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Gene: RYR1 |
Gene summary for RYR1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RYR1 | Gene ID | 6261 |
| Gene name | ryanodine receptor 1 | |
| Gene Alias | CCO | |
| Cytomap | 19q13.2 | |
| Gene Type | protein-coding | GO ID | GO:0001501 | UniProtAcc | P21817 |
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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 |
| 6261 | RYR1 | C30 | Human | Oral cavity | OSCC | 3.12e-30 | 1.22e+00 | 0.3055 |
| 6261 | RYR1 | C38 | Human | Oral cavity | OSCC | 6.65e-03 | 5.69e-01 | 0.172 |
| 6261 | RYR1 | C43 | Human | Oral cavity | OSCC | 2.51e-13 | 3.14e-01 | 0.1704 |
| 6261 | RYR1 | C46 | Human | Oral cavity | OSCC | 1.36e-14 | 4.59e-01 | 0.1673 |
| 6261 | RYR1 | C51 | Human | Oral cavity | OSCC | 1.14e-03 | 2.89e-01 | 0.2674 |
| 6261 | RYR1 | C08 | Human | Oral cavity | OSCC | 1.39e-04 | 1.11e-01 | 0.1919 |
| 6261 | RYR1 | LN22 | Human | Oral cavity | OSCC | 2.07e-15 | 1.69e+00 | 0.1733 |
| 6261 | RYR1 | LN38 | Human | Oral cavity | OSCC | 4.22e-02 | 4.88e-01 | 0.168 |
| 6261 | RYR1 | LN46 | Human | Oral cavity | OSCC | 5.70e-06 | 3.17e-01 | 0.1666 |
| 6261 | RYR1 | SYSMH1 | Human | Oral cavity | OSCC | 8.31e-10 | 2.02e-01 | 0.1127 |
| 6261 | RYR1 | SYSMH2 | Human | Oral cavity | OSCC | 2.37e-03 | 2.78e-01 | 0.2326 |
| 6261 | RYR1 | SYSMH3 | Human | Oral cavity | OSCC | 6.45e-09 | 3.20e-01 | 0.2442 |
| 6261 | RYR1 | SYSMH5 | Human | Oral cavity | OSCC | 5.66e-03 | 2.24e-01 | 0.0647 |
| 6261 | RYR1 | male-WTA | Human | Thyroid | PTC | 2.77e-07 | 9.50e-02 | 0.1037 |
| 6261 | RYR1 | PTC01 | Human | Thyroid | PTC | 1.68e-15 | 3.62e-01 | 0.1899 |
| 6261 | RYR1 | PTC04 | Human | Thyroid | PTC | 5.88e-09 | 2.15e-01 | 0.1927 |
| 6261 | RYR1 | PTC05 | Human | Thyroid | PTC | 2.38e-23 | 6.87e-01 | 0.2065 |
| 6261 | RYR1 | PTC06 | Human | Thyroid | PTC | 9.53e-20 | 4.81e-01 | 0.2057 |
| 6261 | RYR1 | PTC07 | Human | Thyroid | PTC | 5.57e-37 | 6.58e-01 | 0.2044 |
| 6261 | RYR1 | ATC13 | Human | Thyroid | ATC | 2.62e-100 | 2.73e+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:007048219 | Oral cavity | OSCC | response to oxygen levels | 200/7305 | 347/18723 | 1.17e-12 | 5.13e-11 | 200 |
| GO:000166619 | Oral cavity | OSCC | response to hypoxia | 177/7305 | 307/18723 | 2.21e-11 | 7.50e-10 | 177 |
| GO:003629319 | Oral cavity | OSCC | response to decreased oxygen levels | 182/7305 | 322/18723 | 1.14e-10 | 3.41e-09 | 182 |
| GO:005123518 | Oral cavity | OSCC | maintenance of location | 182/7305 | 327/18723 | 6.16e-10 | 1.58e-08 | 182 |
| GO:005165120 | Oral cavity | OSCC | maintenance of location in cell | 121/7305 | 214/18723 | 1.39e-07 | 2.32e-06 | 121 |
| GO:00435887 | Oral cavity | OSCC | skin development | 143/7305 | 263/18723 | 2.77e-07 | 4.27e-06 | 143 |
| GO:001003820 | Oral cavity | OSCC | response to metal ion | 188/7305 | 373/18723 | 4.34e-06 | 5.00e-05 | 188 |
| GO:000150310 | Oral cavity | OSCC | ossification | 203/7305 | 408/18723 | 5.54e-06 | 6.19e-05 | 203 |
| GO:0051259 | Oral cavity | OSCC | protein complex oligomerization | 121/7305 | 238/18723 | 1.29e-04 | 9.21e-04 | 121 |
| GO:007124115 | Oral cavity | OSCC | cellular response to inorganic substance | 111/7305 | 226/18723 | 1.22e-03 | 6.10e-03 | 111 |
| GO:00512622 | Oral cavity | OSCC | protein tetramerization | 48/7305 | 87/18723 | 1.60e-03 | 7.62e-03 | 48 |
| GO:00605378 | Oral cavity | OSCC | muscle tissue development | 185/7305 | 403/18723 | 2.60e-03 | 1.14e-02 | 185 |
| GO:00603484 | Oral cavity | OSCC | bone development | 99/7305 | 205/18723 | 4.13e-03 | 1.68e-02 | 99 |
| GO:00426927 | Oral cavity | OSCC | muscle cell differentiation | 175/7305 | 384/18723 | 4.79e-03 | 1.92e-02 | 175 |
| GO:00147067 | Oral cavity | OSCC | striated muscle tissue development | 174/7305 | 384/18723 | 6.45e-03 | 2.40e-02 | 174 |
| GO:007124816 | Oral cavity | OSCC | cellular response to metal ion | 93/7305 | 197/18723 | 1.14e-02 | 3.85e-02 | 93 |
| GO:0070482113 | Thyroid | PTC | response to oxygen levels | 167/5968 | 347/18723 | 1.51e-10 | 5.03e-09 | 167 |
| GO:0036293113 | Thyroid | PTC | response to decreased oxygen levels | 153/5968 | 322/18723 | 2.71e-09 | 7.52e-08 | 153 |
| GO:0001666113 | Thyroid | PTC | response to hypoxia | 145/5968 | 307/18723 | 1.14e-08 | 2.74e-07 | 145 |
| GO:0051235112 | Thyroid | PTC | maintenance of location | 148/5968 | 327/18723 | 2.30e-07 | 4.07e-06 | 148 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0502228 | Oral cavity | OSCC | Pathways of neurodegeneration - multiple diseases | 292/3704 | 476/8465 | 1.60e-15 | 4.47e-14 | 2.28e-14 | 292 |
| hsa0502028 | Oral cavity | OSCC | Prion disease | 181/3704 | 273/8465 | 2.05e-14 | 5.30e-13 | 2.70e-13 | 181 |
| hsa0501725 | Oral cavity | OSCC | Spinocerebellar ataxia | 86/3704 | 143/8465 | 5.21e-05 | 2.08e-04 | 1.06e-04 | 86 |
| hsa05022112 | Oral cavity | OSCC | Pathways of neurodegeneration - multiple diseases | 292/3704 | 476/8465 | 1.60e-15 | 4.47e-14 | 2.28e-14 | 292 |
| hsa05020112 | Oral cavity | OSCC | Prion disease | 181/3704 | 273/8465 | 2.05e-14 | 5.30e-13 | 2.70e-13 | 181 |
| hsa05017111 | Oral cavity | OSCC | Spinocerebellar ataxia | 86/3704 | 143/8465 | 5.21e-05 | 2.08e-04 | 1.06e-04 | 86 |
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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. |
| 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 |
| RYR1 | SNV | Missense_Mutation | rs866533672 | c.4060G>A | p.Glu1354Lys | p.E1354K | P21817 | protein_coding | tolerated(0.28) | benign(0.092) | TCGA-A1-A0SO-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | SD | |
| RYR1 | SNV | Missense_Mutation | rs200291321 | c.7483G>A | p.Val2495Met | p.V2495M | P21817 | protein_coding | deleterious(0.03) | possibly_damaging(0.707) | TCGA-A2-A25B-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | PD |
| RYR1 | SNV | Missense_Mutation | novel | c.13834T>A | p.Trp4612Arg | p.W4612R | P21817 | protein_coding | tolerated(0.26) | benign(0.001) | TCGA-A7-A56D-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD |
| RYR1 | SNV | Missense_Mutation | rs368516354 | c.224N>A | p.Arg75Gln | p.R75Q | P21817 | protein_coding | deleterious(0) | possibly_damaging(0.856) | TCGA-A8-A06Y-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | PD |
| RYR1 | SNV | Missense_Mutation | rs201276068 | c.9859N>T | p.Arg3287Cys | p.R3287C | P21817 | protein_coding | deleterious(0.02) | possibly_damaging(0.585) | TCGA-A8-A08G-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR |
| RYR1 | SNV | Missense_Mutation | c.2077N>T | p.Pro693Ser | p.P693S | P21817 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A8-A09B-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | 5-fluorouracil | SD | |
| RYR1 | SNV | Missense_Mutation | rs142548565 | c.2488C>T | p.Arg830Trp | p.R830W | P21817 | protein_coding | tolerated(0.08) | probably_damaging(0.96) | TCGA-A8-A0A1-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD |
| RYR1 | SNV | Missense_Mutation | novel | c.5671N>A | p.Glu1891Lys | p.E1891K | P21817 | protein_coding | tolerated(0.33) | benign(0.202) | TCGA-AC-A3TN-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD |
| RYR1 | SNV | Missense_Mutation | novel | c.7717G>C | p.Glu2573Gln | p.E2573Q | P21817 | protein_coding | tolerated(0.07) | benign(0.19) | TCGA-AC-A5XS-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | femara | SD |
| RYR1 | SNV | Missense_Mutation | rs750753962 | c.8551N>T | p.Pro2851Ser | p.P2851S | P21817 | protein_coding | tolerated(0.28) | benign(0.003) | TCGA-AC-A8OQ-01 | Breast | breast invasive 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 |
| 6261 | RYR1 | ION CHANNEL, B30_2 SPRY DOMAIN, DRUGGABLE GENOME | Sevoflurane | SEVOFLURANE | ||
| 6261 | RYR1 | ION CHANNEL, B30_2 SPRY DOMAIN, DRUGGABLE GENOME | chlorocresol | CHLOROCRESOL | 29344738,25086907 | |
| 6261 | RYR1 | ION CHANNEL, B30_2 SPRY DOMAIN, DRUGGABLE GENOME | haloperidol | HALOPERIDOL | 27023437 | |
| 6261 | RYR1 | ION CHANNEL, B30_2 SPRY DOMAIN, DRUGGABLE GENOME | enflurane | ENFLURANE | 25989378,12411786,26951757,8828983,19919814,17710899,7829078,9334205,21965348,11063719,10823104,20681998,25611019,19648156,25256590,12220451,11668625,23736090,14500992,9066328,14641996,18945287,25960145,7889656,11575529,18212565,16284304,8602662,18306019,28326467,11928716,18502356,10352931,12151923,11525881,17122579,16917943,8220422,10700782,16163667,17226826,9389851,16732128,16835904,11448278,29101530,9450902,7547049,23628358,9543323,24361844,26994242,12208234,15448513,16621918,21455645,11553045,12124989,19020143,19191329,27918309,8220423,12059893,10612851,16732084,10793526,27382027,15108991,12709367,12123492,26381711,25268394,28063098,11493496,12434264,12411788,19685112,25735680,8902717,29608462,27663056,7751854,8012359,9520251,15731587,15210166,1510267,10888602,22030266,25466363,17483490,28403410,12237752,1774074,17081152,18564801,10484775,21282829,16244001,7586638,19191333,25086907,7633940,17667581,12883402,19346234,1354642,22415532 | |
| 6261 | RYR1 | ION CHANNEL, B30_2 SPRY DOMAIN, DRUGGABLE GENOME | desflurane | DESFLURANE | 25989378,12411786,26951757,8828983,19919814,17710899,7829078,9334205,21965348,11063719,10823104,20681998,25611019,19648156,25256590,12220451,11668625,23736090,14500992,9066328,14641996,18945287,25960145,7889656,11575529,18212565,16284304,8602662,18306019,28326467,11928716,18502356,10352931,12151923,11525881,17122579,16917943,8220422,10700782,16163667,17226826,9389851,16732128,16835904,11448278,29101530,9450902,7547049,23628358,9543323,24361844,26994242,12208234,15448513,16621918,21455645,11553045,12124989,19020143,19191329,27918309,8220423,12059893,10612851,16732084,10793526,27382027,15108991,12709367,12123492,26381711,25268394,28063098,11493496,12434264,12411788,19685112,25735680,8902717,29608462,27663056,7751854,8012359,9520251,15731587,15210166,1510267,10888602,22030266,25466363,17483490,28403410,12237752,1774074,17081152,18564801,10484775,21282829,16244001,7586638,19191333,25086907,7633940,17667581,12883402,19346234,1354642,22415532 | |
| 6261 | RYR1 | ION CHANNEL, B30_2 SPRY DOMAIN, DRUGGABLE GENOME | volatile anesthetics | 25989378,12411786,21965348,20837722,20301325,9037193,12467748,19648156,23223104,25960145,26031886,28326467,25424378,12761368,11725865,16917943,24291096,16163667,23628358,19807743,18313359,21455645,10625004,12124989,3177917,15537710,12059893,23069638,27382027,19018722,10360872,17182726,25735680,27663056,15731587,26068069,28403410,9873004,20888934,15299003,19346234,22415532 | ||
| 6261 | RYR1 | ION CHANNEL, B30_2 SPRY DOMAIN, DRUGGABLE GENOME | caffeine | CAFFEINE | 9334205,11525881,29344738 | |
| 6261 | RYR1 | ION CHANNEL, B30_2 SPRY DOMAIN, DRUGGABLE GENOME | hmg coa reductase inhibitors | 21795085 | ||
| 6261 | RYR1 | ION CHANNEL, B30_2 SPRY DOMAIN, DRUGGABLE GENOME | blocker | 135652746 | ||
| 6261 | RYR1 | ION CHANNEL, B30_2 SPRY DOMAIN, DRUGGABLE GENOME | isoflurane | ISOFLURANE | 25989378,12411786,26951757,8828983,19919814,17710899,7829078,9334205,21965348,11063719,10823104,20681998,25611019,19648156,25256590,12220451,11668625,23736090,14500992,9066328,14641996,18945287,25960145,7889656,11575529,18212565,16284304,8602662,18306019,28326467,11928716,18502356,10352931,12151923,11525881,17122579,16917943,8220422,10700782,16163667,17226826,9389851,16732128,16835904,11448278,29101530,9450902,7547049,23628358,9543323,24361844,26994242,12208234,15448513,16621918,21455645,11553045,12124989,19020143,19191329,27918309,8220423,12059893,10612851,16732084,10793526,27382027,15108991,12709367,12123492,26381711,25268394,28063098,11493496,12434264,12411788,19685112,25735680,8902717,29608462,27663056,7751854,8012359,9520251,15731587,15210166,1510267,10888602,22030266,25466363,17483490,28403410,12237752,1774074,17081152,18564801,10484775,21282829,16244001,7586638,19191333,25086907,7633940,17667581,12883402,19346234,1354642,22415532 |
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