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Gene: PDS5B |
Gene summary for PDS5B |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PDS5B | Gene ID | 23047 |
| Gene name | PDS5 cohesin associated factor B | |
| Gene Alias | APRIN | |
| Cytomap | 13q13.1 | |
| Gene Type | protein-coding | GO ID | GO:0000070 | UniProtAcc | Q9NTI5 |
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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 |
| 23047 | PDS5B | CCI_1 | Human | Cervix | CC | 1.23e-03 | 6.84e-01 | 0.528 |
| 23047 | PDS5B | CCI_2 | Human | Cervix | CC | 4.64e-09 | 9.19e-01 | 0.5249 |
| 23047 | PDS5B | CCI_3 | Human | Cervix | CC | 5.95e-16 | 8.94e-01 | 0.516 |
| 23047 | PDS5B | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.46e-18 | -5.59e-01 | 0.0155 |
| 23047 | PDS5B | HTA11_866_3004761011 | Human | Colorectum | AD | 4.43e-11 | -4.94e-01 | 0.096 |
| 23047 | PDS5B | HTA11_9408_2000001011 | Human | Colorectum | AD | 8.62e-04 | -6.77e-01 | 0.0451 |
| 23047 | PDS5B | HTA11_8622_2000001021 | Human | Colorectum | SER | 1.06e-03 | -5.82e-01 | 0.0528 |
| 23047 | PDS5B | HTA11_10711_2000001011 | Human | Colorectum | AD | 1.51e-04 | -4.47e-01 | 0.0338 |
| 23047 | PDS5B | HTA11_7696_3000711011 | Human | Colorectum | AD | 5.16e-04 | -3.58e-01 | 0.0674 |
| 23047 | PDS5B | HTA11_99999974143_84620 | Human | Colorectum | MSS | 2.59e-04 | -3.69e-01 | 0.3005 |
| 23047 | PDS5B | F007 | Human | Colorectum | FAP | 1.45e-03 | -8.02e-02 | 0.1176 |
| 23047 | PDS5B | A001-C-207 | Human | Colorectum | FAP | 7.21e-06 | -1.07e-01 | 0.1278 |
| 23047 | PDS5B | A015-C-203 | Human | Colorectum | FAP | 9.61e-25 | -2.94e-01 | -0.1294 |
| 23047 | PDS5B | A015-C-204 | Human | Colorectum | FAP | 1.64e-07 | -2.29e-01 | -0.0228 |
| 23047 | PDS5B | A014-C-040 | Human | Colorectum | FAP | 6.95e-06 | -1.72e-01 | -0.1184 |
| 23047 | PDS5B | A002-C-201 | Human | Colorectum | FAP | 3.74e-14 | -2.59e-01 | 0.0324 |
| 23047 | PDS5B | A002-C-203 | Human | Colorectum | FAP | 2.38e-05 | -9.49e-02 | 0.2786 |
| 23047 | PDS5B | A001-C-119 | Human | Colorectum | FAP | 1.96e-07 | -3.28e-01 | -0.1557 |
| 23047 | PDS5B | A001-C-108 | Human | Colorectum | FAP | 9.40e-16 | -2.40e-01 | -0.0272 |
| 23047 | PDS5B | A002-C-205 | Human | Colorectum | FAP | 1.21e-25 | -4.11e-01 | -0.1236 |
| 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 | ||
| 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 | ||
| 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:00070646 | Cervix | CC | mitotic sister chromatid cohesion | 12/2311 | 28/18723 | 5.47e-05 | 8.06e-04 | 12 |
| GO:01400143 | Cervix | CC | mitotic nuclear division | 50/2311 | 287/18723 | 7.27e-03 | 3.91e-02 | 50 |
| GO:00070625 | Cervix | CC | sister chromatid cohesion | 15/2311 | 62/18723 | 7.30e-03 | 3.92e-02 | 15 |
| GO:00482851 | Cervix | CC | organelle fission | 78/2311 | 488/18723 | 9.70e-03 | 4.79e-02 | 78 |
| GO:0007064 | Colorectum | AD | mitotic sister chromatid cohesion | 13/3918 | 28/18723 | 2.22e-03 | 1.75e-02 | 13 |
| GO:0007062 | Colorectum | AD | sister chromatid cohesion | 23/3918 | 62/18723 | 2.51e-03 | 1.92e-02 | 23 |
| GO:0140014 | Colorectum | AD | mitotic nuclear division | 78/3918 | 287/18723 | 6.48e-03 | 4.05e-02 | 78 |
| GO:00070621 | Colorectum | MSS | sister chromatid cohesion | 20/3467 | 62/18723 | 6.63e-03 | 4.38e-02 | 20 |
| GO:01400141 | Colorectum | MSS | mitotic nuclear division | 70/3467 | 287/18723 | 7.48e-03 | 4.72e-02 | 70 |
| GO:00070641 | Colorectum | MSS | mitotic sister chromatid cohesion | 11/3467 | 28/18723 | 8.30e-03 | 5.00e-02 | 11 |
| GO:00070642 | Colorectum | FAP | mitotic sister chromatid cohesion | 11/2622 | 28/18723 | 8.55e-04 | 8.79e-03 | 11 |
| GO:00070622 | Colorectum | FAP | sister chromatid cohesion | 18/2622 | 62/18723 | 1.60e-03 | 1.42e-02 | 18 |
| GO:00070623 | Colorectum | CRC | sister chromatid cohesion | 16/2078 | 62/18723 | 9.40e-04 | 1.15e-02 | 16 |
| GO:00070643 | Colorectum | CRC | mitotic sister chromatid cohesion | 9/2078 | 28/18723 | 2.43e-03 | 2.30e-02 | 9 |
| GO:014001414 | Esophagus | ESCC | mitotic nuclear division | 218/8552 | 287/18723 | 6.17e-26 | 1.78e-23 | 218 |
| GO:000007011 | Esophagus | ESCC | mitotic sister chromatid segregation | 138/8552 | 168/18723 | 1.37e-22 | 2.63e-20 | 138 |
| GO:00008194 | Esophagus | ESCC | sister chromatid segregation | 157/8552 | 202/18723 | 8.41e-21 | 1.33e-18 | 157 |
| GO:000705911 | Esophagus | ESCC | chromosome segregation | 238/8552 | 346/18723 | 1.72e-18 | 1.82e-16 | 238 |
| GO:00482853 | Esophagus | ESCC | organelle fission | 301/8552 | 488/18723 | 4.64e-13 | 2.12e-11 | 301 |
| GO:00988133 | Esophagus | ESCC | nuclear chromosome segregation | 187/8552 | 281/18723 | 1.00e-12 | 4.36e-11 | 187 |
| Page: 1 2 3 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa041106 | Cervix | CC | Cell cycle | 36/1267 | 157/8465 | 4.94e-03 | 1.67e-02 | 9.86e-03 | 36 |
| hsa0411013 | Cervix | CC | Cell cycle | 36/1267 | 157/8465 | 4.94e-03 | 1.67e-02 | 9.86e-03 | 36 |
| hsa04110 | Colorectum | FAP | Cell cycle | 37/1404 | 157/8465 | 1.44e-02 | 4.77e-02 | 2.90e-02 | 37 |
| hsa041101 | Colorectum | FAP | Cell cycle | 37/1404 | 157/8465 | 1.44e-02 | 4.77e-02 | 2.90e-02 | 37 |
| hsa0411023 | Esophagus | ESCC | Cell cycle | 126/4205 | 157/8465 | 1.34e-15 | 5.60e-14 | 2.87e-14 | 126 |
| hsa0411033 | Esophagus | ESCC | Cell cycle | 126/4205 | 157/8465 | 1.34e-15 | 5.60e-14 | 2.87e-14 | 126 |
| hsa041102 | Liver | HCC | Cell cycle | 106/4020 | 157/8465 | 2.54e-07 | 3.04e-06 | 1.69e-06 | 106 |
| hsa041103 | Liver | HCC | Cell cycle | 106/4020 | 157/8465 | 2.54e-07 | 3.04e-06 | 1.69e-06 | 106 |
| 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 |
| PDS5B | deletion | Frame_Shift_Del | rs759495724 | c.4161delN | p.Asn1390MetfsTer4 | p.N1390Mfs*4 | Q9NTI5 | protein_coding | TCGA-BR-4280-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | ||
| PDS5B | deletion | Frame_Shift_Del | rs747131399 | c.3946delN | p.Lys1318AsnfsTer76 | p.K1318Nfs*76 | Q9NTI5 | protein_coding | TCGA-BR-4292-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| PDS5B | deletion | Frame_Shift_Del | rs747131399 | c.3946delN | p.Lys1318AsnfsTer76 | p.K1318Nfs*76 | Q9NTI5 | protein_coding | TCGA-BR-4361-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | ||
| PDS5B | deletion | Frame_Shift_Del | novel | c.3934delN | p.Gly1314GlufsTer80 | p.G1314Efs*80 | Q9NTI5 | protein_coding | TCGA-BR-4368-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | ||
| PDS5B | deletion | Frame_Shift_Del | rs747131399 | c.3946delN | p.Lys1318AsnfsTer76 | p.K1318Nfs*76 | Q9NTI5 | protein_coding | TCGA-BR-8059-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD | ||
| PDS5B | deletion | Frame_Shift_Del | rs759495724 | c.4161delN | p.Asn1390MetfsTer4 | p.N1390Mfs*4 | Q9NTI5 | protein_coding | TCGA-CG-4442-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | ||
| PDS5B | deletion | Frame_Shift_Del | rs759495724 | c.4161delN | p.Asn1390MetfsTer4 | p.N1390Mfs*4 | Q9NTI5 | protein_coding | TCGA-CG-4460-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Chemotherapy | capecitabine | PD | ||
| PDS5B | deletion | Frame_Shift_Del | c.2170delC | p.Arg724ValfsTer32 | p.R724Vfs*32 | Q9NTI5 | protein_coding | TCGA-CG-5723-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |||
| PDS5B | deletion | Frame_Shift_Del | rs747131399 | c.3946delN | p.Lys1318AsnfsTer76 | p.K1318Nfs*76 | Q9NTI5 | protein_coding | TCGA-HU-8602-01 | Stomach | stomach adenocarcinoma | Female | <65 | I/II | Chemotherapy | xeloda | CR | ||
| PDS5B | insertion | Frame_Shift_Ins | rs746601412 | c.2163_2164insC | p.Arg724ProfsTer16 | p.R724Pfs*16 | Q9NTI5 | protein_coding | TCGA-HU-A4G9-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 |
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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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