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Gene: OPTN |
Gene summary for OPTN |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | OPTN | Gene ID | 10133 |
| Gene name | optineurin | |
| Gene Alias | ALS12 | |
| Cytomap | 10p13 | |
| Gene Type | protein-coding | GO ID | GO:0000422 | UniProtAcc | Q96CV9 |
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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 |
| 10133 | OPTN | HTA11_2487_2000001011 | Human | Colorectum | SER | 1.43e-07 | 5.95e-01 | -0.1808 |
| 10133 | OPTN | HTA11_1938_2000001011 | Human | Colorectum | AD | 6.11e-10 | 5.25e-01 | -0.0811 |
| 10133 | OPTN | HTA11_78_2000001011 | Human | Colorectum | AD | 1.53e-03 | 3.34e-01 | -0.1088 |
| 10133 | OPTN | HTA11_347_2000001011 | Human | Colorectum | AD | 3.11e-18 | 5.76e-01 | -0.1954 |
| 10133 | OPTN | HTA11_411_2000001011 | Human | Colorectum | SER | 4.96e-09 | 1.33e+00 | -0.2602 |
| 10133 | OPTN | HTA11_2112_2000001011 | Human | Colorectum | SER | 5.24e-08 | 9.52e-01 | -0.2196 |
| 10133 | OPTN | HTA11_3361_2000001011 | Human | Colorectum | AD | 3.08e-03 | 3.26e-01 | -0.1207 |
| 10133 | OPTN | HTA11_696_2000001011 | Human | Colorectum | AD | 6.66e-08 | 4.46e-01 | -0.1464 |
| 10133 | OPTN | HTA11_866_2000001011 | Human | Colorectum | AD | 3.61e-07 | 3.08e-01 | -0.1001 |
| 10133 | OPTN | HTA11_1391_2000001011 | Human | Colorectum | AD | 4.49e-07 | 3.66e-01 | -0.059 |
| 10133 | OPTN | HTA11_2992_2000001011 | Human | Colorectum | SER | 1.63e-05 | 6.25e-01 | -0.1706 |
| 10133 | OPTN | HTA11_99999970781_79442 | Human | Colorectum | MSS | 6.46e-08 | 3.61e-01 | 0.294 |
| 10133 | OPTN | HTA11_99999965062_69753 | Human | Colorectum | MSI-H | 9.37e-03 | 8.78e-01 | 0.3487 |
| 10133 | OPTN | HTA11_99999971662_82457 | Human | Colorectum | MSS | 3.13e-08 | 3.97e-01 | 0.3859 |
| 10133 | OPTN | LZE4T | Human | Esophagus | ESCC | 2.76e-10 | 4.61e-01 | 0.0811 |
| 10133 | OPTN | LZE7T | Human | Esophagus | ESCC | 3.99e-04 | 2.46e-01 | 0.0667 |
| 10133 | OPTN | LZE8T | Human | Esophagus | ESCC | 1.86e-07 | 2.48e-01 | 0.067 |
| 10133 | OPTN | LZE20T | Human | Esophagus | ESCC | 2.91e-07 | 1.24e-01 | 0.0662 |
| 10133 | OPTN | LZE22D1 | Human | Esophagus | HGIN | 1.48e-03 | -4.74e-02 | 0.0595 |
| 10133 | OPTN | LZE22T | Human | Esophagus | ESCC | 9.46e-09 | 4.54e-01 | 0.068 |
| Page: 1 2 3 4 5 6 7 8 |
| 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 | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| 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:0072659 | Colorectum | AD | protein localization to plasma membrane | 122/3918 | 284/18723 | 2.86e-17 | 1.49e-14 | 122 |
| GO:0009896 | Colorectum | AD | positive regulation of catabolic process | 180/3918 | 492/18723 | 4.33e-16 | 1.94e-13 | 180 |
| GO:0031331 | Colorectum | AD | positive regulation of cellular catabolic process | 156/3918 | 427/18723 | 4.68e-14 | 1.05e-11 | 156 |
| GO:1990778 | Colorectum | AD | protein localization to cell periphery | 129/3918 | 333/18723 | 5.51e-14 | 1.15e-11 | 129 |
| GO:0090150 | Colorectum | AD | establishment of protein localization to membrane | 100/3918 | 260/18723 | 6.01e-11 | 6.33e-09 | 100 |
| GO:0048193 | Colorectum | AD | Golgi vesicle transport | 109/3918 | 296/18723 | 1.80e-10 | 1.68e-08 | 109 |
| GO:0022411 | Colorectum | AD | cellular component disassembly | 147/3918 | 443/18723 | 8.53e-10 | 6.76e-08 | 147 |
| GO:0010506 | Colorectum | AD | regulation of autophagy | 111/3918 | 317/18723 | 3.57e-09 | 2.35e-07 | 111 |
| GO:0016236 | Colorectum | AD | macroautophagy | 103/3918 | 291/18723 | 6.76e-09 | 4.15e-07 | 103 |
| GO:0098876 | Colorectum | AD | vesicle-mediated transport to the plasma membrane | 57/3918 | 136/18723 | 2.30e-08 | 1.27e-06 | 57 |
| GO:0061951 | Colorectum | AD | establishment of protein localization to plasma membrane | 31/3918 | 60/18723 | 1.37e-07 | 6.42e-06 | 31 |
| GO:0006892 | Colorectum | AD | post-Golgi vesicle-mediated transport | 45/3918 | 104/18723 | 2.22e-07 | 9.26e-06 | 45 |
| GO:0043112 | Colorectum | AD | receptor metabolic process | 62/3918 | 166/18723 | 8.18e-07 | 2.85e-05 | 62 |
| GO:1903008 | Colorectum | AD | organelle disassembly | 46/3918 | 114/18723 | 1.81e-06 | 5.48e-05 | 46 |
| GO:0000422 | Colorectum | AD | autophagy of mitochondrion | 35/3918 | 81/18723 | 4.94e-06 | 1.29e-04 | 35 |
| GO:0061726 | Colorectum | AD | mitochondrion disassembly | 35/3918 | 81/18723 | 4.94e-06 | 1.29e-04 | 35 |
| GO:0043001 | Colorectum | AD | Golgi to plasma membrane protein transport | 21/3918 | 40/18723 | 1.03e-05 | 2.40e-04 | 21 |
| GO:0001881 | Colorectum | AD | receptor recycling | 18/3918 | 33/18723 | 2.23e-05 | 4.40e-04 | 18 |
| GO:0006893 | Colorectum | AD | Golgi to plasma membrane transport | 27/3918 | 60/18723 | 2.41e-05 | 4.66e-04 | 27 |
| GO:0061912 | Colorectum | AD | selective autophagy | 29/3918 | 68/18723 | 4.20e-05 | 7.39e-04 | 29 |
| 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 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa05014 | Colorectum | AD | Amyotrophic lateral sclerosis | 164/2092 | 364/8465 | 4.28e-18 | 1.27e-16 | 8.09e-17 | 164 |
| hsa05022 | Colorectum | AD | Pathways of neurodegeneration - multiple diseases | 201/2092 | 476/8465 | 4.54e-18 | 1.27e-16 | 8.09e-17 | 201 |
| hsa04137 | Colorectum | AD | Mitophagy - animal | 29/2092 | 72/8465 | 2.49e-03 | 1.35e-02 | 8.59e-03 | 29 |
| hsa050141 | Colorectum | AD | Amyotrophic lateral sclerosis | 164/2092 | 364/8465 | 4.28e-18 | 1.27e-16 | 8.09e-17 | 164 |
| hsa050221 | Colorectum | AD | Pathways of neurodegeneration - multiple diseases | 201/2092 | 476/8465 | 4.54e-18 | 1.27e-16 | 8.09e-17 | 201 |
| hsa041371 | Colorectum | AD | Mitophagy - animal | 29/2092 | 72/8465 | 2.49e-03 | 1.35e-02 | 8.59e-03 | 29 |
| hsa050222 | Colorectum | SER | Pathways of neurodegeneration - multiple diseases | 168/1580 | 476/8465 | 6.23e-19 | 2.07e-17 | 1.50e-17 | 168 |
| hsa050142 | Colorectum | SER | Amyotrophic lateral sclerosis | 138/1580 | 364/8465 | 9.89e-19 | 2.99e-17 | 2.17e-17 | 138 |
| hsa041372 | Colorectum | SER | Mitophagy - animal | 22/1580 | 72/8465 | 9.93e-03 | 4.78e-02 | 3.47e-02 | 22 |
| hsa050223 | Colorectum | SER | Pathways of neurodegeneration - multiple diseases | 168/1580 | 476/8465 | 6.23e-19 | 2.07e-17 | 1.50e-17 | 168 |
| hsa050143 | Colorectum | SER | Amyotrophic lateral sclerosis | 138/1580 | 364/8465 | 9.89e-19 | 2.99e-17 | 2.17e-17 | 138 |
| hsa041373 | Colorectum | SER | Mitophagy - animal | 22/1580 | 72/8465 | 9.93e-03 | 4.78e-02 | 3.47e-02 | 22 |
| hsa050224 | Colorectum | MSS | Pathways of neurodegeneration - multiple diseases | 192/1875 | 476/8465 | 2.79e-20 | 1.04e-18 | 6.36e-19 | 192 |
| hsa050144 | Colorectum | MSS | Amyotrophic lateral sclerosis | 156/1875 | 364/8465 | 1.43e-19 | 4.62e-18 | 2.83e-18 | 156 |
| hsa041374 | Colorectum | MSS | Mitophagy - animal | 27/1875 | 72/8465 | 2.17e-03 | 1.10e-02 | 6.76e-03 | 27 |
| hsa050225 | Colorectum | MSS | Pathways of neurodegeneration - multiple diseases | 192/1875 | 476/8465 | 2.79e-20 | 1.04e-18 | 6.36e-19 | 192 |
| hsa050145 | Colorectum | MSS | Amyotrophic lateral sclerosis | 156/1875 | 364/8465 | 1.43e-19 | 4.62e-18 | 2.83e-18 | 156 |
| hsa041375 | Colorectum | MSS | Mitophagy - animal | 27/1875 | 72/8465 | 2.17e-03 | 1.10e-02 | 6.76e-03 | 27 |
| hsa050146 | Colorectum | MSI-H | Amyotrophic lateral sclerosis | 95/797 | 364/8465 | 2.31e-21 | 1.50e-19 | 1.26e-19 | 95 |
| hsa050226 | Colorectum | MSI-H | Pathways of neurodegeneration - multiple diseases | 107/797 | 476/8465 | 1.24e-18 | 5.72e-17 | 4.80e-17 | 107 |
| Page: 1 2 3 4 |
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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 |
| OPTN | SNV | Missense_Mutation | c.943N>A | p.Glu315Lys | p.E315K | Q96CV9 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-BH-A0HN-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| OPTN | SNV | Missense_Mutation | novel | c.117N>T | p.Glu39Asp | p.E39D | Q96CV9 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-D8-A147-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine | SD |
| OPTN | SNV | Missense_Mutation | c.994N>C | p.Glu332Gln | p.E332Q | Q96CV9 | protein_coding | deleterious(0.01) | probably_damaging(0.953) | TCGA-D8-A147-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine | SD | |
| OPTN | insertion | Nonsense_Mutation | novel | c.728_729insAATATA | p.Gly243_Asn244insIleTer | p.G243_N244insI* | Q96CV9 | protein_coding | TCGA-A8-A08H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| OPTN | SNV | Missense_Mutation | novel | c.1375G>A | p.Glu459Lys | p.E459K | Q96CV9 | protein_coding | deleterious(0) | possibly_damaging(0.575) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| OPTN | SNV | Missense_Mutation | novel | c.187C>G | p.Gln63Glu | p.Q63E | Q96CV9 | protein_coding | deleterious(0.02) | possibly_damaging(0.615) | TCGA-JW-A5VL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| OPTN | SNV | Missense_Mutation | c.248N>A | p.Arg83His | p.R83H | Q96CV9 | protein_coding | deleterious(0) | probably_damaging(0.969) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
| OPTN | SNV | Missense_Mutation | c.1111N>A | p.Glu371Lys | p.E371K | Q96CV9 | protein_coding | deleterious(0.01) | probably_damaging(0.952) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR | |
| OPTN | SNV | Missense_Mutation | c.455C>T | p.Ala152Val | p.A152V | Q96CV9 | protein_coding | deleterious(0.01) | possibly_damaging(0.786) | TCGA-AU-6004-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| OPTN | SNV | Missense_Mutation | rs778107336 | c.669G>T | p.Lys223Asn | p.K223N | Q96CV9 | protein_coding | tolerated(0.16) | possibly_damaging(0.628) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 |
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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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