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Gene: IFT88 |
Gene summary for IFT88 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | IFT88 | Gene ID | 8100 |
| Gene name | intraflagellar transport 88 | |
| Gene Alias | D13S1056E | |
| Cytomap | 13q12.11 | |
| Gene Type | protein-coding | GO ID | GO:0000045 | UniProtAcc | B3KX42 |
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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 |
| 8100 | IFT88 | NAFLD1 | Human | Liver | NAFLD | 7.76e-06 | 8.93e-01 | -0.04 |
| 8100 | IFT88 | S43 | Human | Liver | Cirrhotic | 1.16e-05 | -1.41e-01 | -0.0187 |
| 8100 | IFT88 | HCC1_Meng | Human | Liver | HCC | 1.92e-32 | -1.25e-01 | 0.0246 |
| 8100 | IFT88 | HCC2_Meng | Human | Liver | HCC | 1.51e-18 | -6.05e-02 | 0.0107 |
| 8100 | IFT88 | HCC2 | Human | Liver | HCC | 4.68e-08 | 3.47e+00 | 0.5341 |
| 8100 | IFT88 | Pt13.a | Human | Liver | HCC | 2.53e-02 | -1.92e-01 | 0.021 |
| 8100 | IFT88 | S028 | Human | Liver | HCC | 1.78e-02 | 3.83e-01 | 0.2503 |
| 8100 | IFT88 | S029 | Human | Liver | HCC | 8.39e-03 | 4.49e-01 | 0.2581 |
| 8100 | IFT88 | HTA12-23-1 | Human | Pancreas | PDAC | 4.93e-04 | 6.06e-01 | 0.3405 |
| 8100 | IFT88 | HTA12-26-1 | Human | Pancreas | PDAC | 1.35e-17 | 7.64e-01 | 0.3728 |
| 8100 | IFT88 | HTA12-29-1 | Human | Pancreas | PDAC | 2.56e-18 | 5.14e-01 | 0.3722 |
| 8100 | IFT88 | male-WTA | Human | Thyroid | PTC | 2.77e-13 | 6.72e-02 | 0.1037 |
| 8100 | IFT88 | PTC01 | Human | Thyroid | PTC | 5.39e-11 | 1.76e-01 | 0.1899 |
| 8100 | IFT88 | PTC03 | Human | Thyroid | PTC | 1.31e-05 | 1.06e-01 | 0.1784 |
| 8100 | IFT88 | PTC04 | Human | Thyroid | PTC | 2.13e-14 | 1.89e-01 | 0.1927 |
| 8100 | IFT88 | PTC05 | Human | Thyroid | PTC | 1.66e-16 | 3.20e-01 | 0.2065 |
| 8100 | IFT88 | PTC06 | Human | Thyroid | PTC | 1.53e-21 | 4.55e-01 | 0.2057 |
| 8100 | IFT88 | PTC07 | Human | Thyroid | PTC | 3.42e-31 | 4.20e-01 | 0.2044 |
| 8100 | IFT88 | ATC09 | Human | Thyroid | ATC | 4.83e-03 | 8.04e-02 | 0.2871 |
| 8100 | IFT88 | ATC13 | Human | Thyroid | ATC | 2.19e-27 | 4.91e-01 | 0.34 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| 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:00307055 | Liver | NAFLD | cytoskeleton-dependent intracellular transport | 33/1882 | 195/18723 | 1.98e-03 | 1.98e-02 | 33 |
| GO:00162365 | Liver | NAFLD | macroautophagy | 45/1882 | 291/18723 | 2.31e-03 | 2.19e-02 | 45 |
| GO:00109703 | Liver | NAFLD | transport along microtubule | 26/1882 | 155/18723 | 6.30e-03 | 4.69e-02 | 26 |
| GO:001623611 | Liver | Cirrhotic | macroautophagy | 129/4634 | 291/18723 | 1.75e-13 | 1.41e-11 | 129 |
| GO:00070332 | Liver | Cirrhotic | vacuole organization | 80/4634 | 180/18723 | 5.73e-09 | 2.25e-07 | 80 |
| GO:0000045 | Liver | Cirrhotic | autophagosome assembly | 43/4634 | 99/18723 | 3.56e-05 | 4.32e-04 | 43 |
| GO:1905037 | Liver | Cirrhotic | autophagosome organization | 44/4634 | 103/18723 | 4.74e-05 | 5.50e-04 | 44 |
| GO:0044088 | Liver | Cirrhotic | regulation of vacuole organization | 23/4634 | 45/18723 | 1.23e-04 | 1.22e-03 | 23 |
| GO:1902115 | Liver | Cirrhotic | regulation of organelle assembly | 66/4634 | 186/18723 | 6.66e-04 | 5.04e-03 | 66 |
| GO:003070511 | Liver | Cirrhotic | cytoskeleton-dependent intracellular transport | 68/4634 | 195/18723 | 9.54e-04 | 6.77e-03 | 68 |
| GO:0031503 | Liver | Cirrhotic | protein-containing complex localization | 75/4634 | 220/18723 | 1.13e-03 | 7.73e-03 | 75 |
| GO:2000785 | Liver | Cirrhotic | regulation of autophagosome assembly | 18/4634 | 39/18723 | 2.93e-03 | 1.67e-02 | 18 |
| GO:01200326 | Liver | Cirrhotic | regulation of plasma membrane bounded cell projection assembly | 63/4634 | 186/18723 | 3.16e-03 | 1.78e-02 | 63 |
| GO:00604915 | Liver | Cirrhotic | regulation of cell projection assembly | 63/4634 | 188/18723 | 4.17e-03 | 2.22e-02 | 63 |
| GO:00109701 | Liver | Cirrhotic | transport along microtubule | 52/4634 | 155/18723 | 8.42e-03 | 3.91e-02 | 52 |
| GO:001623621 | Liver | HCC | macroautophagy | 204/7958 | 291/18723 | 8.66e-22 | 1.41e-19 | 204 |
| GO:000703311 | Liver | HCC | vacuole organization | 119/7958 | 180/18723 | 1.22e-10 | 4.25e-09 | 119 |
| GO:19050371 | Liver | HCC | autophagosome organization | 70/7958 | 103/18723 | 1.52e-07 | 2.82e-06 | 70 |
| GO:00000451 | Liver | HCC | autophagosome assembly | 67/7958 | 99/18723 | 3.56e-07 | 6.07e-06 | 67 |
| GO:00315031 | Liver | HCC | protein-containing complex localization | 129/7958 | 220/18723 | 9.38e-07 | 1.42e-05 | 129 |
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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 |
| IFT88 | SNV | Missense_Mutation | c.767N>T | p.Arg256Ile | p.R256I | Q13099 | protein_coding | tolerated(0.05) | possibly_damaging(0.69) | TCGA-A2-A0CM-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | PD | |
| IFT88 | SNV | Missense_Mutation | c.1796N>T | p.Ser599Phe | p.S599F | Q13099 | protein_coding | tolerated(0.27) | benign(0.276) | TCGA-A8-A08L-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| IFT88 | SNV | Missense_Mutation | c.1020N>C | p.Leu340Phe | p.L340F | Q13099 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| IFT88 | SNV | Missense_Mutation | c.243N>T | p.Lys81Asn | p.K81N | Q13099 | protein_coding | tolerated(0.44) | benign(0.272) | TCGA-C8-A12W-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
| IFT88 | SNV | Missense_Mutation | c.1420G>C | p.Asp474His | p.D474H | Q13099 | protein_coding | deleterious(0) | possibly_damaging(0.498) | TCGA-E2-A14V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD | |
| IFT88 | SNV | Missense_Mutation | c.1722N>A | p.Met574Ile | p.M574I | Q13099 | protein_coding | tolerated(0.3) | benign(0.06) | TCGA-E2-A1LA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | arimidex | SD | |
| IFT88 | insertion | Nonsense_Mutation | novel | c.2376_2377insTAAGAACCTACAGTTAAGAAAAAGTATGCATGC | p.Glu792_Ile793insTer | p.E792_I793ins* | Q13099 | protein_coding | TCGA-A8-A08H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| IFT88 | SNV | Missense_Mutation | novel | c.1358A>G | p.Lys453Arg | p.K453R | Q13099 | protein_coding | tolerated(0.17) | probably_damaging(0.98) | TCGA-C5-A7UE-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
| IFT88 | SNV | Missense_Mutation | novel | c.1367N>C | p.Arg456Thr | p.R456T | Q13099 | protein_coding | deleterious(0.05) | benign(0.115) | TCGA-C5-A902-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
| IFT88 | SNV | Missense_Mutation | c.1366A>G | p.Arg456Gly | p.R456G | Q13099 | protein_coding | deleterious(0.01) | benign(0.079) | TCGA-AA-3715-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | 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 |
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