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Gene: PATL1 |
Gene summary for PATL1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PATL1 | Gene ID | 219988 |
| Gene name | PAT1 homolog 1, processing body mRNA decay factor | |
| Gene Alias | Pat1b | |
| Cytomap | 11q12.1 | |
| Gene Type | protein-coding | GO ID | GO:0000288 | UniProtAcc | Q86TB9 |
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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 |
| 219988 | PATL1 | HTA11_1938_2000001011 | Human | Colorectum | AD | 4.74e-04 | 3.44e-01 | -0.0811 |
| 219988 | PATL1 | HTA11_347_2000001011 | Human | Colorectum | AD | 1.71e-04 | 2.86e-01 | -0.1954 |
| 219988 | PATL1 | HTA11_1391_2000001011 | Human | Colorectum | AD | 3.20e-04 | 3.53e-01 | -0.059 |
| 219988 | PATL1 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 1.83e-33 | 9.08e-01 | 0.294 |
| 219988 | PATL1 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 6.70e-03 | 3.46e-01 | 0.281 |
| 219988 | PATL1 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 2.32e-02 | 3.44e-01 | 0.3859 |
| 219988 | PATL1 | A002-C-116 | Human | Colorectum | FAP | 8.99e-03 | -1.15e-01 | -0.0452 |
| 219988 | PATL1 | LZE2T | Human | Esophagus | ESCC | 1.11e-05 | 3.86e-01 | 0.082 |
| 219988 | PATL1 | LZE4T | Human | Esophagus | ESCC | 1.80e-10 | 2.07e-01 | 0.0811 |
| 219988 | PATL1 | LZE7T | Human | Esophagus | ESCC | 1.05e-07 | 4.49e-01 | 0.0667 |
| 219988 | PATL1 | LZE8T | Human | Esophagus | ESCC | 2.70e-03 | 1.26e-01 | 0.067 |
| 219988 | PATL1 | LZE20T | Human | Esophagus | ESCC | 6.58e-06 | 4.66e-02 | 0.0662 |
| 219988 | PATL1 | LZE22T | Human | Esophagus | ESCC | 1.76e-03 | 9.35e-02 | 0.068 |
| 219988 | PATL1 | LZE24T | Human | Esophagus | ESCC | 1.55e-12 | 4.69e-01 | 0.0596 |
| 219988 | PATL1 | LZE21T | Human | Esophagus | ESCC | 4.89e-03 | 5.33e-02 | 0.0655 |
| 219988 | PATL1 | LZE6T | Human | Esophagus | ESCC | 2.55e-06 | 1.37e-01 | 0.0845 |
| 219988 | PATL1 | P2T-E | Human | Esophagus | ESCC | 1.47e-21 | 2.55e-01 | 0.1177 |
| 219988 | PATL1 | P4T-E | Human | Esophagus | ESCC | 2.73e-13 | 3.03e-01 | 0.1323 |
| 219988 | PATL1 | P5T-E | Human | Esophagus | ESCC | 4.75e-18 | 1.35e-01 | 0.1327 |
| 219988 | PATL1 | P8T-E | Human | Esophagus | ESCC | 2.84e-25 | 3.89e-01 | 0.0889 |
| Page: 1 2 3 4 5 |
| 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 | ||
| 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 |
| ∗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:006101319 | Esophagus | ESCC | regulation of mRNA catabolic process | 115/8552 | 166/18723 | 5.90e-10 | 1.49e-08 | 115 |
| GO:004348719 | Esophagus | ESCC | regulation of RNA stability | 117/8552 | 170/18723 | 7.91e-10 | 1.94e-08 | 117 |
| GO:004348819 | Esophagus | ESCC | regulation of mRNA stability | 109/8552 | 158/18723 | 2.40e-09 | 5.35e-08 | 109 |
| GO:006101416 | Esophagus | ESCC | positive regulation of mRNA catabolic process | 63/8552 | 87/18723 | 3.70e-07 | 5.15e-06 | 63 |
| GO:006115716 | Esophagus | ESCC | mRNA destabilization | 61/8552 | 84/18723 | 4.81e-07 | 6.49e-06 | 61 |
| GO:005077916 | Esophagus | ESCC | RNA destabilization | 63/8552 | 88/18723 | 7.23e-07 | 9.40e-06 | 63 |
| GO:000028816 | Esophagus | ESCC | nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay | 40/8552 | 56/18723 | 8.36e-05 | 6.08e-04 | 40 |
| GO:003396214 | Esophagus | ESCC | P-body assembly | 16/8552 | 21/18723 | 4.47e-03 | 1.76e-02 | 16 |
| GO:0110154 | Esophagus | ESCC | RNA decapping | 14/8552 | 18/18723 | 5.77e-03 | 2.14e-02 | 14 |
| GO:003424914 | Esophagus | ESCC | negative regulation of cellular amide metabolic process | 144/8552 | 273/18723 | 1.08e-02 | 3.67e-02 | 144 |
| GO:000989622 | Liver | HCC | positive regulation of catabolic process | 335/7958 | 492/18723 | 3.83e-31 | 1.87e-28 | 335 |
| GO:003133122 | Liver | HCC | positive regulation of cellular catabolic process | 295/7958 | 427/18723 | 3.20e-29 | 1.45e-26 | 295 |
| GO:004427021 | Liver | HCC | cellular nitrogen compound catabolic process | 303/7958 | 451/18723 | 9.76e-27 | 3.64e-24 | 303 |
| GO:004670021 | Liver | HCC | heterocycle catabolic process | 299/7958 | 445/18723 | 2.07e-26 | 7.29e-24 | 299 |
| GO:190136121 | Liver | HCC | organic cyclic compound catabolic process | 325/7958 | 495/18723 | 6.52e-26 | 2.18e-23 | 325 |
| GO:001943921 | Liver | HCC | aromatic compound catabolic process | 309/7958 | 467/18723 | 1.56e-25 | 4.94e-23 | 309 |
| GO:000640121 | Liver | HCC | RNA catabolic process | 201/7958 | 278/18723 | 3.88e-24 | 1.02e-21 | 201 |
| GO:003465521 | Liver | HCC | nucleobase-containing compound catabolic process | 273/7958 | 407/18723 | 4.84e-24 | 1.23e-21 | 273 |
| GO:190331121 | Liver | HCC | regulation of mRNA metabolic process | 205/7958 | 288/18723 | 3.38e-23 | 6.90e-21 | 205 |
| GO:000640221 | Liver | HCC | mRNA catabolic process | 169/7958 | 232/18723 | 4.50e-21 | 6.96e-19 | 169 |
| Page: 1 2 3 4 5 6 7 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0301824 | Esophagus | ESCC | RNA degradation | 62/4205 | 79/8465 | 1.18e-07 | 9.39e-07 | 4.81e-07 | 62 |
| hsa0301834 | Esophagus | ESCC | RNA degradation | 62/4205 | 79/8465 | 1.18e-07 | 9.39e-07 | 4.81e-07 | 62 |
| hsa030182 | Liver | HCC | RNA degradation | 58/4020 | 79/8465 | 2.29e-06 | 2.19e-05 | 1.22e-05 | 58 |
| hsa030183 | Liver | HCC | RNA degradation | 58/4020 | 79/8465 | 2.29e-06 | 2.19e-05 | 1.22e-05 | 58 |
| hsa030189 | Oral cavity | OSCC | RNA degradation | 59/3704 | 79/8465 | 2.05e-08 | 1.91e-07 | 9.70e-08 | 59 |
| hsa0301814 | Oral cavity | OSCC | RNA degradation | 59/3704 | 79/8465 | 2.05e-08 | 1.91e-07 | 9.70e-08 | 59 |
| 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 |
| PATL1 | SNV | Missense_Mutation | c.30T>G | p.Cys10Trp | p.C10W | Q86TB9 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.97) | TCGA-AR-A251-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | SD | |
| PATL1 | insertion | Frame_Shift_Ins | novel | c.1962_1963insA | p.Leu655ThrfsTer43 | p.L655Tfs*43 | Q86TB9 | protein_coding | TCGA-A7-A0CD-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | ||
| PATL1 | insertion | Frame_Shift_Ins | novel | c.1961_1962insGCTGGAGCGCAATGGTGCGATCTTGGCTCACTGCAACCTC | p.Ser654ArgfsTer57 | p.S654Rfs*57 | Q86TB9 | protein_coding | TCGA-A7-A0CD-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | ||
| PATL1 | SNV | Missense_Mutation | rs762892994 | c.1373G>A | p.Arg458His | p.R458H | Q86TB9 | protein_coding | tolerated(0.36) | benign(0.171) | TCGA-EA-A410-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| PATL1 | SNV | Missense_Mutation | c.1066N>T | p.His356Tyr | p.H356Y | Q86TB9 | protein_coding | deleterious(0) | probably_damaging(0.988) | TCGA-EK-A2RN-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| PATL1 | SNV | Missense_Mutation | c.388G>C | p.Glu130Gln | p.E130Q | Q86TB9 | protein_coding | tolerated(0.45) | benign(0.114) | TCGA-IR-A3LA-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| PATL1 | insertion | Nonsense_Mutation | novel | c.1903_1904insTCTA | p.Cys635PhefsTer2 | p.C635Ffs*2 | Q86TB9 | protein_coding | TCGA-DS-A1OA-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | carboplatin | PD | ||
| PATL1 | insertion | In_Frame_Ins | novel | c.1905_1906insCGG | p.Cys635_Leu636insArg | p.C635_L636insR | Q86TB9 | protein_coding | TCGA-DS-A1OC-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | gemcitabine | SD | ||
| PATL1 | insertion | Nonsense_Mutation | novel | c.1903_1904insA | p.Cys635Ter | p.C635* | Q86TB9 | protein_coding | TCGA-DS-A1OC-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | gemcitabine | SD | ||
| PATL1 | SNV | Missense_Mutation | c.1663N>G | p.Met555Val | p.M555V | Q86TB9 | protein_coding | tolerated(0.55) | benign(0) | TCGA-A6-3809-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 |
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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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