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Gene: YLPM1 |
Gene summary for YLPM1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | YLPM1 | Gene ID | 56252 |
| Gene name | YLP motif containing 1 | |
| Gene Alias | C14orf170 | |
| Cytomap | 14q24.3 | |
| Gene Type | protein-coding | GO ID | GO:0000723 | UniProtAcc | P49750 |
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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 |
| 56252 | YLPM1 | P52T-E | Human | Esophagus | ESCC | 3.61e-20 | 2.35e-01 | 0.1555 |
| 56252 | YLPM1 | P54T-E | Human | Esophagus | ESCC | 1.06e-12 | 3.62e-01 | 0.0975 |
| 56252 | YLPM1 | P56T-E | Human | Esophagus | ESCC | 2.89e-03 | 7.97e-01 | 0.1613 |
| 56252 | YLPM1 | P57T-E | Human | Esophagus | ESCC | 1.01e-20 | 2.31e-01 | 0.0926 |
| 56252 | YLPM1 | P61T-E | Human | Esophagus | ESCC | 4.90e-29 | 8.00e-01 | 0.099 |
| 56252 | YLPM1 | P62T-E | Human | Esophagus | ESCC | 1.54e-19 | 4.20e-01 | 0.1302 |
| 56252 | YLPM1 | P65T-E | Human | Esophagus | ESCC | 3.19e-22 | 3.70e-01 | 0.0978 |
| 56252 | YLPM1 | P74T-E | Human | Esophagus | ESCC | 1.43e-23 | 5.45e-01 | 0.1479 |
| 56252 | YLPM1 | P75T-E | Human | Esophagus | ESCC | 1.48e-17 | 3.66e-01 | 0.1125 |
| 56252 | YLPM1 | P76T-E | Human | Esophagus | ESCC | 1.08e-16 | 2.01e-01 | 0.1207 |
| 56252 | YLPM1 | P79T-E | Human | Esophagus | ESCC | 1.61e-28 | 4.79e-01 | 0.1154 |
| 56252 | YLPM1 | P80T-E | Human | Esophagus | ESCC | 1.03e-15 | 5.79e-01 | 0.155 |
| 56252 | YLPM1 | P82T-E | Human | Esophagus | ESCC | 1.23e-05 | 3.05e-01 | 0.1072 |
| 56252 | YLPM1 | P83T-E | Human | Esophagus | ESCC | 9.04e-25 | 6.45e-01 | 0.1738 |
| 56252 | YLPM1 | P84T-E | Human | Esophagus | ESCC | 1.28e-07 | 2.87e-01 | 0.0933 |
| 56252 | YLPM1 | P89T-E | Human | Esophagus | ESCC | 1.22e-03 | 5.34e-01 | 0.1752 |
| 56252 | YLPM1 | P91T-E | Human | Esophagus | ESCC | 1.87e-09 | 1.21e+00 | 0.1828 |
| 56252 | YLPM1 | P104T-E | Human | Esophagus | ESCC | 9.12e-06 | 2.22e-01 | 0.0931 |
| 56252 | YLPM1 | P107T-E | Human | Esophagus | ESCC | 8.42e-16 | 4.23e-01 | 0.171 |
| 56252 | YLPM1 | P127T-E | Human | Esophagus | ESCC | 1.72e-20 | 4.27e-01 | 0.0826 |
| Page: 1 2 3 4 5 6 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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:003304416 | Esophagus | ESCC | regulation of chromosome organization | 145/8552 | 187/18723 | 3.80e-19 | 4.31e-17 | 145 |
| GO:005105215 | Esophagus | ESCC | regulation of DNA metabolic process | 232/8552 | 359/18723 | 2.40e-13 | 1.13e-11 | 232 |
| GO:000072319 | Esophagus | ESCC | telomere maintenance | 99/8552 | 131/18723 | 2.68e-12 | 1.08e-10 | 99 |
| GO:003220417 | Esophagus | ESCC | regulation of telomere maintenance | 65/8552 | 80/18723 | 6.02e-11 | 1.90e-09 | 65 |
| GO:003220014 | Esophagus | ESCC | telomere organization | 99/8552 | 159/18723 | 1.77e-05 | 1.57e-04 | 99 |
| GO:00330444 | Liver | NAFLD | regulation of chromosome organization | 34/1882 | 187/18723 | 4.69e-04 | 6.74e-03 | 34 |
| GO:00510526 | Liver | NAFLD | regulation of DNA metabolic process | 56/1882 | 359/18723 | 5.95e-04 | 7.92e-03 | 56 |
| GO:003304421 | Liver | HCC | regulation of chromosome organization | 125/7958 | 187/18723 | 1.35e-11 | 5.40e-10 | 125 |
| GO:000072311 | Liver | HCC | telomere maintenance | 85/7958 | 131/18723 | 1.86e-07 | 3.40e-06 | 85 |
| GO:005105221 | Liver | HCC | regulation of DNA metabolic process | 198/7958 | 359/18723 | 7.62e-07 | 1.17e-05 | 198 |
| GO:003220411 | Liver | HCC | regulation of telomere maintenance | 55/7958 | 80/18723 | 1.83e-06 | 2.54e-05 | 55 |
| GO:00322001 | Liver | HCC | telomere organization | 86/7958 | 159/18723 | 2.06e-03 | 1.04e-02 | 86 |
| GO:00330448 | Oral cavity | OSCC | regulation of chromosome organization | 123/7305 | 187/18723 | 9.87e-14 | 5.17e-12 | 123 |
| GO:005105210 | Oral cavity | OSCC | regulation of DNA metabolic process | 207/7305 | 359/18723 | 4.45e-13 | 2.17e-11 | 207 |
| GO:000072316 | Oral cavity | OSCC | telomere maintenance | 85/7305 | 131/18723 | 1.72e-09 | 4.09e-08 | 85 |
| GO:003220410 | Oral cavity | OSCC | regulation of telomere maintenance | 55/7305 | 80/18723 | 6.67e-08 | 1.19e-06 | 55 |
| GO:00322006 | Oral cavity | OSCC | telomere organization | 85/7305 | 159/18723 | 1.47e-04 | 1.04e-03 | 85 |
| GO:003304422 | Oral cavity | EOLP | regulation of chromosome organization | 50/2218 | 187/18723 | 1.80e-08 | 7.94e-07 | 50 |
| GO:005105222 | Oral cavity | EOLP | regulation of DNA metabolic process | 75/2218 | 359/18723 | 5.81e-07 | 1.53e-05 | 75 |
| GO:000072322 | Oral cavity | EOLP | telomere maintenance | 36/2218 | 131/18723 | 8.39e-07 | 2.10e-05 | 36 |
| Page: 1 2 3 |
| 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 |
| YLPM1 | SNV | Missense_Mutation | c.6013N>T | p.Asp2005Tyr | p.D2005Y | P49750 | protein_coding | deleterious(0) | probably_damaging(0.989) | TCGA-A1-A0SI-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| YLPM1 | SNV | Missense_Mutation | c.2722N>A | p.Glu908Lys | p.E908K | P49750 | protein_coding | tolerated_low_confidence(0.08) | benign(0.223) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| YLPM1 | SNV | Missense_Mutation | novel | c.877C>G | p.Gln293Glu | p.Q293E | P49750 | protein_coding | deleterious_low_confidence(0.03) | probably_damaging(0.979) | TCGA-AC-A3W5-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | docetaxel | CR |
| YLPM1 | SNV | Missense_Mutation | c.1129N>C | p.Asp377His | p.D377H | P49750 | protein_coding | deleterious_low_confidence(0.01) | possibly_damaging(0.73) | TCGA-AO-A03T-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD | |
| YLPM1 | SNV | Missense_Mutation | novel | c.5174N>G | p.Val1725Gly | p.V1725G | P49750 | protein_coding | tolerated_low_confidence(0.27) | benign(0.001) | TCGA-AO-A128-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
| YLPM1 | SNV | Missense_Mutation | c.2973T>G | p.His991Gln | p.H991Q | P49750 | protein_coding | tolerated_low_confidence(0.46) | benign(0.001) | TCGA-AR-A1AY-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unspecific | Doxorubicin | SD | |
| YLPM1 | SNV | Missense_Mutation | c.2488C>T | p.Pro830Ser | p.P830S | P49750 | protein_coding | tolerated_low_confidence(0.52) | benign(0.147) | TCGA-B6-A0RM-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| YLPM1 | SNV | Missense_Mutation | c.3199G>A | p.Asp1067Asn | p.D1067N | P49750 | protein_coding | tolerated_low_confidence(0.09) | benign(0.082) | TCGA-C8-A12T-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| YLPM1 | SNV | Missense_Mutation | rs757763862 | c.4088N>A | p.Arg1363Gln | p.R1363Q | P49750 | protein_coding | deleterious_low_confidence(0.01) | benign(0.018) | TCGA-C8-A26Y-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| YLPM1 | SNV | Missense_Mutation | novel | c.4513N>T | p.Met1505Leu | p.M1505L | P49750 | protein_coding | tolerated_low_confidence(0.53) | benign(0) | TCGA-C8-A8HR-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | 5-fluorouracil | CR |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 |
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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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