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Gene: SHFM1 |
Gene summary for SHFM1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SHFM1 | Gene ID | 7979 |
| Gene name | SEM1 26S proteasome subunit | |
| Gene Alias | C7orf76 | |
| Cytomap | 7q21.3 | |
| Gene Type | protein-coding | GO ID | NA | UniProtAcc | P60896 |
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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 |
| 7979 | SHFM1 | GSM4909280 | Human | Breast | Precancer | 2.58e-03 | -4.59e-01 | 0.0305 |
| 7979 | SHFM1 | GSM4909281 | Human | Breast | IDC | 9.92e-21 | -4.59e-01 | 0.21 |
| 7979 | SHFM1 | GSM4909282 | Human | Breast | IDC | 3.31e-22 | -4.59e-01 | -0.0288 |
| 7979 | SHFM1 | GSM4909285 | Human | Breast | IDC | 4.25e-21 | -4.59e-01 | 0.21 |
| 7979 | SHFM1 | GSM4909286 | Human | Breast | IDC | 2.31e-20 | -4.59e-01 | 0.1081 |
| 7979 | SHFM1 | GSM4909287 | Human | Breast | IDC | 3.47e-27 | -4.59e-01 | 0.2057 |
| 7979 | SHFM1 | GSM4909288 | Human | Breast | IDC | 5.54e-07 | -4.59e-01 | 0.0988 |
| 7979 | SHFM1 | GSM4909289 | Human | Breast | IDC | 4.60e-05 | -4.59e-01 | 0.1064 |
| 7979 | SHFM1 | GSM4909290 | Human | Breast | IDC | 9.70e-20 | -4.59e-01 | 0.2096 |
| 7979 | SHFM1 | GSM4909291 | Human | Breast | IDC | 3.67e-16 | -4.59e-01 | 0.1753 |
| 7979 | SHFM1 | GSM4909292 | Human | Breast | IDC | 2.45e-02 | -4.59e-01 | 0.1236 |
| 7979 | SHFM1 | GSM4909293 | Human | Breast | IDC | 3.31e-22 | -4.59e-01 | 0.1581 |
| 7979 | SHFM1 | GSM4909294 | Human | Breast | IDC | 4.25e-21 | -4.59e-01 | 0.2022 |
| 7979 | SHFM1 | GSM4909295 | Human | Breast | IDC | 7.13e-13 | -4.59e-01 | 0.0898 |
| 7979 | SHFM1 | GSM4909296 | Human | Breast | IDC | 1.82e-21 | -4.59e-01 | 0.1524 |
| 7979 | SHFM1 | GSM4909297 | Human | Breast | IDC | 5.96e-23 | -4.59e-01 | 0.1517 |
| 7979 | SHFM1 | GSM4909298 | Human | Breast | IDC | 2.31e-20 | -4.59e-01 | 0.1551 |
| 7979 | SHFM1 | GSM4909299 | Human | Breast | IDC | 2.31e-20 | -4.59e-01 | 0.035 |
| 7979 | SHFM1 | GSM4909300 | Human | Breast | IDC | 1.87e-11 | -4.59e-01 | 0.0334 |
| 7979 | SHFM1 | GSM4909301 | Human | Breast | IDC | 9.92e-21 | -4.59e-01 | 0.1577 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| GC |  | CAG: Chronic atrophic gastritis |
| CAG with IM: Chronic atrophic gastritis with intestinal metaplasia | ||
| CSG: Chronic superficial gastritis | ||
| GC: Gastric cancer | ||
| SIM: Severe intestinal metaplasia | ||
| WIM: Wild intestinal metaplasia | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗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 |
| Page: 1 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0516925 | Endometrium | EEC | Epstein-Barr virus infection | 47/1237 | 202/8465 | 6.17e-04 | 4.41e-03 | 3.29e-03 | 47 |
| hsa0501236 | Endometrium | EEC | Parkinson disease | 117/1237 | 266/8465 | 5.97e-32 | 9.82e-30 | 7.32e-30 | 117 |
| hsa0501635 | Endometrium | EEC | Huntington disease | 120/1237 | 306/8465 | 3.86e-27 | 4.23e-25 | 3.15e-25 | 120 |
| hsa0502035 | Endometrium | EEC | Prion disease | 111/1237 | 273/8465 | 1.01e-26 | 8.27e-25 | 6.16e-25 | 111 |
| hsa0501435 | Endometrium | EEC | Amyotrophic lateral sclerosis | 128/1237 | 364/8465 | 9.83e-24 | 4.04e-22 | 3.01e-22 | 128 |
| hsa0501035 | Endometrium | EEC | Alzheimer disease | 126/1237 | 384/8465 | 2.25e-20 | 7.40e-19 | 5.52e-19 | 126 |
| hsa0502235 | Endometrium | EEC | Pathways of neurodegeneration - multiple diseases | 140/1237 | 476/8465 | 9.49e-18 | 2.60e-16 | 1.94e-16 | 140 |
| hsa0305034 | Endometrium | EEC | Proteasome | 23/1237 | 46/8465 | 1.41e-08 | 2.33e-07 | 1.73e-07 | 23 |
| hsa0501733 | Endometrium | EEC | Spinocerebellar ataxia | 43/1237 | 143/8465 | 1.46e-06 | 2.01e-05 | 1.50e-05 | 43 |
| hsa0516934 | Endometrium | EEC | Epstein-Barr virus infection | 47/1237 | 202/8465 | 6.17e-04 | 4.41e-03 | 3.29e-03 | 47 |
| hsa0501239 | Esophagus | HGIN | Parkinson disease | 124/1383 | 266/8465 | 5.95e-32 | 9.70e-30 | 7.70e-30 | 124 |
| hsa0501630 | Esophagus | HGIN | Huntington disease | 129/1383 | 306/8465 | 6.81e-28 | 7.41e-26 | 5.88e-26 | 129 |
| hsa0502030 | Esophagus | HGIN | Prion disease | 117/1383 | 273/8465 | 4.15e-26 | 3.38e-24 | 2.69e-24 | 117 |
| hsa0501430 | Esophagus | HGIN | Amyotrophic lateral sclerosis | 140/1383 | 364/8465 | 2.13e-25 | 1.16e-23 | 9.19e-24 | 140 |
| hsa0502230 | Esophagus | HGIN | Pathways of neurodegeneration - multiple diseases | 153/1383 | 476/8465 | 1.22e-18 | 4.41e-17 | 3.50e-17 | 153 |
| hsa0501030 | Esophagus | HGIN | Alzheimer disease | 130/1383 | 384/8465 | 5.26e-18 | 1.71e-16 | 1.36e-16 | 130 |
| hsa0305027 | Esophagus | HGIN | Proteasome | 34/1383 | 46/8465 | 6.45e-18 | 1.91e-16 | 1.52e-16 | 34 |
| hsa0501727 | Esophagus | HGIN | Spinocerebellar ataxia | 43/1383 | 143/8465 | 2.68e-05 | 3.64e-04 | 2.89e-04 | 43 |
| hsa0516930 | Esophagus | HGIN | Epstein-Barr virus infection | 55/1383 | 202/8465 | 5.13e-05 | 6.19e-04 | 4.92e-04 | 55 |
| hsa05012114 | Esophagus | HGIN | Parkinson disease | 124/1383 | 266/8465 | 5.95e-32 | 9.70e-30 | 7.70e-30 | 124 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 |
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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 |
| Page: 1 |
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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 |
| Page: 1 |
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