.Ser516Thr | p.S516T | Q8TEV9 | protein_coding | deleterious(0.01) | probably_damaging(0.994) | TCGA-A2-A3XU-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | arimidex | PD |
| SMCR8 | SNV | Missense_Mutation | c.2221N>A | p.Ala741Thr | p.A741T | Q8TEV9 | protein_coding | tolerated(0.42) | benign(0) | TCGA-A7-A13F-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | SD | |
| SMCR8 | SNV | Missense_Mutation | c.1469N>T | p.Gln490Leu | p.Q490L | Q8TEV9 | protein_coding | tolerated(0.05) | probably_damaging(0.994) | TCGA-A8-A06Z-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| SMCR8 | SNV | Missense_Mutation | novel | c.2423N>A | p.Ser808Asn | p.S808N | Q8TEV9 | protein_coding | deleterious(0) | probably_damaging(0.946) | TCGA-AO-A128-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
| SMCR8 | SNV | Missense_Mutation | c.1476C>A | p.Ser492Arg | p.S492R | Q8TEV9 | protein_coding | tolerated(0.18) | benign(0.003) | TCGA-B6-A0IC-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| SMCR8 | SNV | Missense_Mutation | novel | c.1534N>C | p.Ile512Leu | p.I512L | Q8TEV9 | protein_coding | tolerated(0.13) | benign(0.034) | TCGA-B6-A0IN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD |
| SMCR8 | insertion | Frame_Shift_Ins | novel | c.2792_2793insAGGCAGAAAGAAGAGGTTTTTTTGTTTGTTTTGTTTTTTAAGA | p.Ser932GlyfsTer19 | p.S932Gfs*19 | Q8TEV9 | protein_coding | TCGA-A2-A0D4-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | ||
| SMCR8 | insertion | Frame_Shift_Ins | novel | c.327_328insAGTTCTCCAGGAAACCATTTCAGGATCTACTTTTGTTATCTGAGATATT | p.Ala111SerfsTer35 | p.A111Sfs*35 | Q8TEV9 | protein_coding | TCGA-BH-A0AY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | SD | |||
| SMCR8 | insertion | In_Frame_Ins | novel | c.142_143insCCATGCTCTTAGAAAAGTTCTCCAGAAAACCAT | p.Lys47_Leu48insProMetLeuLeuGluLysPheSerArgLysPro | p.K47_L48insPMLLEKFSRKP | Q8TEV9 | protein_coding | TCGA-BH-A0HK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | ||
| SMCR8 | deletion | Frame_Shift_Del | novel | c.2024delN | p.Ser676AlafsTer3 | p.S676Afs*3 | Q8TEV9 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
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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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