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Gene: PRF1 |
Gene summary for PRF1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PRF1 | Gene ID | 5551 |
| Gene name | perforin 1 | |
| Gene Alias | HPLH2 | |
| Cytomap | 10q22.1 | |
| Gene Type | protein-coding | GO ID | GO:0001771 | UniProtAcc | P14222 |
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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 |
| 5551 | PRF1 | C21 | Human | Oral cavity | OSCC | 7.24e-15 | 6.01e-01 | 0.2678 |
| 5551 | PRF1 | C38 | Human | Oral cavity | OSCC | 6.69e-06 | 5.61e-01 | 0.172 |
| 5551 | PRF1 | ATC2 | Human | Thyroid | ATC | 6.74e-16 | 3.15e+00 | 0.34 |
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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 | ||
| 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:000961515 | Oral cavity | OSCC | response to virus | 215/7305 | 367/18723 | 1.63e-14 | 9.41e-13 | 215 |
| GO:00516074 | Oral cavity | OSCC | defense response to virus | 154/7305 | 265/18723 | 1.96e-10 | 5.63e-09 | 154 |
| GO:01405464 | Oral cavity | OSCC | defense response to symbiont | 154/7305 | 265/18723 | 1.96e-10 | 5.63e-09 | 154 |
| GO:00358218 | Oral cavity | OSCC | modulation of process of other organism | 64/7305 | 106/18723 | 6.70e-06 | 7.36e-05 | 64 |
| GO:0051259 | Oral cavity | OSCC | protein complex oligomerization | 121/7305 | 238/18723 | 1.29e-04 | 9.21e-04 | 121 |
| GO:0009615111 | Thyroid | ATC | response to virus | 173/6293 | 367/18723 | 4.23e-08 | 7.71e-07 | 173 |
| GO:003582121 | Thyroid | ATC | modulation of process of other organism | 55/6293 | 106/18723 | 7.71e-05 | 5.82e-04 | 55 |
| GO:005160712 | Thyroid | ATC | defense response to virus | 115/6293 | 265/18723 | 5.31e-04 | 3.09e-03 | 115 |
| GO:014054612 | Thyroid | ATC | defense response to symbiont | 115/6293 | 265/18723 | 5.31e-04 | 3.09e-03 | 115 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0421018 | Oral cavity | OSCC | Apoptosis | 101/3704 | 136/8465 | 3.34e-13 | 7.00e-12 | 3.56e-12 | 101 |
| hsa0541629 | Oral cavity | OSCC | Viral myocarditis | 39/3704 | 60/8465 | 7.13e-04 | 2.09e-03 | 1.07e-03 | 39 |
| hsa0421019 | Oral cavity | OSCC | Apoptosis | 101/3704 | 136/8465 | 3.34e-13 | 7.00e-12 | 3.56e-12 | 101 |
| hsa05416113 | Oral cavity | OSCC | Viral myocarditis | 39/3704 | 60/8465 | 7.13e-04 | 2.09e-03 | 1.07e-03 | 39 |
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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 |
| PRF1 | SNV | Missense_Mutation | rs754079962 | c.1018G>A | p.Asp340Asn | p.D340N | P14222 | protein_coding | tolerated(0.15) | benign(0.08) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| PRF1 | SNV | Missense_Mutation | c.1435N>T | p.Arg479Trp | p.R479W | P14222 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-AO-A0J4-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| PRF1 | SNV | Missense_Mutation | rs551046401 | c.1153C>T | p.Arg385Trp | p.R385W | P14222 | protein_coding | deleterious(0.02) | benign(0.443) | TCGA-BH-A0E7-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD |
| PRF1 | SNV | Missense_Mutation | novel | c.848N>T | p.Lys283Met | p.K283M | P14222 | protein_coding | deleterious(0) | probably_damaging(0.97) | TCGA-S3-AA15-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | CR |
| PRF1 | insertion | Frame_Shift_Ins | novel | c.1507_1508insGGCAAAGCCTTCATTGC | p.Ser503TrpfsTer12 | p.S503Wfs*12 | P14222 | protein_coding | TCGA-A8-A07J-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | ||
| PRF1 | insertion | In_Frame_Ins | novel | c.1505_1506insCCCTTCCCTTGAGCCCTCTATGGT | p.Lys502delinsAsnProSerLeuGluProSerMetVal | p.K502delinsNPSLEPSMV | P14222 | protein_coding | TCGA-A8-A07J-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | ||
| PRF1 | SNV | Missense_Mutation | rs200589152 | c.1501N>T | p.Pro501Ser | p.P501S | P14222 | protein_coding | tolerated(0.06) | benign(0.172) | TCGA-EA-A3QD-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Chemotherapy | cisplatin | CR |
| PRF1 | SNV | Missense_Mutation | c.212G>T | p.Gly71Val | p.G71V | P14222 | protein_coding | deleterious(0) | possibly_damaging(0.567) | TCGA-ZJ-AB0I-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| PRF1 | SNV | Missense_Mutation | c.83G>A | p.Arg28His | p.R28H | P14222 | protein_coding | tolerated(0.24) | benign(0.251) | TCGA-AA-3947-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| PRF1 | SNV | Missense_Mutation | rs28933376 | c.1304N>T | p.Thr435Met | p.T435M | P14222 | protein_coding | deleterious(0) | probably_damaging(0.981) | TCGA-AA-A01R-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5-fluorouracil | PD |
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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 |
| 5551 | PRF1 | TRANSPORTER, CLINICALLY ACTIONABLE, DRUGGABLE GENOME | IL-2 | ALDESLEUKIN | 15893691 | |
| 5551 | PRF1 | TRANSPORTER, CLINICALLY ACTIONABLE, DRUGGABLE GENOME | emapalumab | EMAPALUMAB | ||
| 5551 | PRF1 | TRANSPORTER, CLINICALLY ACTIONABLE, DRUGGABLE GENOME | inhibitor | 387065583 | ||
| 5551 | PRF1 | TRANSPORTER, CLINICALLY ACTIONABLE, DRUGGABLE GENOME | Emapalumab-lzsg | EMAPALUMAB |
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