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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. |
∗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 |
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 | insertion | Frame_Shift_Ins | novel | c.2180_2181insTTATAATTATTTGTCTGTTAGTAGCTATCCACTAAGAT | p.Lys727AsnfsTer14 | p.K727Nfs*14 | Q13099 | protein_coding | TCGA-B5-A11V-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
IFT88 | insertion | Frame_Shift_Ins | novel | c.2180_2181insTTATAATTATTTGTCTGTTAGT | p.Lys727AsnfsTer36 | p.K727Nfs*36 | Q13099 | protein_coding | TCGA-D1-A0ZR-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
IFT88 | insertion | Frame_Shift_Ins | novel | c.2180_2181insTTATAATTATTTGTCTGTTAGT | p.Lys727AsnfsTer36 | p.K727Nfs*36 | Q13099 | protein_coding | TCGA-D1-A102-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
IFT88 | insertion | Frame_Shift_Ins | novel | c.420dupA | p.Asp141ArgfsTer2 | p.D141Rfs*2 | Q13099 | protein_coding | TCGA-E6-A1LX-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
IFT88 | SNV | Missense_Mutation | novel | c.971A>G | p.Tyr324Cys | p.Y324C | Q13099 | protein_coding | tolerated(0.09) | benign(0.003) | TCGA-2Y-A9H6-01 | Liver | liver hepatocellular carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
IFT88 | SNV | Missense_Mutation | c.2359N>G | p.Ser787Gly | p.S787G | Q13099 | protein_coding | tolerated(0.25) | benign(0.039) | TCGA-DD-A11D-01 | Liver | liver hepatocellular carcinoma | Female | <65 | I/II | Targeted Molecular therapy | sorafenib | PD | |
IFT88 | SNV | Missense_Mutation | c.569A>T | p.Gln190Leu | p.Q190L | Q13099 | protein_coding | tolerated(1) | benign(0.003) | TCGA-44-3918-01 | Lung | lung adenocarcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | SD | |
IFT88 | SNV | Missense_Mutation | c.1789G>T | p.Val597Phe | p.V597F | Q13099 | protein_coding | deleterious(0.01) | benign(0.188) | TCGA-44-6778-01 | Lung | lung adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
IFT88 | SNV | Missense_Mutation | c.421N>C | p.Asp141His | p.D141H | Q13099 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-49-4488-01 | Lung | lung adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
IFT88 | SNV | Missense_Mutation | novel | c.2467N>C | p.Asp823His | p.D823H | Q13099 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-49-6742-01 | Lung | lung adenocarcinoma | Male | >=65 | I/II | Chemotherapy | alimta | 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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