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Gene: CFAP54 |
Gene summary for CFAP54 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CFAP54 | Gene ID | 144535 |
| Gene name | cilia and flagella associated protein 54 | |
| Gene Alias | C12orf55 | |
| Cytomap | 12q23.1 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | Q96N23 |
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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 |
| 144535 | CFAP54 | RNA-P6T1-P6T1-2 | Human | Lung | MIAC | 4.12e-03 | 5.19e-01 | -0.0186 |
| 144535 | CFAP54 | RNA-P6T1-P6T1-3 | Human | Lung | MIAC | 2.58e-05 | 7.76e-01 | -0.0296 |
| 144535 | CFAP54 | RNA-P6T1-P6T1-4 | Human | Lung | MIAC | 2.24e-04 | 6.15e-01 | -0.0263 |
| 144535 | CFAP54 | RNA-P6T2-P6T2-1 | Human | Lung | IAC | 1.39e-03 | 2.07e-01 | -0.0166 |
| 144535 | CFAP54 | RNA-P6T2-P6T2-2 | Human | Lung | IAC | 1.88e-06 | 2.75e-01 | -0.0132 |
| 144535 | CFAP54 | RNA-P6T2-P6T2-3 | Human | Lung | IAC | 1.43e-02 | 1.48e-01 | -0.013 |
| 144535 | CFAP54 | RNA-P6T2-P6T2-4 | Human | Lung | IAC | 6.01e-04 | 2.40e-01 | -0.0121 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma |
| ∗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:0060271 | Lung | IAC | cilium assembly | 55/2061 | 337/18723 | 1.84e-03 | 1.88e-02 | 55 |
| GO:0044782 | Lung | IAC | cilium organization | 58/2061 | 368/18723 | 3.15e-03 | 2.75e-02 | 58 |
| GO:00602711 | Lung | MIAC | cilium assembly | 37/967 | 337/18723 | 1.29e-05 | 9.85e-04 | 37 |
| GO:00447821 | Lung | MIAC | cilium organization | 38/967 | 368/18723 | 3.93e-05 | 2.08e-03 | 38 |
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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. |
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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 |
| CFAP54 | SNV | Missense_Mutation | rs763234756 | c.5722N>T | p.Leu1908Phe | p.L1908F | Q96N23 | protein_coding | deleterious(0.03) | probably_damaging(0.998) | TCGA-5L-AAT0-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD |
| CFAP54 | SNV | Missense_Mutation | novel | c.6415N>C | p.Tyr2139His | p.Y2139H | Q96N23 | protein_coding | tolerated(0.54) | benign(0.001) | TCGA-A2-A0YK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD |
| CFAP54 | SNV | Missense_Mutation | novel | c.6955G>T | p.Ala2319Ser | p.A2319S | Q96N23 | protein_coding | tolerated(0.17) | benign(0.028) | TCGA-A2-A25A-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Cytoxan | SD |
| CFAP54 | SNV | Missense_Mutation | rs537859109 | c.8063N>T | p.Ser2688Phe | p.S2688F | Q96N23 | protein_coding | deleterious(0.01) | possibly_damaging(0.645) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| CFAP54 | SNV | Missense_Mutation | novel | c.7420C>G | p.Gln2474Glu | p.Q2474E | Q96N23 | protein_coding | tolerated(0.9) | benign(0.031) | TCGA-D8-A1JA-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD |
| CFAP54 | SNV | Missense_Mutation | novel | c.4948N>A | p.Leu1650Ile | p.L1650I | Q96N23 | protein_coding | tolerated(0.09) | benign(0.239) | TCGA-E2-A158-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | arimidex | SD |
| CFAP54 | SNV | Missense_Mutation | novel | c.3848C>T | p.Ala1283Val | p.A1283V | Q96N23 | protein_coding | tolerated(0.33) | benign(0.015) | TCGA-OL-A6VQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| CFAP54 | SNV | Missense_Mutation | novel | c.2989N>T | p.Val997Phe | p.V997F | Q96N23 | protein_coding | deleterious(0) | benign(0.055) | TCGA-UL-AAZ6-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | herceptin | SD |
| CFAP54 | insertion | In_Frame_Ins | novel | c.5214_5215insTTCTCA | p.Val1738_Asp1739insPheSer | p.V1738_D1739insFS | Q96N23 | protein_coding | TCGA-A2-A04Y-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
| CFAP54 | insertion | Frame_Shift_Ins | novel | c.5215_5216insTGTTGTTTATTTCTCAATGTTGCCAA | p.Asp1739ValfsTer11 | p.D1739Vfs*11 | Q96N23 | protein_coding | TCGA-A2-A04Y-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 |
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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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