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Gene: PPP4C |
Gene summary for PPP4C |
Gene summary. |
Gene information | Species | Human | Gene symbol | PPP4C | Gene ID | 5531 |
Gene name | protein phosphatase 4 catalytic subunit | |
Gene Alias | PP-X | |
Cytomap | 16p11.2 | |
Gene Type | protein-coding | GO ID | GO:0000018 | UniProtAcc | A0A024R625 |
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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 |
5531 | PPP4C | GSM4909288 | Human | Breast | IDC | 4.04e-02 | -2.43e-01 | 0.0988 |
5531 | PPP4C | GSM4909294 | Human | Breast | IDC | 2.69e-04 | -2.13e-01 | 0.2022 |
5531 | PPP4C | GSM4909296 | Human | Breast | IDC | 1.13e-11 | 9.52e-02 | 0.1524 |
5531 | PPP4C | GSM4909297 | Human | Breast | IDC | 9.76e-14 | -1.56e-01 | 0.1517 |
5531 | PPP4C | GSM4909301 | Human | Breast | IDC | 1.37e-02 | -1.13e-01 | 0.1577 |
5531 | PPP4C | GSM4909306 | Human | Breast | IDC | 3.89e-07 | 3.81e-01 | 0.1564 |
5531 | PPP4C | GSM4909311 | Human | Breast | IDC | 5.04e-37 | -2.79e-01 | 0.1534 |
5531 | PPP4C | GSM4909312 | Human | Breast | IDC | 1.52e-17 | -9.56e-02 | 0.1552 |
5531 | PPP4C | GSM4909313 | Human | Breast | IDC | 3.68e-04 | -1.99e-01 | 0.0391 |
5531 | PPP4C | GSM4909319 | Human | Breast | IDC | 2.34e-43 | -1.40e-01 | 0.1563 |
5531 | PPP4C | GSM4909321 | Human | Breast | IDC | 4.60e-21 | 3.25e-02 | 0.1559 |
5531 | PPP4C | brca1 | Human | Breast | Precancer | 6.66e-16 | 5.13e-01 | -0.0338 |
5531 | PPP4C | brca2 | Human | Breast | Precancer | 8.66e-06 | 3.26e-01 | -0.024 |
5531 | PPP4C | brca3 | Human | Breast | Precancer | 4.70e-03 | 2.59e-01 | -0.0263 |
5531 | PPP4C | NCCBC14 | Human | Breast | DCIS | 1.78e-07 | -9.71e-02 | 0.2021 |
5531 | PPP4C | NCCBC3 | Human | Breast | DCIS | 3.95e-04 | -1.05e-01 | 0.1198 |
5531 | PPP4C | NCCBC5 | Human | Breast | DCIS | 2.38e-14 | 3.53e-02 | 0.2046 |
5531 | PPP4C | NCCBC6 | Human | Breast | DCIS | 5.28e-03 | 2.06e-01 | 0.2095 |
5531 | PPP4C | P1 | Human | Breast | IDC | 2.66e-20 | -1.17e-01 | 0.1527 |
5531 | PPP4C | DCIS2 | Human | Breast | DCIS | 1.41e-49 | -2.06e-02 | 0.0085 |
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Transcriptomic changes along malignancy continuum. |
∗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). |
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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:000647013 | Endometrium | EEC | protein dephosphorylation | 51/2168 | 281/18723 | 7.38e-04 | 7.01e-03 | 51 |
GO:200102014 | Endometrium | EEC | regulation of response to DNA damage stimulus | 40/2168 | 219/18723 | 2.30e-03 | 1.70e-02 | 40 |
GO:00380612 | Endometrium | EEC | NIK/NF-kappaB signaling | 27/2168 | 143/18723 | 6.99e-03 | 4.01e-02 | 27 |
GO:005105214 | Esophagus | HGIN | regulation of DNA metabolic process | 79/2587 | 359/18723 | 1.38e-05 | 3.85e-04 | 79 |
GO:200102019 | Esophagus | HGIN | regulation of response to DNA damage stimulus | 52/2587 | 219/18723 | 5.00e-05 | 1.19e-03 | 52 |
GO:000647017 | Esophagus | HGIN | protein dephosphorylation | 61/2587 | 281/18723 | 1.86e-04 | 3.51e-03 | 61 |
GO:005105215 | Esophagus | ESCC | regulation of DNA metabolic process | 232/8552 | 359/18723 | 2.40e-13 | 1.13e-11 | 232 |
GO:2001020110 | Esophagus | ESCC | regulation of response to DNA damage stimulus | 145/8552 | 219/18723 | 5.97e-10 | 1.50e-08 | 145 |
GO:001631110 | Esophagus | ESCC | dephosphorylation | 251/8552 | 417/18723 | 1.26e-09 | 2.99e-08 | 251 |
GO:000647018 | Esophagus | ESCC | protein dephosphorylation | 177/8552 | 281/18723 | 3.13e-09 | 6.72e-08 | 177 |
GO:00063024 | Esophagus | ESCC | double-strand break repair | 152/8552 | 251/18723 | 1.33e-06 | 1.62e-05 | 152 |
GO:00062826 | Esophagus | ESCC | regulation of DNA repair | 82/8552 | 130/18723 | 4.65e-05 | 3.66e-04 | 82 |
GO:00063101 | Esophagus | ESCC | DNA recombination | 168/8552 | 305/18723 | 5.58e-04 | 3.05e-03 | 168 |
GO:20007793 | Esophagus | ESCC | regulation of double-strand break repair | 52/8552 | 85/18723 | 2.86e-03 | 1.21e-02 | 52 |
GO:00007241 | Esophagus | ESCC | double-strand break repair via homologous recombination | 79/8552 | 138/18723 | 4.05e-03 | 1.62e-02 | 79 |
GO:00007251 | Esophagus | ESCC | recombinational repair | 80/8552 | 140/18723 | 4.10e-03 | 1.63e-02 | 80 |
GO:00380615 | Esophagus | ESCC | NIK/NF-kappaB signaling | 81/8552 | 143/18723 | 5.33e-03 | 2.00e-02 | 81 |
GO:000647011 | Liver | Cirrhotic | protein dephosphorylation | 96/4634 | 281/18723 | 2.32e-04 | 2.11e-03 | 96 |
GO:0038061 | Liver | Cirrhotic | NIK/NF-kappaB signaling | 54/4634 | 143/18723 | 3.64e-04 | 3.07e-03 | 54 |
GO:200102011 | Liver | Cirrhotic | regulation of response to DNA damage stimulus | 75/4634 | 219/18723 | 9.75e-04 | 6.89e-03 | 75 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa04922 | Colorectum | AD | Glucagon signaling pathway | 41/2092 | 107/8465 | 1.18e-03 | 7.75e-03 | 4.94e-03 | 41 |
hsa049221 | Colorectum | AD | Glucagon signaling pathway | 41/2092 | 107/8465 | 1.18e-03 | 7.75e-03 | 4.94e-03 | 41 |
hsa049222 | Colorectum | SER | Glucagon signaling pathway | 38/1580 | 107/8465 | 2.57e-05 | 3.28e-04 | 2.38e-04 | 38 |
hsa049223 | Colorectum | SER | Glucagon signaling pathway | 38/1580 | 107/8465 | 2.57e-05 | 3.28e-04 | 2.38e-04 | 38 |
hsa049224 | Colorectum | MSS | Glucagon signaling pathway | 39/1875 | 107/8465 | 5.00e-04 | 3.45e-03 | 2.11e-03 | 39 |
hsa049225 | Colorectum | MSS | Glucagon signaling pathway | 39/1875 | 107/8465 | 5.00e-04 | 3.45e-03 | 2.11e-03 | 39 |
hsa0492214 | Esophagus | ESCC | Glucagon signaling pathway | 64/4205 | 107/8465 | 2.18e-02 | 4.80e-02 | 2.46e-02 | 64 |
hsa0492215 | Esophagus | ESCC | Glucagon signaling pathway | 64/4205 | 107/8465 | 2.18e-02 | 4.80e-02 | 2.46e-02 | 64 |
hsa0492221 | Liver | Cirrhotic | Glucagon signaling pathway | 43/2530 | 107/8465 | 1.42e-02 | 4.35e-02 | 2.68e-02 | 43 |
hsa0492231 | Liver | Cirrhotic | Glucagon signaling pathway | 43/2530 | 107/8465 | 1.42e-02 | 4.35e-02 | 2.68e-02 | 43 |
hsa0492241 | Liver | HCC | Glucagon signaling pathway | 64/4020 | 107/8465 | 6.70e-03 | 1.87e-02 | 1.04e-02 | 64 |
hsa0492251 | Liver | HCC | Glucagon signaling pathway | 64/4020 | 107/8465 | 6.70e-03 | 1.87e-02 | 1.04e-02 | 64 |
hsa0492212 | Prostate | BPH | Glucagon signaling pathway | 32/1718 | 107/8465 | 1.13e-02 | 3.43e-02 | 2.12e-02 | 32 |
hsa0492213 | Prostate | BPH | Glucagon signaling pathway | 32/1718 | 107/8465 | 1.13e-02 | 3.43e-02 | 2.12e-02 | 32 |
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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 |
PPP4C | SNV | Missense_Mutation | c.357G>C | p.Gln119His | p.Q119H | P60510 | protein_coding | deleterious(0) | possibly_damaging(0.889) | TCGA-A2-A0YD-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | |
PPP4C | SNV | Missense_Mutation | c.578G>A | p.Cys193Tyr | p.C193Y | P60510 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AZ-6598-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
PPP4C | SNV | Missense_Mutation | c.365N>G | p.Gln122Arg | p.Q122R | P60510 | protein_coding | deleterious(0) | possibly_damaging(0.679) | TCGA-CM-6169-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Ancillary | leucovorin | SD | |
PPP4C | SNV | Missense_Mutation | c.850N>G | p.Ile284Val | p.I284V | P60510 | protein_coding | tolerated(0.56) | benign(0) | TCGA-DM-A1HB-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD | |
PPP4C | SNV | Missense_Mutation | novel | c.856N>G | p.Phe286Val | p.F286V | P60510 | protein_coding | deleterious(0) | probably_damaging(0.985) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
PPP4C | SNV | Missense_Mutation | rs546535681 | c.274G>A | p.Glu92Lys | p.E92K | P60510 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-A5-A2K5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
PPP4C | SNV | Missense_Mutation | rs546535681 | c.274N>A | p.Glu92Lys | p.E92K | P60510 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AJ-A5DW-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
PPP4C | SNV | Missense_Mutation | c.394N>T | p.Arg132Cys | p.R132C | P60510 | protein_coding | deleterious(0) | probably_damaging(0.99) | TCGA-AP-A054-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatin | PD | |
PPP4C | SNV | Missense_Mutation | rs546535681 | c.274N>A | p.Glu92Lys | p.E92K | P60510 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AP-A056-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
PPP4C | SNV | Missense_Mutation | novel | c.80N>T | p.Ala27Val | p.A27V | P60510 | protein_coding | tolerated(0.27) | benign(0) | TCGA-AX-A1CE-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | 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 |
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