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Gene: GNLY |
Gene summary for GNLY |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | GNLY | Gene ID | 10578 |
| Gene name | granulysin | |
| Gene Alias | D2S69E | |
| Cytomap | 2p11.2 | |
| Gene Type | protein-coding | GO ID | GO:0001906 | UniProtAcc | B4E3H9 |
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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 |
| 10578 | GNLY | C21 | Human | Oral cavity | OSCC | 7.74e-71 | 2.10e+00 | 0.2678 |
| 10578 | GNLY | C30 | Human | Oral cavity | OSCC | 3.82e-29 | 1.32e+00 | 0.3055 |
| 10578 | GNLY | C38 | Human | Oral cavity | OSCC | 6.76e-08 | 9.78e-01 | 0.172 |
| 10578 | GNLY | C43 | Human | Oral cavity | OSCC | 5.50e-03 | 7.34e-02 | 0.1704 |
| 10578 | GNLY | C46 | Human | Oral cavity | OSCC | 1.26e-23 | 5.15e-01 | 0.1673 |
| 10578 | GNLY | C51 | Human | Oral cavity | OSCC | 1.85e-19 | 1.16e+00 | 0.2674 |
| 10578 | GNLY | C57 | Human | Oral cavity | OSCC | 3.16e-08 | 2.47e-01 | 0.1679 |
| 10578 | GNLY | C06 | Human | Oral cavity | OSCC | 3.16e-12 | 9.78e-01 | 0.2699 |
| 10578 | GNLY | C07 | Human | Oral cavity | OSCC | 1.82e-07 | 1.11e+00 | 0.2491 |
| 10578 | GNLY | C08 | Human | Oral cavity | OSCC | 1.10e-20 | 4.41e-01 | 0.1919 |
| 10578 | GNLY | C86 | Human | Oral cavity | OSCC | 5.12e-04 | 5.31e-01 | 0.161 |
| 10578 | GNLY | C09 | Human | Oral cavity | OSCC | 4.07e-07 | 1.62e-01 | 0.1431 |
| 10578 | GNLY | LN22 | Human | Oral cavity | OSCC | 2.12e-03 | 6.41e-01 | 0.1733 |
| 10578 | GNLY | LN46 | Human | Oral cavity | OSCC | 7.02e-20 | 4.58e-01 | 0.1666 |
| 10578 | GNLY | LP15 | Human | Oral cavity | LP | 1.36e-03 | 1.39e+00 | 0.2174 |
| 10578 | GNLY | SYSMH2 | Human | Oral cavity | OSCC | 2.80e-09 | 6.36e-01 | 0.2326 |
| 10578 | GNLY | SYSMH5 | Human | Oral cavity | OSCC | 2.62e-02 | 2.34e+00 | 0.0647 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma |
| ∗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). |
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| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
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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. |
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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 |
| GNLY | SNV | Missense_Mutation | c.281N>T | p.Arg94Met | p.R94M | protein_coding | tolerated(0.26) | benign(0.01) | TCGA-D8-A27K-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin+cyclophosphamid | SD | ||
| GNLY | SNV | Missense_Mutation | c.146N>T | p.Ser49Phe | p.S49F | protein_coding | deleterious(0) | possibly_damaging(0.657) | TCGA-EW-A1IZ-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | taxotere | SD | ||
| GNLY | insertion | In_Frame_Ins | novel | c.513_514insAAATCTGGTCTCCAT | p.Pro171_Leu172insLysSerGlyLeuHis | p.P171_L172insKSGLH | protein_coding | TCGA-AN-A03X-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |||
| GNLY | SNV | Missense_Mutation | novel | c.158N>A | p.Pro53His | p.P53H | protein_coding | deleterious(0) | possibly_damaging(0.879) | TCGA-ZX-AA5X-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD | |
| GNLY | SNV | Missense_Mutation | c.329N>A | p.Pro110His | p.P110H | protein_coding | deleterious(0.05) | probably_damaging(0.979) | TCGA-AZ-4313-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| GNLY | SNV | Missense_Mutation | rs201165294 | c.148C>T | p.Arg50Cys | p.R50C | protein_coding | deleterious(0.03) | benign(0.255) | TCGA-AG-4007-01 | Colorectum | rectum adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD | |
| GNLY | SNV | Missense_Mutation | rs778757101 | c.356N>T | p.Ala119Val | p.A119V | protein_coding | tolerated(0.13) | possibly_damaging(0.457) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
| GNLY | SNV | Missense_Mutation | novel | c.514N>A | p.Leu172Ile | p.L172I | protein_coding | deleterious_low_confidence(0) | benign(0.005) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD | |
| GNLY | SNV | Missense_Mutation | c.338N>T | p.Arg113Ile | p.R113I | protein_coding | tolerated(0.06) | benign(0.009) | TCGA-AX-A05Z-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | SD | ||
| GNLY | SNV | Missense_Mutation | rs767011139 | c.386G>A | p.Arg129Gln | p.R129Q | protein_coding | tolerated(0.47) | benign(0) | TCGA-BG-A0VX-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
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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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