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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:19033112 | Colorectum | MSS | regulation of mRNA metabolic process | 115/3467 | 288/18723 | 1.23e-17 | 6.41e-15 | 115 |
| GO:00064012 | Colorectum | MSS | RNA catabolic process | 102/3467 | 278/18723 | 5.07e-13 | 1.02e-10 | 102 |
| GO:00064022 | Colorectum | MSS | mRNA catabolic process | 89/3467 | 232/18723 | 8.70e-13 | 1.60e-10 | 89 |
| GO:00442702 | Colorectum | MSS | cellular nitrogen compound catabolic process | 141/3467 | 451/18723 | 2.95e-11 | 3.83e-09 | 141 |
| GO:00467002 | Colorectum | MSS | heterocycle catabolic process | 139/3467 | 445/18723 | 4.37e-11 | 5.05e-09 | 139 |
| GO:00346552 | Colorectum | MSS | nucleobase-containing compound catabolic process | 129/3467 | 407/18723 | 7.48e-11 | 8.18e-09 | 129 |
| GO:00610132 | Colorectum | MSS | regulation of mRNA catabolic process | 66/3467 | 166/18723 | 1.25e-10 | 1.26e-08 | 66 |
| GO:19013612 | Colorectum | MSS | organic cyclic compound catabolic process | 148/3467 | 495/18723 | 3.47e-10 | 3.18e-08 | 148 |
| GO:00434872 | Colorectum | MSS | regulation of RNA stability | 66/3467 | 170/18723 | 4.14e-10 | 3.49e-08 | 66 |
| GO:00434882 | Colorectum | MSS | regulation of mRNA stability | 62/3467 | 158/18723 | 8.41e-10 | 6.81e-08 | 62 |
| GO:00194392 | Colorectum | MSS | aromatic compound catabolic process | 140/3467 | 467/18723 | 8.56e-10 | 6.85e-08 | 140 |
| GO:00069132 | Colorectum | MSS | nucleocytoplasmic transport | 99/3467 | 301/18723 | 1.35e-09 | 1.03e-07 | 99 |
| GO:00511692 | Colorectum | MSS | nuclear transport | 99/3467 | 301/18723 | 1.35e-09 | 1.03e-07 | 99 |
| GO:00064032 | Colorectum | MSS | RNA localization | 69/3467 | 201/18723 | 6.33e-08 | 3.26e-06 | 69 |
| GO:00525472 | Colorectum | MSS | regulation of peptidase activity | 130/3467 | 461/18723 | 1.81e-07 | 8.13e-06 | 130 |
| GO:00106392 | Colorectum | MSS | negative regulation of organelle organization | 102/3467 | 348/18723 | 5.36e-07 | 2.05e-05 | 102 |
| GO:00009561 | Colorectum | MSS | nuclear-transcribed mRNA catabolic process | 42/3467 | 112/18723 | 1.75e-06 | 5.60e-05 | 42 |
| GO:00159312 | Colorectum | MSS | nucleobase-containing compound transport | 70/3467 | 222/18723 | 1.92e-06 | 6.01e-05 | 70 |
| GO:20001162 | Colorectum | MSS | regulation of cysteine-type endopeptidase activity | 72/3467 | 235/18723 | 4.39e-06 | 1.24e-04 | 72 |
| GO:00512362 | Colorectum | MSS | establishment of RNA localization | 55/3467 | 166/18723 | 4.54e-06 | 1.27e-04 | 55 |
| 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 |
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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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