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Gene: PCID2 |
Gene summary for PCID2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PCID2 | Gene ID | 55795 |
| Gene name | PCI domain containing 2 | |
| Gene Alias | F10 | |
| Cytomap | 13q34 | |
| Gene Type | protein-coding | GO ID | GO:0000070 | UniProtAcc | Q5JVF3 |
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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 |
| 55795 | PCID2 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 5.01e-13 | 8.03e-01 | 0.281 |
| 55795 | PCID2 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 4.99e-13 | 7.49e-01 | 0.3859 |
| 55795 | PCID2 | A015-C-203 | Human | Colorectum | FAP | 1.02e-05 | -9.66e-02 | -0.1294 |
| 55795 | PCID2 | A001-C-119 | Human | Colorectum | FAP | 1.39e-04 | -2.97e-01 | -0.1557 |
| 55795 | PCID2 | A001-C-108 | Human | Colorectum | FAP | 2.07e-03 | -1.16e-01 | -0.0272 |
| 55795 | PCID2 | A002-C-205 | Human | Colorectum | FAP | 3.71e-07 | -2.45e-01 | -0.1236 |
| 55795 | PCID2 | A015-C-006 | Human | Colorectum | FAP | 8.41e-03 | 6.79e-02 | -0.0994 |
| 55795 | PCID2 | A002-C-114 | Human | Colorectum | FAP | 2.89e-05 | -2.26e-01 | -0.1561 |
| 55795 | PCID2 | A015-C-104 | Human | Colorectum | FAP | 1.69e-10 | -2.31e-01 | -0.1899 |
| 55795 | PCID2 | A002-C-116 | Human | Colorectum | FAP | 2.17e-07 | -1.94e-01 | -0.0452 |
| 55795 | PCID2 | A014-C-008 | Human | Colorectum | FAP | 3.37e-02 | -2.11e-01 | -0.191 |
| 55795 | PCID2 | A018-E-020 | Human | Colorectum | FAP | 5.16e-03 | -1.60e-01 | -0.2034 |
| 55795 | PCID2 | F034 | Human | Colorectum | FAP | 2.46e-02 | -8.74e-02 | -0.0665 |
| 55795 | PCID2 | LZE4T | Human | Esophagus | ESCC | 1.23e-08 | 2.62e-01 | 0.0811 |
| 55795 | PCID2 | LZE7T | Human | Esophagus | ESCC | 1.68e-05 | 4.40e-01 | 0.0667 |
| 55795 | PCID2 | LZE8T | Human | Esophagus | ESCC | 1.68e-07 | 2.08e-01 | 0.067 |
| 55795 | PCID2 | LZE24T | Human | Esophagus | ESCC | 3.68e-07 | 2.02e-01 | 0.0596 |
| 55795 | PCID2 | LZE6T | Human | Esophagus | ESCC | 6.15e-04 | 3.68e-01 | 0.0845 |
| 55795 | PCID2 | P1T-E | Human | Esophagus | ESCC | 8.29e-05 | 2.39e-01 | 0.0875 |
| 55795 | PCID2 | P2T-E | Human | Esophagus | ESCC | 6.70e-13 | 3.68e-01 | 0.1177 |
| Page: 1 2 3 4 5 6 |
| 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 | ||
| 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:00008194 | Esophagus | ESCC | sister chromatid segregation | 157/8552 | 202/18723 | 8.41e-21 | 1.33e-18 | 157 |
| GO:005123617 | Esophagus | ESCC | establishment of RNA localization | 134/8552 | 166/18723 | 1.23e-20 | 1.81e-18 | 134 |
| GO:0051168110 | Esophagus | ESCC | nuclear export | 126/8552 | 154/18723 | 1.88e-20 | 2.65e-18 | 126 |
| GO:005102815 | Esophagus | ESCC | mRNA transport | 110/8552 | 130/18723 | 2.76e-20 | 3.80e-18 | 110 |
| GO:005065717 | Esophagus | ESCC | nucleic acid transport | 131/8552 | 163/18723 | 6.94e-20 | 8.46e-18 | 131 |
| GO:005065817 | Esophagus | ESCC | RNA transport | 131/8552 | 163/18723 | 6.94e-20 | 8.46e-18 | 131 |
| GO:003304416 | Esophagus | ESCC | regulation of chromosome organization | 145/8552 | 187/18723 | 3.80e-19 | 4.31e-17 | 145 |
| GO:000705911 | Esophagus | ESCC | chromosome segregation | 238/8552 | 346/18723 | 1.72e-18 | 1.82e-16 | 238 |
| GO:0034655110 | Esophagus | ESCC | nucleobase-containing compound catabolic process | 272/8552 | 407/18723 | 2.92e-18 | 2.90e-16 | 272 |
| GO:004477216 | Esophagus | ESCC | mitotic cell cycle phase transition | 281/8552 | 424/18723 | 4.63e-18 | 4.45e-16 | 281 |
| GO:0006402110 | Esophagus | ESCC | mRNA catabolic process | 170/8552 | 232/18723 | 8.70e-18 | 8.00e-16 | 170 |
| GO:001593117 | Esophagus | ESCC | nucleobase-containing compound transport | 162/8552 | 222/18723 | 9.87e-17 | 7.93e-15 | 162 |
| GO:000734615 | Esophagus | ESCC | regulation of mitotic cell cycle | 293/8552 | 457/18723 | 8.00e-16 | 5.64e-14 | 293 |
| GO:004670018 | Esophagus | ESCC | heterocycle catabolic process | 286/8552 | 445/18723 | 1.12e-15 | 7.47e-14 | 286 |
| GO:004427019 | Esophagus | ESCC | cellular nitrogen compound catabolic process | 288/8552 | 451/18723 | 3.03e-15 | 1.79e-13 | 288 |
| GO:001943918 | Esophagus | ESCC | aromatic compound catabolic process | 295/8552 | 467/18723 | 1.09e-14 | 5.98e-13 | 295 |
| GO:000635414 | Esophagus | ESCC | DNA-templated transcription, elongation | 76/8552 | 91/18723 | 8.35e-14 | 4.11e-12 | 76 |
| GO:190136118 | Esophagus | ESCC | organic cyclic compound catabolic process | 307/8552 | 495/18723 | 9.99e-14 | 4.80e-12 | 307 |
| GO:007116612 | Esophagus | ESCC | ribonucleoprotein complex localization | 66/8552 | 77/18723 | 2.94e-13 | 1.38e-11 | 66 |
| GO:00482853 | Esophagus | ESCC | organelle fission | 301/8552 | 488/18723 | 4.64e-13 | 2.12e-11 | 301 |
| 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 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| 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 |
| PCID2 | SNV | Missense_Mutation | c.509N>C | p.Arg170Pro | p.R170P | Q5JVF3 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-A8-A08L-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| PCID2 | SNV | Missense_Mutation | rs750326771 | c.301A>G | p.Arg101Gly | p.R101G | Q5JVF3 | protein_coding | tolerated(0.09) | benign(0) | TCGA-A8-A09W-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| PCID2 | SNV | Missense_Mutation | c.419N>T | p.Ser140Leu | p.S140L | Q5JVF3 | protein_coding | tolerated(0.44) | benign(0) | TCGA-C8-A12P-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| PCID2 | SNV | Missense_Mutation | c.331G>C | p.Glu111Gln | p.E111Q | Q5JVF3 | protein_coding | tolerated(0.42) | benign(0) | TCGA-D8-A1JA-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD | |
| PCID2 | insertion | Nonsense_Mutation | novel | c.1295_1296insTCCCAAGTAGCTGGGAGCACAGGTGCATGCCACCACACCCA | p.His433ProfsTer3 | p.H433Pfs*3 | Q5JVF3 | protein_coding | TCGA-AN-A04C-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| PCID2 | insertion | In_Frame_Ins | novel | c.1027_1028insTACCACATTTCATCA | p.Gly343delinsValProHisPheIleSer | p.G343delinsVPHFIS | Q5JVF3 | protein_coding | TCGA-AN-A0FK-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | ||
| PCID2 | SNV | Missense_Mutation | novel | c.814C>T | p.Arg272Cys | p.R272C | Q5JVF3 | protein_coding | deleterious(0.05) | possibly_damaging(0.854) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| PCID2 | SNV | Missense_Mutation | rs768260894 | c.497C>T | p.Ala166Val | p.A166V | Q5JVF3 | protein_coding | tolerated(0.27) | benign(0.038) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| PCID2 | SNV | Missense_Mutation | c.912N>A | p.Met304Ile | p.M304I | Q5JVF3 | protein_coding | deleterious(0.04) | benign(0.015) | TCGA-Q1-A73O-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| PCID2 | SNV | Missense_Mutation | c.811N>A | p.Gly271Arg | p.G271R | Q5JVF3 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-4T-AA8H-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 |
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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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