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Gene: GRN |
Gene summary for GRN |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | GRN | Gene ID | 2896 |
| Gene name | granulin precursor | |
| Gene Alias | CLN11 | |
| Cytomap | 17q21.31 | |
| Gene Type | protein-coding | GO ID | GO:0001525 | UniProtAcc | P28799 |
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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 |
| 2896 | GRN | GSM4909281 | Human | Breast | IDC | 2.91e-07 | 3.28e-01 | 0.21 |
| 2896 | GRN | GSM4909285 | Human | Breast | IDC | 2.22e-18 | 4.80e-01 | 0.21 |
| 2896 | GRN | GSM4909286 | Human | Breast | IDC | 8.29e-08 | 2.18e-01 | 0.1081 |
| 2896 | GRN | GSM4909295 | Human | Breast | IDC | 1.62e-06 | 4.85e-01 | 0.0898 |
| 2896 | GRN | GSM4909296 | Human | Breast | IDC | 3.69e-03 | -1.69e-01 | 0.1524 |
| 2896 | GRN | GSM4909297 | Human | Breast | IDC | 8.68e-05 | -2.82e-02 | 0.1517 |
| 2896 | GRN | GSM4909305 | Human | Breast | IDC | 4.85e-02 | 2.44e-01 | 0.0436 |
| 2896 | GRN | GSM4909306 | Human | Breast | IDC | 1.12e-02 | 2.12e-01 | 0.1564 |
| 2896 | GRN | GSM4909311 | Human | Breast | IDC | 6.52e-20 | 1.10e-01 | 0.1534 |
| 2896 | GRN | GSM4909312 | Human | Breast | IDC | 4.34e-05 | 1.66e-01 | 0.1552 |
| 2896 | GRN | GSM4909317 | Human | Breast | IDC | 3.20e-17 | 5.66e-01 | 0.1355 |
| 2896 | GRN | GSM4909319 | Human | Breast | IDC | 1.87e-23 | 5.04e-02 | 0.1563 |
| 2896 | GRN | GSM4909321 | Human | Breast | IDC | 4.37e-15 | 3.42e-01 | 0.1559 |
| 2896 | GRN | brca2 | Human | Breast | Precancer | 2.95e-14 | 4.05e-01 | -0.024 |
| 2896 | GRN | brca3 | Human | Breast | Precancer | 4.34e-09 | 3.58e-01 | -0.0263 |
| 2896 | GRN | NCCBC11 | Human | Breast | DCIS | 1.26e-04 | 2.77e-01 | 0.1232 |
| 2896 | GRN | NCCBC14 | Human | Breast | DCIS | 5.06e-09 | 5.59e-02 | 0.2021 |
| 2896 | GRN | NCCBC2 | Human | Breast | DCIS | 1.60e-03 | 2.27e-01 | 0.1554 |
| 2896 | GRN | NCCBC3 | Human | Breast | DCIS | 2.36e-22 | 6.80e-01 | 0.1198 |
| 2896 | GRN | NCCBC5 | Human | Breast | DCIS | 5.74e-12 | 1.36e-01 | 0.2046 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 |
| 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 | ||
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| 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 | ||
| 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 |
| GO:00311033 | Esophagus | ESCC | axon regeneration | 37/8552 | 52/18723 | 1.75e-04 | 1.14e-03 | 37 |
| GO:00070423 | Esophagus | ESCC | lysosomal lumen acidification | 11/8552 | 11/18723 | 1.80e-04 | 1.16e-03 | 11 |
| GO:006156415 | Esophagus | ESCC | axon development | 251/8552 | 467/18723 | 2.41e-04 | 1.49e-03 | 251 |
| GO:001097516 | Esophagus | ESCC | regulation of neuron projection development | 240/8552 | 445/18723 | 2.48e-04 | 1.53e-03 | 240 |
| GO:006049118 | Esophagus | ESCC | regulation of cell projection assembly | 110/8552 | 188/18723 | 2.60e-04 | 1.58e-03 | 110 |
| GO:00100016 | Esophagus | ESCC | glial cell differentiation | 129/8552 | 225/18723 | 2.73e-04 | 1.65e-03 | 129 |
| GO:0043525110 | Esophagus | ESCC | positive regulation of neuron apoptotic process | 40/8552 | 58/18723 | 2.83e-04 | 1.71e-03 | 40 |
| GO:003432918 | Esophagus | ESCC | cell junction assembly | 227/8552 | 420/18723 | 3.06e-04 | 1.83e-03 | 227 |
| GO:004352317 | Esophagus | ESCC | regulation of neuron apoptotic process | 122/8552 | 212/18723 | 3.21e-04 | 1.90e-03 | 122 |
| GO:00311024 | Esophagus | ESCC | neuron projection regeneration | 41/8552 | 60/18723 | 3.25e-04 | 1.91e-03 | 41 |
| GO:00450885 | Esophagus | ESCC | regulation of innate immune response | 125/8552 | 218/18723 | 3.34e-04 | 1.96e-03 | 125 |
| GO:012003218 | Esophagus | ESCC | regulation of plasma membrane bounded cell projection assembly | 108/8552 | 186/18723 | 4.37e-04 | 2.46e-03 | 108 |
| GO:00507775 | Esophagus | ESCC | negative regulation of immune response | 112/8552 | 194/18723 | 4.67e-04 | 2.62e-03 | 112 |
| GO:004408812 | Esophagus | ESCC | regulation of vacuole organization | 32/8552 | 45/18723 | 4.87e-04 | 2.70e-03 | 32 |
| GO:00519606 | Esophagus | ESCC | regulation of nervous system development | 237/8552 | 443/18723 | 5.02e-04 | 2.78e-03 | 237 |
| GO:005067817 | Esophagus | ESCC | regulation of epithelial cell proliferation | 206/8552 | 381/18723 | 5.51e-04 | 3.02e-03 | 206 |
| GO:000268316 | Esophagus | ESCC | negative regulation of immune system process | 231/8552 | 434/18723 | 8.48e-04 | 4.36e-03 | 231 |
| GO:01200347 | Esophagus | ESCC | positive regulation of plasma membrane bounded cell projection assembly | 64/8552 | 105/18723 | 1.15e-03 | 5.70e-03 | 64 |
| GO:000166720 | Esophagus | ESCC | ameboidal-type cell migration | 250/8552 | 475/18723 | 1.22e-03 | 5.97e-03 | 250 |
| GO:00519625 | Esophagus | ESCC | positive regulation of nervous system development | 149/8552 | 272/18723 | 1.50e-03 | 7.06e-03 | 149 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| GRN | SORT1 | GRN_SORT1 | GRN | Breast | DCIS |
| GRN | SORT1 | GRN_SORT1 | GRN | Cervix | ADJ |
| GRN | SORT1 | GRN_SORT1 | GRN | Cervix | CC |
| GRN | SORT1 | GRN_SORT1 | GRN | Cervix | Precancer |
| GRN | SORT1 | GRN_SORT1 | GRN | CRC | AD |
| GRN | SORT1 | GRN_SORT1 | GRN | CRC | ADJ |
| GRN | SORT1 | GRN_SORT1 | GRN | CRC | MSI-H |
| GRN | SORT1 | GRN_SORT1 | GRN | CRC | MSS |
| GRN | SORT1 | GRN_SORT1 | GRN | CRC | SER |
| GRN | SORT1 | GRN_SORT1 | GRN | Endometrium | ADJ |
| GRN | SORT1 | GRN_SORT1 | GRN | Endometrium | AEH |
| GRN | SORT1 | GRN_SORT1 | GRN | Endometrium | Healthy |
| GRN | SORT1 | GRN_SORT1 | GRN | Esophagus | ESCC |
| GRN | SORT1 | GRN_SORT1 | GRN | GC | ADJ |
| GRN | SORT1 | GRN_SORT1 | GRN | HNSCC | ADJ |
| GRN | SORT1 | GRN_SORT1 | GRN | HNSCC | OSCC |
| GRN | SORT1 | GRN_SORT1 | GRN | HNSCC | Precancer |
| GRN | SORT1 | GRN_SORT1 | GRN | Liver | HCC |
| GRN | SORT1 | GRN_SORT1 | GRN | Lung | AAH |
| GRN | SORT1 | GRN_SORT1 | GRN | Lung | ADJ |
| Page: 1 2 |
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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 |
| GRN | SNV | Missense_Mutation | novel | c.340N>G | p.Gln114Glu | p.Q114E | P28799 | protein_coding | tolerated(0.45) | benign(0.257) | TCGA-AC-A5XS-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | femara | SD |
| GRN | SNV | Missense_Mutation | novel | c.1623G>T | p.Trp541Cys | p.W541C | P28799 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-B6-A402-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | PD |
| GRN | SNV | Missense_Mutation | c.1292N>T | p.Ala431Val | p.A431V | P28799 | protein_coding | deleterious(0.04) | benign(0.037) | TCGA-D8-A1XQ-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| GRN | insertion | Frame_Shift_Ins | novel | c.159_160insGCTA | p.Ser54AlafsTer12 | p.S54Afs*12 | P28799 | protein_coding | TCGA-BH-A0AY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | SD | |||
| GRN | insertion | In_Frame_Ins | novel | c.161_162insTGAAAGAAGCCAGTTGCAGAT | p.Ser54_Arg55insGluArgSerGlnLeuGlnIle | p.S54_R55insERSQLQI | P28799 | protein_coding | TCGA-BH-A0AY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | SD | |||
| GRN | deletion | Frame_Shift_Del | novel | c.1015delN | p.His340ThrfsTer21 | p.H340Tfs*21 | P28799 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| GRN | deletion | Frame_Shift_Del | novel | c.1331delG | p.Cys444LeufsTer47 | p.C444Lfs*47 | P28799 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | ||
| GRN | SNV | Missense_Mutation | c.1404N>C | p.Gln468His | p.Q468H | P28799 | protein_coding | tolerated(0.08) | probably_damaging(0.909) | TCGA-BI-A0VS-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| GRN | SNV | Missense_Mutation | rs751651838 | c.529N>T | p.Arg177Cys | p.R177C | P28799 | protein_coding | deleterious(0) | probably_damaging(0.984) | TCGA-C5-A1M6-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PD |
| GRN | SNV | Missense_Mutation | c.104G>A | p.Gly35Glu | p.G35E | P28799 | protein_coding | tolerated(0.09) | benign(0.129) | TCGA-EK-A3GK-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 |
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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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