|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: PAN3 |
Gene summary for PAN3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PAN3 | Gene ID | 255967 |
| Gene name | poly(A) specific ribonuclease subunit PAN3 | |
| Gene Alias | PAN3 | |
| Cytomap | 13q12.2 | |
| Gene Type | protein-coding | GO ID | GO:0000288 | UniProtAcc | Q58A45 |
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 |
| 255967 | PAN3 | CCI_1 | Human | Cervix | CC | 1.81e-09 | 1.10e+00 | 0.528 |
| 255967 | PAN3 | CCI_2 | Human | Cervix | CC | 7.52e-13 | 1.86e+00 | 0.5249 |
| 255967 | PAN3 | CCI_3 | Human | Cervix | CC | 9.35e-20 | 1.22e+00 | 0.516 |
| 255967 | PAN3 | HTA11_3410_2000001011 | Human | Colorectum | AD | 3.49e-34 | -7.85e-01 | 0.0155 |
| 255967 | PAN3 | HTA11_2487_2000001011 | Human | Colorectum | SER | 2.85e-04 | -5.18e-01 | -0.1808 |
| 255967 | PAN3 | HTA11_2951_2000001011 | Human | Colorectum | AD | 3.08e-04 | -8.62e-01 | 0.0216 |
| 255967 | PAN3 | HTA11_347_2000001011 | Human | Colorectum | AD | 2.03e-04 | 4.10e-01 | -0.1954 |
| 255967 | PAN3 | HTA11_3361_2000001011 | Human | Colorectum | AD | 4.48e-05 | -5.20e-01 | -0.1207 |
| 255967 | PAN3 | HTA11_696_2000001011 | Human | Colorectum | AD | 7.62e-05 | -3.29e-01 | -0.1464 |
| 255967 | PAN3 | HTA11_2992_2000001011 | Human | Colorectum | SER | 8.41e-04 | -5.46e-01 | -0.1706 |
| 255967 | PAN3 | HTA11_5212_2000001011 | Human | Colorectum | AD | 3.22e-10 | -8.75e-01 | -0.2061 |
| 255967 | PAN3 | HTA11_5216_2000001011 | Human | Colorectum | SER | 9.55e-05 | -6.25e-01 | -0.1462 |
| 255967 | PAN3 | HTA11_9341_2000001011 | Human | Colorectum | SER | 1.82e-02 | -7.72e-01 | -0.00410000000000005 |
| 255967 | PAN3 | HTA11_866_3004761011 | Human | Colorectum | AD | 5.76e-06 | -4.94e-01 | 0.096 |
| 255967 | PAN3 | HTA11_10711_2000001011 | Human | Colorectum | AD | 3.45e-11 | -5.71e-01 | 0.0338 |
| 255967 | PAN3 | HTA11_7696_3000711011 | Human | Colorectum | AD | 6.15e-06 | -4.91e-01 | 0.0674 |
| 255967 | PAN3 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 1.96e-05 | -4.31e-01 | 0.294 |
| 255967 | PAN3 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 7.45e-35 | 1.56e+00 | 0.281 |
| 255967 | PAN3 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 6.18e-05 | 6.33e-01 | 0.3859 |
| 255967 | PAN3 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 2.62e-04 | 9.88e-01 | 0.2585 |
| Page: 1 2 3 4 5 6 7 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| 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 | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| 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 |
| ∗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:000989610 | Cervix | CC | positive regulation of catabolic process | 109/2311 | 492/18723 | 5.26e-10 | 6.99e-08 | 109 |
| GO:003133110 | Cervix | CC | positive regulation of cellular catabolic process | 91/2311 | 427/18723 | 9.64e-08 | 5.25e-06 | 91 |
| GO:00064029 | Cervix | CC | mRNA catabolic process | 56/2311 | 232/18723 | 4.81e-07 | 1.83e-05 | 56 |
| GO:19033119 | Cervix | CC | regulation of mRNA metabolic process | 64/2311 | 288/18723 | 1.71e-06 | 5.64e-05 | 64 |
| GO:00064019 | Cervix | CC | RNA catabolic process | 62/2311 | 278/18723 | 2.18e-06 | 6.56e-05 | 62 |
| GO:00002896 | Cervix | CC | nuclear-transcribed mRNA poly(A) tail shortening | 13/2311 | 29/18723 | 1.48e-05 | 2.93e-04 | 13 |
| GO:000641710 | Cervix | CC | regulation of translation | 89/2311 | 468/18723 | 1.86e-05 | 3.46e-04 | 89 |
| GO:00009567 | Cervix | CC | nuclear-transcribed mRNA catabolic process | 30/2311 | 112/18723 | 2.60e-05 | 4.37e-04 | 30 |
| GO:00002886 | Cervix | CC | nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay | 18/2311 | 56/18723 | 8.42e-05 | 1.13e-03 | 18 |
| GO:00610139 | Cervix | CC | regulation of mRNA catabolic process | 38/2311 | 166/18723 | 1.07e-04 | 1.36e-03 | 38 |
| GO:19033136 | Cervix | CC | positive regulation of mRNA metabolic process | 29/2311 | 118/18723 | 1.86e-04 | 2.18e-03 | 29 |
| GO:19021153 | Cervix | CC | regulation of organelle assembly | 40/2311 | 186/18723 | 2.92e-04 | 3.15e-03 | 40 |
| GO:00467008 | Cervix | CC | heterocycle catabolic process | 80/2311 | 445/18723 | 3.23e-04 | 3.42e-03 | 80 |
| GO:19021171 | Cervix | CC | positive regulation of organelle assembly | 19/2311 | 67/18723 | 3.42e-04 | 3.58e-03 | 19 |
| GO:00346559 | Cervix | CC | nucleobase-containing compound catabolic process | 74/2311 | 407/18723 | 3.77e-04 | 3.88e-03 | 74 |
| GO:00434889 | Cervix | CC | regulation of mRNA stability | 35/2311 | 158/18723 | 3.80e-04 | 3.89e-03 | 35 |
| GO:00611576 | Cervix | CC | mRNA destabilization | 22/2311 | 84/18723 | 4.18e-04 | 4.23e-03 | 22 |
| GO:00610146 | Cervix | CC | positive regulation of mRNA catabolic process | 22/2311 | 87/18723 | 7.03e-04 | 6.40e-03 | 22 |
| GO:00434879 | Cervix | CC | regulation of RNA stability | 36/2311 | 170/18723 | 7.72e-04 | 6.86e-03 | 36 |
| GO:00442709 | Cervix | CC | cellular nitrogen compound catabolic process | 79/2311 | 451/18723 | 7.80e-04 | 6.91e-03 | 79 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa030187 | Endometrium | EEC | RNA degradation | 20/1237 | 79/8465 | 8.36e-03 | 3.88e-02 | 2.89e-02 | 20 |
| hsa0301812 | Endometrium | EEC | RNA degradation | 20/1237 | 79/8465 | 8.36e-03 | 3.88e-02 | 2.89e-02 | 20 |
| hsa03018 | Liver | Cirrhotic | RNA degradation | 44/2530 | 79/8465 | 1.43e-06 | 1.65e-05 | 1.02e-05 | 44 |
| hsa030181 | Liver | Cirrhotic | RNA degradation | 44/2530 | 79/8465 | 1.43e-06 | 1.65e-05 | 1.02e-05 | 44 |
| 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 |
| hsa0301841 | Oral cavity | EOLP | RNA degradation | 22/1218 | 79/8465 | 1.33e-03 | 4.80e-03 | 2.83e-03 | 22 |
| hsa0301851 | Oral cavity | EOLP | RNA degradation | 22/1218 | 79/8465 | 1.33e-03 | 4.80e-03 | 2.83e-03 | 22 |
| hsa0301861 | Oral cavity | NEOLP | RNA degradation | 18/1112 | 79/8465 | 1.25e-02 | 4.06e-02 | 2.56e-02 | 18 |
| hsa0301871 | Oral cavity | NEOLP | RNA degradation | 18/1112 | 79/8465 | 1.25e-02 | 4.06e-02 | 2.56e-02 | 18 |
| hsa030188 | Prostate | BPH | RNA degradation | 29/1718 | 79/8465 | 5.17e-04 | 2.67e-03 | 1.65e-03 | 29 |
| hsa0301813 | Prostate | BPH | RNA degradation | 29/1718 | 79/8465 | 5.17e-04 | 2.67e-03 | 1.65e-03 | 29 |
| hsa0301822 | Prostate | Tumor | RNA degradation | 30/1791 | 79/8465 | 4.48e-04 | 2.35e-03 | 1.46e-03 | 30 |
| hsa0301832 | Prostate | Tumor | RNA degradation | 30/1791 | 79/8465 | 4.48e-04 | 2.35e-03 | 1.46e-03 | 30 |
| Page: 1 |
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 |
| ∗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 |
| PAN3 | SNV | Missense_Mutation | novel | c.2433N>T | p.Leu811Phe | p.L811F | Q58A45 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AR-A2LE-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | PD |
| PAN3 | SNV | Missense_Mutation | novel | c.2436A>C | p.Lys812Asn | p.K812N | Q58A45 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-B6-A0IN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD |
| PAN3 | SNV | Missense_Mutation | c.1202C>T | p.Thr401Met | p.T401M | Q58A45 | protein_coding | deleterious(0.01) | probably_damaging(0.999) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| PAN3 | SNV | Missense_Mutation | c.2561C>T | p.Ser854Phe | p.S854F | Q58A45 | protein_coding | deleterious(0) | probably_damaging(0.987) | TCGA-C5-A1BL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| PAN3 | SNV | Missense_Mutation | novel | c.1734G>A | p.Met578Ile | p.M578I | Q58A45 | protein_coding | deleterious(0.02) | benign(0.019) | TCGA-C5-A2LZ-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | Unknown | Unknown | PD |
| PAN3 | SNV | Missense_Mutation | rs769103468 | c.2219N>A | p.Arg740Gln | p.R740Q | Q58A45 | protein_coding | deleterious(0.03) | possibly_damaging(0.73) | TCGA-FU-A3HZ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| PAN3 | SNV | Missense_Mutation | c.1856N>T | p.Ala619Val | p.A619V | Q58A45 | protein_coding | deleterious(0.02) | possibly_damaging(0.672) | TCGA-A6-5661-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PAN3 | SNV | Missense_Mutation | c.1549N>T | p.Pro517Ser | p.P517S | Q58A45 | protein_coding | tolerated(0.18) | benign(0.384) | TCGA-AA-3492-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PAN3 | SNV | Missense_Mutation | c.2231N>G | p.Asp744Gly | p.D744G | Q58A45 | protein_coding | deleterious(0.04) | probably_damaging(0.999) | TCGA-AA-3492-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PAN3 | SNV | Missense_Mutation | rs765586023 | c.1318N>A | p.Ala440Thr | p.A440T | Q58A45 | protein_coding | tolerated(0.16) | possibly_damaging(0.748) | TCGA-AA-3845-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| Page: 1 2 3 4 5 6 7 8 9 |
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 |
| Page: 1 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |