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Gene: RAB11FIP3 |
Gene summary for RAB11FIP3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RAB11FIP3 | Gene ID | 9727 |
| Gene name | RAB11 family interacting protein 3 | |
| Gene Alias | CART1 | |
| Cytomap | 16p13.3 | |
| Gene Type | protein-coding | GO ID | GO:0000910 | UniProtAcc | O75154 |
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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 |
| 9727 | RAB11FIP3 | HTA11_1391_2000001011 | Human | Colorectum | AD | 9.55e-03 | 5.91e-01 | -0.059 |
| 9727 | RAB11FIP3 | HTA11_866_3004761011 | Human | Colorectum | AD | 5.53e-04 | 4.36e-01 | 0.096 |
| 9727 | RAB11FIP3 | HTA11_7696_3000711011 | Human | Colorectum | AD | 9.72e-12 | 4.87e-01 | 0.0674 |
| 9727 | RAB11FIP3 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 9.73e-05 | 5.59e-01 | 0.281 |
| 9727 | RAB11FIP3 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 3.00e-12 | 6.46e-01 | 0.3859 |
| 9727 | RAB11FIP3 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 1.18e-07 | 9.54e-01 | 0.2585 |
| 9727 | RAB11FIP3 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 4.56e-02 | 2.66e-01 | 0.3005 |
| 9727 | RAB11FIP3 | A015-C-203 | Human | Colorectum | FAP | 2.35e-07 | -2.34e-02 | -0.1294 |
| 9727 | RAB11FIP3 | A002-C-201 | Human | Colorectum | FAP | 3.76e-04 | -1.36e-01 | 0.0324 |
| 9727 | RAB11FIP3 | A001-C-108 | Human | Colorectum | FAP | 1.65e-02 | -8.44e-02 | -0.0272 |
| 9727 | RAB11FIP3 | A002-C-205 | Human | Colorectum | FAP | 8.23e-06 | -1.27e-01 | -0.1236 |
| 9727 | RAB11FIP3 | A015-C-006 | Human | Colorectum | FAP | 8.72e-04 | -8.62e-02 | -0.0994 |
| 9727 | RAB11FIP3 | A002-C-114 | Human | Colorectum | FAP | 4.85e-04 | -6.56e-02 | -0.1561 |
| 9727 | RAB11FIP3 | A015-C-104 | Human | Colorectum | FAP | 7.64e-11 | -1.12e-01 | -0.1899 |
| 9727 | RAB11FIP3 | A001-C-014 | Human | Colorectum | FAP | 2.42e-02 | -8.94e-02 | 0.0135 |
| 9727 | RAB11FIP3 | A015-C-002 | Human | Colorectum | FAP | 3.72e-02 | -1.65e-01 | -0.0763 |
| 9727 | RAB11FIP3 | A002-C-116 | Human | Colorectum | FAP | 4.00e-09 | -1.74e-01 | -0.0452 |
| 9727 | RAB11FIP3 | A014-C-008 | Human | Colorectum | FAP | 4.19e-02 | -6.49e-02 | -0.191 |
| 9727 | RAB11FIP3 | A018-E-020 | Human | Colorectum | FAP | 1.37e-05 | -1.68e-01 | -0.2034 |
| 9727 | RAB11FIP3 | F034 | Human | Colorectum | FAP | 1.42e-03 | -6.08e-02 | -0.0665 |
| Page: 1 2 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal 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:0016197 | Colorectum | AD | endosomal transport | 90/3918 | 230/18723 | 1.88e-10 | 1.73e-08 | 90 |
| GO:0098876 | Colorectum | AD | vesicle-mediated transport to the plasma membrane | 57/3918 | 136/18723 | 2.30e-08 | 1.27e-06 | 57 |
| GO:0000910 | Colorectum | AD | cytokinesis | 59/3918 | 173/18723 | 3.74e-05 | 6.75e-04 | 59 |
| GO:0050708 | Colorectum | AD | regulation of protein secretion | 83/3918 | 268/18723 | 6.59e-05 | 1.07e-03 | 83 |
| GO:0009306 | Colorectum | AD | protein secretion | 105/3918 | 359/18723 | 1.05e-04 | 1.57e-03 | 105 |
| GO:0035592 | Colorectum | AD | establishment of protein localization to extracellular region | 105/3918 | 360/18723 | 1.18e-04 | 1.73e-03 | 105 |
| GO:0071692 | Colorectum | AD | protein localization to extracellular region | 106/3918 | 368/18723 | 1.86e-04 | 2.49e-03 | 106 |
| GO:0032456 | Colorectum | AD | endocytic recycling | 28/3918 | 73/18723 | 4.87e-04 | 5.30e-03 | 28 |
| GO:00988762 | Colorectum | MSS | vesicle-mediated transport to the plasma membrane | 54/3467 | 136/18723 | 6.20e-09 | 3.95e-07 | 54 |
| GO:00161972 | Colorectum | MSS | endosomal transport | 79/3467 | 230/18723 | 7.04e-09 | 4.39e-07 | 79 |
| GO:00507082 | Colorectum | MSS | regulation of protein secretion | 78/3467 | 268/18723 | 1.47e-05 | 3.33e-04 | 78 |
| GO:00093062 | Colorectum | MSS | protein secretion | 98/3467 | 359/18723 | 2.43e-05 | 5.09e-04 | 98 |
| GO:00355922 | Colorectum | MSS | establishment of protein localization to extracellular region | 98/3467 | 360/18723 | 2.75e-05 | 5.58e-04 | 98 |
| GO:00716922 | Colorectum | MSS | protein localization to extracellular region | 99/3467 | 368/18723 | 4.17e-05 | 7.83e-04 | 99 |
| GO:00324561 | Colorectum | MSS | endocytic recycling | 26/3467 | 73/18723 | 4.05e-04 | 4.99e-03 | 26 |
| GO:00009102 | Colorectum | MSS | cytokinesis | 49/3467 | 173/18723 | 1.02e-03 | 1.02e-02 | 49 |
| GO:00510511 | Colorectum | MSS | negative regulation of transport | 110/3467 | 470/18723 | 4.20e-03 | 3.04e-02 | 110 |
| GO:00988763 | Colorectum | FAP | vesicle-mediated transport to the plasma membrane | 42/2622 | 136/18723 | 3.16e-07 | 1.78e-05 | 42 |
| GO:00507083 | Colorectum | FAP | regulation of protein secretion | 66/2622 | 268/18723 | 2.21e-06 | 8.87e-05 | 66 |
| GO:00161973 | Colorectum | FAP | endosomal transport | 56/2622 | 230/18723 | 1.79e-05 | 4.53e-04 | 56 |
| Page: 1 2 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa04144 | Colorectum | AD | Endocytosis | 111/2092 | 251/8465 | 5.95e-12 | 1.42e-10 | 9.08e-11 | 111 |
| hsa041441 | Colorectum | AD | Endocytosis | 111/2092 | 251/8465 | 5.95e-12 | 1.42e-10 | 9.08e-11 | 111 |
| hsa041444 | Colorectum | MSS | Endocytosis | 102/1875 | 251/8465 | 1.85e-11 | 4.43e-10 | 2.71e-10 | 102 |
| hsa041445 | Colorectum | MSS | Endocytosis | 102/1875 | 251/8465 | 1.85e-11 | 4.43e-10 | 2.71e-10 | 102 |
| hsa041446 | Colorectum | FAP | Endocytosis | 78/1404 | 251/8465 | 6.20e-09 | 2.96e-07 | 1.80e-07 | 78 |
| hsa041447 | Colorectum | FAP | Endocytosis | 78/1404 | 251/8465 | 6.20e-09 | 2.96e-07 | 1.80e-07 | 78 |
| hsa041448 | Colorectum | CRC | Endocytosis | 65/1091 | 251/8465 | 1.27e-08 | 1.06e-06 | 7.19e-07 | 65 |
| hsa041449 | Colorectum | CRC | Endocytosis | 65/1091 | 251/8465 | 1.27e-08 | 1.06e-06 | 7.19e-07 | 65 |
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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 |
| RAB11FIP3 | SNV | Missense_Mutation | c.721N>T | p.Asp241Tyr | p.D241Y | O75154 | protein_coding | deleterious(0.05) | probably_damaging(0.993) | TCGA-C8-A26Y-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| RAB11FIP3 | deletion | Frame_Shift_Del | novel | c.948delC | p.Tyr317ThrfsTer67 | p.Y317Tfs*67 | O75154 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | ||
| RAB11FIP3 | SNV | Missense_Mutation | novel | c.1679N>T | p.Ser560Phe | p.S560F | O75154 | protein_coding | deleterious(0.01) | probably_damaging(0.996) | TCGA-HM-A4S6-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Chemotherapy | cisplatin | CR |
| RAB11FIP3 | SNV | Missense_Mutation | c.1684N>T | p.Thr562Ser | p.T562S | O75154 | protein_coding | tolerated(0.06) | benign(0.164) | TCGA-AA-3952-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | PD | |
| RAB11FIP3 | SNV | Missense_Mutation | c.1970G>A | p.Arg657His | p.R657H | O75154 | protein_coding | deleterious(0.03) | benign(0.139) | TCGA-AZ-6601-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
| RAB11FIP3 | SNV | Missense_Mutation | c.2086N>A | p.Ala696Thr | p.A696T | O75154 | protein_coding | deleterious(0) | probably_damaging(0.992) | TCGA-CM-6163-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| RAB11FIP3 | SNV | Missense_Mutation | rs777219325 | c.1415G>A | p.Arg472His | p.R472H | O75154 | protein_coding | tolerated(0.06) | probably_damaging(0.996) | TCGA-G4-6311-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | oxaliplatin | SD |
| RAB11FIP3 | SNV | Missense_Mutation | rs766981935 | c.971N>T | p.Thr324Met | p.T324M | O75154 | protein_coding | deleterious(0.01) | probably_damaging(0.996) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| RAB11FIP3 | SNV | Missense_Mutation | c.711N>T | p.Glu237Asp | p.E237D | O75154 | protein_coding | tolerated(0.28) | benign(0.054) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| RAB11FIP3 | SNV | Missense_Mutation | c.1424N>C | p.Glu475Ala | p.E475A | O75154 | protein_coding | tolerated(0.06) | probably_damaging(0.989) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | 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 |
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