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Gene: LCA5 |
Gene summary for LCA5 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LCA5 | Gene ID | 167691 |
| Gene name | lebercilin LCA5 | |
| Gene Alias | C6orf152 | |
| Cytomap | 6q14.1 | |
| Gene Type | protein-coding | GO ID | GO:0001894 | UniProtAcc | Q86VQ0 |
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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 |
| 167691 | LCA5 | male-WTA | Human | Thyroid | PTC | 5.74e-15 | 1.91e-01 | 0.1037 |
| 167691 | LCA5 | PTC01 | Human | Thyroid | PTC | 7.03e-10 | 2.43e-01 | 0.1899 |
| 167691 | LCA5 | PTC03 | Human | Thyroid | PTC | 4.05e-03 | 1.08e-01 | 0.1784 |
| 167691 | LCA5 | PTC04 | Human | Thyroid | PTC | 1.82e-16 | 2.50e-01 | 0.1927 |
| 167691 | LCA5 | PTC05 | Human | Thyroid | PTC | 3.00e-31 | 1.12e+00 | 0.2065 |
| 167691 | LCA5 | PTC06 | Human | Thyroid | PTC | 1.02e-35 | 7.74e-01 | 0.2057 |
| 167691 | LCA5 | PTC07 | Human | Thyroid | PTC | 8.04e-38 | 7.06e-01 | 0.2044 |
| 167691 | LCA5 | ATC13 | Human | Thyroid | ATC | 1.17e-31 | 4.74e-01 | 0.34 |
| 167691 | LCA5 | ATC5 | Human | Thyroid | ATC | 3.12e-23 | 5.18e-01 | 0.34 |
| Page: 1 |
| 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:0030705111 | Thyroid | PTC | cytoskeleton-dependent intracellular transport | 104/5968 | 195/18723 | 3.87e-10 | 1.24e-08 | 104 |
| GO:00315037 | Thyroid | PTC | protein-containing complex localization | 107/5968 | 220/18723 | 1.47e-07 | 2.82e-06 | 107 |
| GO:00109709 | Thyroid | PTC | transport along microtubule | 80/5968 | 155/18723 | 2.48e-07 | 4.32e-06 | 80 |
| GO:00991115 | Thyroid | PTC | microtubule-based transport | 88/5968 | 190/18723 | 2.08e-05 | 2.08e-04 | 88 |
| GO:003070532 | Thyroid | ATC | cytoskeleton-dependent intracellular transport | 105/6293 | 195/18723 | 4.31e-09 | 9.70e-08 | 105 |
| GO:001097022 | Thyroid | ATC | transport along microtubule | 83/6293 | 155/18723 | 2.38e-07 | 3.70e-06 | 83 |
| GO:003150316 | Thyroid | ATC | protein-containing complex localization | 108/6293 | 220/18723 | 1.33e-06 | 1.69e-05 | 108 |
| GO:009911112 | Thyroid | ATC | microtubule-based transport | 91/6293 | 190/18723 | 2.97e-05 | 2.48e-04 | 91 |
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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 |
| LCA5 | SNV | Missense_Mutation | rs750681198 | c.556N>A | p.Glu186Lys | p.E186K | Q86VQ0 | protein_coding | deleterious(0.01) | probably_damaging(0.974) | TCGA-C8-A26Y-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| LCA5 | SNV | Missense_Mutation | c.669N>T | p.Lys223Asn | p.K223N | Q86VQ0 | protein_coding | deleterious(0) | probably_damaging(0.974) | TCGA-E9-A24A-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | |
| LCA5 | SNV | Missense_Mutation | novel | c.167N>T | p.Ser56Leu | p.S56L | Q86VQ0 | protein_coding | tolerated(0.16) | probably_damaging(0.998) | TCGA-DS-A1OB-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | carboplatin | PD |
| LCA5 | SNV | Missense_Mutation | novel | c.1599N>C | p.Lys533Asn | p.K533N | Q86VQ0 | protein_coding | deleterious(0.03) | benign(0.018) | TCGA-EA-A3HS-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| LCA5 | SNV | Missense_Mutation | c.1903N>C | p.Asp635His | p.D635H | Q86VQ0 | protein_coding | deleterious(0) | possibly_damaging(0.875) | TCGA-EK-A3GK-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| LCA5 | SNV | Missense_Mutation | c.104N>A | p.Arg35Gln | p.R35Q | Q86VQ0 | protein_coding | tolerated(1) | benign(0.003) | TCGA-A6-A567-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Unknown | Unknown | PD | |
| LCA5 | SNV | Missense_Mutation | c.1061N>G | p.Tyr354Cys | p.Y354C | Q86VQ0 | protein_coding | tolerated(0.17) | possibly_damaging(0.874) | TCGA-AA-3966-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| LCA5 | SNV | Missense_Mutation | rs534689871 | c.1063N>A | p.Glu355Lys | p.E355K | Q86VQ0 | protein_coding | tolerated(0.09) | possibly_damaging(0.617) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| LCA5 | SNV | Missense_Mutation | c.1636G>A | p.Ala546Thr | p.A546T | Q86VQ0 | protein_coding | tolerated(0.69) | benign(0.007) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
| LCA5 | SNV | Missense_Mutation | rs761494084 | c.2012N>A | p.Arg671Gln | p.R671Q | Q86VQ0 | protein_coding | tolerated(0.07) | benign(0.157) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 9 |
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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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