|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: PML |
Gene summary for PML |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PML | Gene ID | 5371 |
| Gene name | PML nuclear body scaffold | |
| Gene Alias | MYL | |
| Cytomap | 15q24.1 | |
| Gene Type | protein-coding | GO ID | GO:0000075 | UniProtAcc | P29590 |
Top |
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 |
| 5371 | PML | LZE4T | Human | Esophagus | ESCC | 1.04e-09 | 1.61e-01 | 0.0811 |
| 5371 | PML | LZE7T | Human | Esophagus | ESCC | 3.26e-07 | 6.24e-01 | 0.0667 |
| 5371 | PML | LZE8T | Human | Esophagus | ESCC | 6.97e-08 | 2.19e-01 | 0.067 |
| 5371 | PML | LZE20T | Human | Esophagus | ESCC | 7.47e-10 | 2.99e-01 | 0.0662 |
| 5371 | PML | LZE22D1 | Human | Esophagus | HGIN | 3.84e-02 | 5.55e-03 | 0.0595 |
| 5371 | PML | LZE24D1 | Human | Esophagus | HGIN | 1.52e-02 | 3.48e-01 | 0.054 |
| 5371 | PML | LZE24T | Human | Esophagus | ESCC | 3.19e-06 | 3.12e-01 | 0.0596 |
| 5371 | PML | LZE22D3 | Human | Esophagus | HGIN | 1.14e-02 | 6.99e-01 | 0.0653 |
| 5371 | PML | LZE21T | Human | Esophagus | ESCC | 4.01e-07 | 6.37e-01 | 0.0655 |
| 5371 | PML | P1T-E | Human | Esophagus | ESCC | 7.79e-20 | 1.04e+00 | 0.0875 |
| 5371 | PML | P2T-E | Human | Esophagus | ESCC | 5.02e-34 | 8.01e-01 | 0.1177 |
| 5371 | PML | P4T-E | Human | Esophagus | ESCC | 1.26e-22 | 2.88e-01 | 0.1323 |
| 5371 | PML | P5T-E | Human | Esophagus | ESCC | 2.95e-13 | 3.19e-01 | 0.1327 |
| 5371 | PML | P8T-E | Human | Esophagus | ESCC | 1.59e-36 | 9.53e-01 | 0.0889 |
| 5371 | PML | P9T-E | Human | Esophagus | ESCC | 2.61e-26 | 6.79e-01 | 0.1131 |
| 5371 | PML | P10T-E | Human | Esophagus | ESCC | 9.89e-09 | 1.51e-01 | 0.116 |
| 5371 | PML | P11T-E | Human | Esophagus | ESCC | 1.54e-32 | 1.51e+00 | 0.1426 |
| 5371 | PML | P12T-E | Human | Esophagus | ESCC | 9.50e-15 | 3.31e-01 | 0.1122 |
| 5371 | PML | P15T-E | Human | Esophagus | ESCC | 1.36e-30 | 6.70e-01 | 0.1149 |
| 5371 | PML | P16T-E | Human | Esophagus | ESCC | 8.60e-18 | 4.39e-01 | 0.1153 |
| 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 | ||
| 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. |
Top |
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:004851124 | Thyroid | ATC | rhythmic process | 141/6293 | 298/18723 | 5.58e-07 | 7.93e-06 | 141 |
| GO:000756924 | Thyroid | ATC | cell aging | 72/6293 | 132/18723 | 5.77e-07 | 8.15e-06 | 72 |
| GO:004814432 | Thyroid | ATC | fibroblast proliferation | 49/6293 | 81/18723 | 6.38e-07 | 8.80e-06 | 49 |
| GO:003220623 | Thyroid | ATC | positive regulation of telomere maintenance | 35/6293 | 52/18723 | 6.97e-07 | 9.40e-06 | 35 |
| GO:005123532 | Thyroid | ATC | maintenance of location | 152/6293 | 327/18723 | 7.84e-07 | 1.04e-05 | 152 |
| GO:200125224 | Thyroid | ATC | positive regulation of chromosome organization | 49/6293 | 82/18723 | 1.07e-06 | 1.39e-05 | 49 |
| GO:004277131 | Thyroid | ATC | intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator | 30/6293 | 43/18723 | 1.36e-06 | 1.71e-05 | 30 |
| GO:001076116 | Thyroid | ATC | fibroblast migration | 32/6293 | 47/18723 | 1.42e-06 | 1.77e-05 | 32 |
| GO:005145722 | Thyroid | ATC | maintenance of protein location in nucleus | 19/6293 | 23/18723 | 1.89e-06 | 2.29e-05 | 19 |
| GO:005165133 | Thyroid | ATC | maintenance of location in cell | 105/6293 | 214/18723 | 1.92e-06 | 2.31e-05 | 105 |
| GO:000863026 | Thyroid | ATC | intrinsic apoptotic signaling pathway in response to DNA damage | 56/6293 | 99/18723 | 2.22e-06 | 2.63e-05 | 56 |
| GO:000709312 | Thyroid | ATC | mitotic cell cycle checkpoint | 69/6293 | 129/18723 | 2.52e-06 | 2.96e-05 | 69 |
| GO:190390028 | Thyroid | ATC | regulation of viral life cycle | 77/6293 | 148/18723 | 2.79e-06 | 3.21e-05 | 77 |
| GO:004328133 | Thyroid | ATC | regulation of cysteine-type endopeptidase activity involved in apoptotic process | 102/6293 | 209/18723 | 3.61e-06 | 4.03e-05 | 102 |
| GO:003009933 | Thyroid | ATC | myeloid cell differentiation | 170/6293 | 381/18723 | 4.26e-06 | 4.68e-05 | 170 |
| GO:000176317 | Thyroid | ATC | morphogenesis of a branching structure | 96/6293 | 196/18723 | 5.68e-06 | 6.04e-05 | 96 |
| GO:000863125 | Thyroid | ATC | intrinsic apoptotic signaling pathway in response to oxidative stress | 30/6293 | 45/18723 | 5.89e-06 | 6.18e-05 | 30 |
| GO:005254734 | Thyroid | ATC | regulation of peptidase activity | 200/6293 | 461/18723 | 6.25e-06 | 6.52e-05 | 200 |
| GO:000628211 | Thyroid | ATC | regulation of DNA repair | 68/6293 | 130/18723 | 8.19e-06 | 8.27e-05 | 68 |
| GO:200011633 | Thyroid | ATC | regulation of cysteine-type endopeptidase activity | 111/6293 | 235/18723 | 9.41e-06 | 9.41e-05 | 111 |
| 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 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0414429 | Esophagus | HGIN | Endocytosis | 76/1383 | 251/8465 | 1.74e-08 | 3.34e-07 | 2.65e-07 | 76 |
| hsa0412026 | Esophagus | HGIN | Ubiquitin mediated proteolysis | 49/1383 | 142/8465 | 7.78e-08 | 1.33e-06 | 1.06e-06 | 49 |
| hsa0516420 | Esophagus | HGIN | Influenza A | 42/1383 | 171/8465 | 3.41e-03 | 2.54e-02 | 2.02e-02 | 42 |
| hsa04144113 | Esophagus | HGIN | Endocytosis | 76/1383 | 251/8465 | 1.74e-08 | 3.34e-07 | 2.65e-07 | 76 |
| hsa04120111 | Esophagus | HGIN | Ubiquitin mediated proteolysis | 49/1383 | 142/8465 | 7.78e-08 | 1.33e-06 | 1.06e-06 | 49 |
| hsa05164110 | Esophagus | HGIN | Influenza A | 42/1383 | 171/8465 | 3.41e-03 | 2.54e-02 | 2.02e-02 | 42 |
| hsa0412027 | Esophagus | ESCC | Ubiquitin mediated proteolysis | 122/4205 | 142/8465 | 6.53e-20 | 7.29e-18 | 3.74e-18 | 122 |
| hsa04144210 | Esophagus | ESCC | Endocytosis | 186/4205 | 251/8465 | 9.74e-16 | 4.66e-14 | 2.39e-14 | 186 |
| hsa0516425 | Esophagus | ESCC | Influenza A | 122/4205 | 171/8465 | 5.01e-09 | 4.79e-08 | 2.45e-08 | 122 |
| hsa052215 | Esophagus | ESCC | Acute myeloid leukemia | 49/4205 | 67/8465 | 7.43e-05 | 3.07e-04 | 1.57e-04 | 49 |
| hsa052028 | Esophagus | ESCC | Transcriptional misregulation in cancer | 116/4205 | 193/8465 | 2.08e-03 | 5.95e-03 | 3.05e-03 | 116 |
| hsa0412036 | Esophagus | ESCC | Ubiquitin mediated proteolysis | 122/4205 | 142/8465 | 6.53e-20 | 7.29e-18 | 3.74e-18 | 122 |
| hsa0414437 | Esophagus | ESCC | Endocytosis | 186/4205 | 251/8465 | 9.74e-16 | 4.66e-14 | 2.39e-14 | 186 |
| hsa0516435 | Esophagus | ESCC | Influenza A | 122/4205 | 171/8465 | 5.01e-09 | 4.79e-08 | 2.45e-08 | 122 |
| hsa0522113 | Esophagus | ESCC | Acute myeloid leukemia | 49/4205 | 67/8465 | 7.43e-05 | 3.07e-04 | 1.57e-04 | 49 |
| hsa0520213 | Esophagus | ESCC | Transcriptional misregulation in cancer | 116/4205 | 193/8465 | 2.08e-03 | 5.95e-03 | 3.05e-03 | 116 |
| hsa0414412 | Liver | Cirrhotic | Endocytosis | 119/2530 | 251/8465 | 2.33e-09 | 4.56e-08 | 2.81e-08 | 119 |
| hsa0412021 | Liver | Cirrhotic | Ubiquitin mediated proteolysis | 72/2530 | 142/8465 | 1.32e-07 | 1.97e-06 | 1.21e-06 | 72 |
| hsa0516410 | Liver | Cirrhotic | Influenza A | 66/2530 | 171/8465 | 8.56e-03 | 2.91e-02 | 1.79e-02 | 66 |
| hsa0414413 | Liver | Cirrhotic | Endocytosis | 119/2530 | 251/8465 | 2.33e-09 | 4.56e-08 | 2.81e-08 | 119 |
| Page: 1 2 3 |
Top |
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 |
Top |
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 |
| PML | PMC | Stomach | ADJ | APOL1,MUC1,RNF213, etc. | 3.30e-01 |  |
| PML | PMC | Stomach | WIM | APOL1,MUC1,RNF213, etc. | 5.86e-01 |  |
| ∗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 |
Top |
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 |
| PML | SNV | Missense_Mutation | novel | c.1022C>T | p.Ser341Leu | p.S341L | P29590 | protein_coding | deleterious(0.03) | probably_damaging(0.983) | TCGA-A2-A0EY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD |
| PML | SNV | Missense_Mutation | c.1228N>G | p.Pro410Ala | p.P410A | P29590 | protein_coding | tolerated(0.06) | probably_damaging(0.95) | TCGA-D8-A1JA-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD | |
| PML | deletion | Frame_Shift_Del | c.208delN | p.Leu70CysfsTer28 | p.L70Cfs*28 | P29590 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | |||
| PML | SNV | Missense_Mutation | rs769540520 | c.2221N>T | p.Arg741Cys | p.R741C | P29590 | protein_coding | deleterious(0.03) | benign(0.003) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| PML | SNV | Missense_Mutation | rs765869727 | c.973C>T | p.Arg325Cys | p.R325C | P29590 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-C5-A1M5-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | PD |
| PML | SNV | Missense_Mutation | c.895G>C | p.Glu299Gln | p.E299Q | P29590 | protein_coding | tolerated(0.23) | benign(0.3) | TCGA-DR-A0ZM-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unspecific | Cisplatin | SD | |
| PML | SNV | Missense_Mutation | c.1702N>A | p.Glu568Lys | p.E568K | P29590 | protein_coding | deleterious(0) | probably_damaging(0.976) | TCGA-EA-A97N-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| PML | SNV | Missense_Mutation | c.502N>A | p.Glu168Lys | p.E168K | P29590 | protein_coding | deleterious(0) | possibly_damaging(0.606) | TCGA-JX-A3Q0-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD | |
| PML | SNV | Missense_Mutation | novel | c.1015N>A | p.Tyr339Asn | p.Y339N | P29590 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-MA-AA43-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD |
| PML | SNV | Missense_Mutation | rs745678082 | c.2218N>A | p.Glu740Lys | p.E740K | P29590 | protein_coding | tolerated(0.2) | benign(0.007) | TCGA-MY-A5BD-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| Page: 1 2 3 4 5 6 7 8 |
Top |
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 |
| 5371 | PML | CLINICALLY ACTIONABLE, TRANSCRIPTION FACTOR, DRUG RESISTANCE | GEMTUZUMAB OZOGAMICIN | 15187030 | ||
| 5371 | PML | CLINICALLY ACTIONABLE, TRANSCRIPTION FACTOR, DRUG RESISTANCE | TRETINOIN | TRETINOIN | 21505136,8674046,21613260,23670176,11704842,30289902 | |
| 5371 | PML | CLINICALLY ACTIONABLE, TRANSCRIPTION FACTOR, DRUG RESISTANCE | arsenic trioxide | 24433361 | ||
| 5371 | PML | CLINICALLY ACTIONABLE, TRANSCRIPTION FACTOR, DRUG RESISTANCE | tretinoin | TRETINOIN | ||
| 5371 | PML | CLINICALLY ACTIONABLE, TRANSCRIPTION FACTOR, DRUG RESISTANCE | TAMIBAROTENE | TAMIBAROTENE | 30289902 | |
| 5371 | PML | CLINICALLY ACTIONABLE, TRANSCRIPTION FACTOR, DRUG RESISTANCE | TAZAROTENE | TAZAROTENE | 16939905 | |
| 5371 | PML | CLINICALLY ACTIONABLE, TRANSCRIPTION FACTOR, DRUG RESISTANCE | Tretinoin | TRETINOIN | ||
| 5371 | PML | CLINICALLY ACTIONABLE, TRANSCRIPTION FACTOR, DRUG RESISTANCE | ARSENIC TRIOXIDE | 26537301,11704842 |
| Page: 1 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |