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Gene: RPGRIP1L |
Gene summary for RPGRIP1L |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RPGRIP1L | Gene ID | 23322 |
| Gene name | RPGRIP1 like | |
| Gene Alias | COACH3 | |
| Cytomap | 16q12.2 | |
| Gene Type | protein-coding | GO ID | GO:0001654 | UniProtAcc | Q68CZ1 |
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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 |
| 23322 | RPGRIP1L | male-WTA | Human | Thyroid | PTC | 2.09e-04 | 7.01e-02 | 0.1037 |
| 23322 | RPGRIP1L | PTC01 | Human | Thyroid | PTC | 3.41e-03 | 3.74e-02 | 0.1899 |
| 23322 | RPGRIP1L | PTC05 | Human | Thyroid | PTC | 4.71e-04 | 1.92e-01 | 0.2065 |
| 23322 | RPGRIP1L | PTC06 | Human | Thyroid | PTC | 9.75e-12 | 2.34e-01 | 0.2057 |
| 23322 | RPGRIP1L | PTC07 | Human | Thyroid | PTC | 1.52e-08 | 1.97e-01 | 0.2044 |
| 23322 | RPGRIP1L | ATC12 | Human | Thyroid | ATC | 2.80e-13 | 1.25e-01 | 0.34 |
| 23322 | RPGRIP1L | ATC13 | Human | Thyroid | ATC | 8.83e-15 | 1.45e-01 | 0.34 |
| 23322 | RPGRIP1L | ATC2 | Human | Thyroid | ATC | 4.42e-07 | 5.21e-01 | 0.34 |
| 23322 | RPGRIP1L | ATC4 | Human | Thyroid | ATC | 1.31e-10 | 1.76e-01 | 0.34 |
| 23322 | RPGRIP1L | ATC5 | Human | Thyroid | ATC | 2.29e-06 | 1.61e-01 | 0.34 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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:0007163111 | Thyroid | PTC | establishment or maintenance of cell polarity | 115/5968 | 218/18723 | 1.15e-10 | 3.90e-09 | 115 |
| GO:0001701111 | Thyroid | PTC | in utero embryonic development | 175/5968 | 367/18723 | 1.40e-10 | 4.73e-09 | 175 |
| GO:0048732113 | Thyroid | PTC | gland development | 193/5968 | 436/18723 | 2.88e-08 | 6.42e-07 | 193 |
| GO:0001889112 | Thyroid | PTC | liver development | 79/5968 | 147/18723 | 3.08e-08 | 6.82e-07 | 79 |
| GO:0061008112 | Thyroid | PTC | hepaticobiliary system development | 80/5968 | 150/18723 | 3.94e-08 | 8.55e-07 | 80 |
| GO:000182215 | Thyroid | PTC | kidney development | 133/5968 | 293/18723 | 7.57e-07 | 1.18e-05 | 133 |
| GO:000165517 | Thyroid | PTC | urogenital system development | 149/5968 | 338/18723 | 1.41e-06 | 2.01e-05 | 149 |
| GO:007200114 | Thyroid | PTC | renal system development | 135/5968 | 302/18723 | 1.76e-06 | 2.43e-05 | 135 |
| GO:002191514 | Thyroid | PTC | neural tube development | 76/5968 | 152/18723 | 2.40e-06 | 3.17e-05 | 76 |
| GO:006054115 | Thyroid | PTC | respiratory system development | 86/5968 | 203/18723 | 1.02e-03 | 6.08e-03 | 86 |
| GO:00220382 | Thyroid | PTC | corpus callosum development | 10/5968 | 14/18723 | 2.77e-03 | 1.38e-02 | 10 |
| GO:00215373 | Thyroid | PTC | telencephalon development | 100/5968 | 248/18723 | 2.90e-03 | 1.44e-02 | 100 |
| GO:00309007 | Thyroid | PTC | forebrain development | 143/5968 | 379/18723 | 8.47e-03 | 3.56e-02 | 143 |
| GO:00017389 | Thyroid | PTC | morphogenesis of a polarized epithelium | 41/5968 | 94/18723 | 1.10e-02 | 4.38e-02 | 41 |
| GO:000716329 | Thyroid | ATC | establishment or maintenance of cell polarity | 122/6293 | 218/18723 | 8.46e-12 | 3.16e-10 | 122 |
| GO:000170126 | Thyroid | ATC | in utero embryonic development | 183/6293 | 367/18723 | 6.62e-11 | 2.11e-09 | 183 |
| GO:004873233 | Thyroid | ATC | gland development | 210/6293 | 436/18723 | 1.50e-10 | 4.59e-09 | 210 |
| GO:000188927 | Thyroid | ATC | liver development | 85/6293 | 147/18723 | 1.37e-09 | 3.43e-08 | 85 |
| GO:006100827 | Thyroid | ATC | hepaticobiliary system development | 86/6293 | 150/18723 | 1.96e-09 | 4.78e-08 | 86 |
| GO:000182222 | Thyroid | ATC | kidney development | 146/6293 | 293/18723 | 5.81e-09 | 1.28e-07 | 146 |
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| 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 |
| 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 |
| RPGRIP1L | SNV | Missense_Mutation | c.55C>A | p.Leu19Ile | p.L19I | Q68CZ1 | protein_coding | tolerated(0.16) | benign(0.018) | TCGA-A2-A25A-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Cytoxan | SD | |
| RPGRIP1L | SNV | Missense_Mutation | novel | c.3742N>A | p.Gln1248Lys | p.Q1248K | Q68CZ1 | protein_coding | deleterious(0) | probably_damaging(0.91) | TCGA-A7-A425-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | adriamycin | PD |
| RPGRIP1L | SNV | Missense_Mutation | rs750930363 | c.3448C>T | p.Arg1150Trp | p.R1150W | Q68CZ1 | protein_coding | deleterious(0) | probably_damaging(0.973) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| RPGRIP1L | SNV | Missense_Mutation | c.1573N>C | p.Asp525His | p.D525H | Q68CZ1 | protein_coding | deleterious(0) | probably_damaging(0.962) | TCGA-AR-A1AL-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | anastrozole | SD | |
| RPGRIP1L | SNV | Missense_Mutation | c.3751G>C | p.Glu1251Gln | p.E1251Q | Q68CZ1 | protein_coding | deleterious(0) | probably_damaging(0.983) | TCGA-BH-A0DZ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | docetaxel | SD | |
| RPGRIP1L | SNV | Missense_Mutation | c.739N>T | p.Leu247Phe | p.L247F | Q68CZ1 | protein_coding | tolerated(0.06) | benign(0.099) | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| RPGRIP1L | SNV | Missense_Mutation | c.1505A>G | p.His502Arg | p.H502R | Q68CZ1 | protein_coding | deleterious(0) | probably_damaging(0.913) | TCGA-D8-A1XK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine+cyclophosphamide | SD | |
| RPGRIP1L | SNV | Missense_Mutation | c.1939G>T | p.Val647Leu | p.V647L | Q68CZ1 | protein_coding | tolerated(0.1) | benign(0.015) | TCGA-D8-A1XT-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin+cyclophosphamide | SD | |
| RPGRIP1L | insertion | Frame_Shift_Ins | novel | c.3164_3165insTGACCTTGGTGGAGACGAACAAACCATATTC | p.Gln1055HisfsTer17 | p.Q1055Hfs*17 | Q68CZ1 | protein_coding | TCGA-A8-A06X-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| RPGRIP1L | insertion | Nonsense_Mutation | novel | c.401_402insAACCTATTTACATTGTTAAAACTTGAATAGAAGA | p.Ser135ThrfsTer6 | p.S135Tfs*6 | Q68CZ1 | protein_coding | TCGA-AN-A049-01 | 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 |
| Page: 1 |
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