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Gene: PKDCC |
Gene summary for PKDCC |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PKDCC | Gene ID | 91461 |
| Gene name | protein kinase domain containing, cytoplasmic | |
| Gene Alias | RLSDF | |
| Cytomap | 2p21 | |
| Gene Type | protein-coding | GO ID | GO:0001501 | UniProtAcc | Q504Y2 |
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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 |
| 91461 | PKDCC | HTA11_1938_2000001011 | Human | Colorectum | AD | 2.61e-02 | 4.55e-01 | -0.0811 |
| 91461 | PKDCC | HTA11_347_2000001011 | Human | Colorectum | AD | 2.45e-05 | 3.96e-01 | -0.1954 |
| 91461 | PKDCC | HTA11_1391_2000001011 | Human | Colorectum | AD | 4.17e-07 | 6.31e-01 | -0.059 |
| 91461 | PKDCC | HTA11_8622_2000001021 | Human | Colorectum | SER | 6.06e-03 | 5.62e-01 | 0.0528 |
| 91461 | PKDCC | HTA11_7663_2000001011 | Human | Colorectum | SER | 1.47e-08 | 8.69e-01 | 0.0131 |
| 91461 | PKDCC | HTA11_99999970781_79442 | Human | Colorectum | MSS | 5.11e-08 | -2.92e-01 | 0.294 |
| 91461 | PKDCC | HTA11_99999971662_82457 | Human | Colorectum | MSS | 3.65e-07 | 6.38e-01 | 0.3859 |
| 91461 | PKDCC | F007 | Human | Colorectum | FAP | 1.08e-03 | -3.12e-01 | 0.1176 |
| 91461 | PKDCC | A002-C-010 | Human | Colorectum | FAP | 4.36e-08 | -3.07e-01 | 0.242 |
| 91461 | PKDCC | A001-C-207 | Human | Colorectum | FAP | 1.76e-07 | -3.50e-01 | 0.1278 |
| 91461 | PKDCC | A015-C-203 | Human | Colorectum | FAP | 6.02e-11 | -2.71e-01 | -0.1294 |
| 91461 | PKDCC | A014-C-040 | Human | Colorectum | FAP | 1.51e-02 | -3.62e-01 | -0.1184 |
| 91461 | PKDCC | A002-C-201 | Human | Colorectum | FAP | 1.61e-09 | -3.12e-01 | 0.0324 |
| 91461 | PKDCC | A002-C-203 | Human | Colorectum | FAP | 2.83e-05 | -1.86e-01 | 0.2786 |
| 91461 | PKDCC | A001-C-119 | Human | Colorectum | FAP | 9.63e-06 | -3.44e-01 | -0.1557 |
| 91461 | PKDCC | A001-C-108 | Human | Colorectum | FAP | 8.47e-13 | -3.27e-01 | -0.0272 |
| 91461 | PKDCC | A002-C-021 | Human | Colorectum | FAP | 5.08e-04 | -2.51e-01 | 0.1171 |
| 91461 | PKDCC | A002-C-205 | Human | Colorectum | FAP | 3.78e-14 | -3.62e-01 | -0.1236 |
| 91461 | PKDCC | A001-C-104 | Human | Colorectum | FAP | 3.68e-07 | -2.85e-01 | 0.0184 |
| 91461 | PKDCC | A015-C-005 | Human | Colorectum | FAP | 3.72e-05 | -2.96e-01 | -0.0336 |
| Page: 1 2 3 |
| 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 | ||
| 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:19907781 | Colorectum | SER | protein localization to cell periphery | 98/2897 | 333/18723 | 6.09e-11 | 9.57e-09 | 98 |
| GO:00481931 | Colorectum | SER | Golgi vesicle transport | 79/2897 | 296/18723 | 4.20e-07 | 2.15e-05 | 79 |
| GO:19030761 | Colorectum | SER | regulation of protein localization to plasma membrane | 36/2897 | 104/18723 | 1.12e-06 | 5.18e-05 | 36 |
| GO:19054751 | Colorectum | SER | regulation of protein localization to membrane | 52/2897 | 175/18723 | 1.31e-06 | 6.04e-05 | 52 |
| GO:19043751 | Colorectum | SER | regulation of protein localization to cell periphery | 40/2897 | 125/18723 | 2.85e-06 | 1.16e-04 | 40 |
| GO:00901501 | Colorectum | SER | establishment of protein localization to membrane | 68/2897 | 260/18723 | 5.55e-06 | 2.01e-04 | 68 |
| GO:00068921 | Colorectum | SER | post-Golgi vesicle-mediated transport | 31/2897 | 104/18723 | 1.59e-04 | 3.08e-03 | 31 |
| GO:00988761 | Colorectum | SER | vesicle-mediated transport to the plasma membrane | 37/2897 | 136/18723 | 3.08e-04 | 5.00e-03 | 37 |
| GO:00619511 | Colorectum | SER | establishment of protein localization to plasma membrane | 20/2897 | 60/18723 | 4.60e-04 | 6.65e-03 | 20 |
| GO:0051051 | Colorectum | SER | negative regulation of transport | 98/2897 | 470/18723 | 1.01e-03 | 1.19e-02 | 98 |
| GO:00487361 | Colorectum | SER | appendage development | 42/2897 | 172/18723 | 1.43e-03 | 1.55e-02 | 42 |
| GO:00601731 | Colorectum | SER | limb development | 42/2897 | 172/18723 | 1.43e-03 | 1.55e-02 | 42 |
| GO:00430011 | Colorectum | SER | Golgi to plasma membrane protein transport | 14/2897 | 40/18723 | 1.88e-03 | 1.90e-02 | 14 |
| GO:19038281 | Colorectum | SER | negative regulation of cellular protein localization | 30/2897 | 117/18723 | 2.96e-03 | 2.62e-02 | 30 |
| GO:0035107 | Colorectum | SER | appendage morphogenesis | 33/2897 | 138/18723 | 6.10e-03 | 4.42e-02 | 33 |
| GO:0035108 | Colorectum | SER | limb morphogenesis | 33/2897 | 138/18723 | 6.10e-03 | 4.42e-02 | 33 |
| GO:00015031 | Colorectum | SER | ossification | 82/2897 | 408/18723 | 6.76e-03 | 4.78e-02 | 82 |
| GO:19030771 | Colorectum | SER | negative regulation of protein localization to plasma membrane | 9/2897 | 24/18723 | 7.19e-03 | 4.99e-02 | 9 |
| GO:00726592 | Colorectum | MSS | protein localization to plasma membrane | 113/3467 | 284/18723 | 3.23e-17 | 1.55e-14 | 113 |
| GO:19907782 | Colorectum | MSS | protein localization to cell periphery | 120/3467 | 333/18723 | 2.02e-14 | 5.47e-12 | 120 |
| Page: 1 2 3 4 5 6 7 8 9 |
| 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 |
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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. |
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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 |
| PKDCC | SNV | Missense_Mutation | novel | c.712C>A | p.Pro238Thr | p.P238T | Q504Y2 | protein_coding | deleterious(0) | probably_damaging(0.993) | TCGA-BH-A0B4-01 | Breast | breast invasive carcinoma | Male | >=65 | III/IV | Hormone Therapy | tamoxiphen | SD |
| PKDCC | SNV | Missense_Mutation | c.787N>G | p.Leu263Val | p.L263V | Q504Y2 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-BH-A0BZ-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | CR | |
| PKDCC | insertion | Nonsense_Mutation | novel | c.713_714insAAAAATTAGCTGGGCATAG | p.Val239LysfsTer6 | p.V239Kfs*6 | Q504Y2 | protein_coding | TCGA-BH-A0B4-01 | Breast | breast invasive carcinoma | Male | >=65 | III/IV | Hormone Therapy | tamoxiphen | SD | ||
| PKDCC | deletion | Frame_Shift_Del | novel | c.1097delG | p.Ser366ThrfsTer124 | p.S366Tfs*124 | Q504Y2 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| PKDCC | SNV | Missense_Mutation | rs749783255 | c.1012C>T | p.Arg338Trp | p.R338W | Q504Y2 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| PKDCC | SNV | Missense_Mutation | c.478G>A | p.Gly160Ser | p.G160S | Q504Y2 | protein_coding | tolerated(0.47) | benign(0.154) | TCGA-IR-A3LA-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| PKDCC | SNV | Missense_Mutation | c.1270N>A | p.Cys424Ser | p.C424S | Q504Y2 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-AA-A022-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PKDCC | SNV | Missense_Mutation | rs144832959 | c.782G>A | p.Arg261His | p.R261H | Q504Y2 | protein_coding | deleterious(0.03) | probably_damaging(0.921) | TCGA-AD-6895-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD |
| PKDCC | SNV | Missense_Mutation | c.569G>T | p.Arg190Leu | p.R190L | Q504Y2 | protein_coding | deleterious(0.02) | possibly_damaging(0.478) | TCGA-AM-5821-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PKDCC | SNV | Missense_Mutation | rs374316779 | c.820N>A | p.Val274Ile | p.V274I | Q504Y2 | protein_coding | tolerated(0.27) | benign(0.12) | TCGA-G4-6628-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
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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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