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Gene: GPCPD1 |
Gene summary for GPCPD1 |
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Gene information | Species | Human | Gene symbol | GPCPD1 | Gene ID | 56261 |
Gene name | glycerophosphocholine phosphodiesterase 1 | |
Gene Alias | EDI3 | |
Cytomap | 20p12.3 | |
Gene Type | protein-coding | GO ID | GO:0006629 | UniProtAcc | Q9NPB8 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
56261 | GPCPD1 | EEC-subject2 | Human | Endometrium | EEC | 4.53e-07 | 4.52e-01 | -0.2607 |
56261 | GPCPD1 | EEC-subject3 | Human | Endometrium | EEC | 6.97e-07 | 3.19e-01 | -0.2525 |
56261 | GPCPD1 | EEC-subject4 | Human | Endometrium | EEC | 7.73e-03 | 2.40e-01 | -0.2571 |
56261 | GPCPD1 | GSM5276934 | Human | Endometrium | EEC | 4.56e-03 | -1.74e-01 | -0.0913 |
56261 | GPCPD1 | GSM6177620_NYU_UCEC1_lib1_lib1 | Human | Endometrium | EEC | 1.32e-09 | 2.03e-01 | -0.1869 |
56261 | GPCPD1 | GSM6177620_NYU_UCEC1_lib2_lib2 | Human | Endometrium | EEC | 2.86e-09 | 3.23e-01 | -0.1875 |
56261 | GPCPD1 | GSM6177620_NYU_UCEC1_lib3_lib3 | Human | Endometrium | EEC | 1.84e-13 | 2.43e-01 | -0.1883 |
56261 | GPCPD1 | GSM6177621_NYU_UCEC2_lib1_lib1 | Human | Endometrium | EEC | 2.77e-06 | 5.68e-02 | -0.1934 |
56261 | GPCPD1 | GSM6177622_NYU_UCEC3_lib1_lib1 | Human | Endometrium | EEC | 6.81e-10 | -7.13e-02 | -0.1917 |
56261 | GPCPD1 | GSM6177622_NYU_UCEC3_lib2_lib2 | Human | Endometrium | EEC | 1.54e-09 | -1.00e-01 | -0.1916 |
56261 | GPCPD1 | LZE4T | Human | Esophagus | ESCC | 2.39e-11 | 4.60e-01 | 0.0811 |
56261 | GPCPD1 | LZE5T | Human | Esophagus | ESCC | 3.17e-07 | 1.08e+00 | 0.0514 |
56261 | GPCPD1 | LZE7T | Human | Esophagus | ESCC | 3.00e-05 | 1.44e-01 | 0.0667 |
56261 | GPCPD1 | LZE8T | Human | Esophagus | ESCC | 1.29e-03 | -1.85e-02 | 0.067 |
56261 | GPCPD1 | LZE20T | Human | Esophagus | ESCC | 2.10e-03 | 2.12e-01 | 0.0662 |
56261 | GPCPD1 | LZE22D1 | Human | Esophagus | HGIN | 2.24e-03 | 4.20e-02 | 0.0595 |
56261 | GPCPD1 | LZE24T | Human | Esophagus | ESCC | 2.59e-11 | 5.04e-01 | 0.0596 |
56261 | GPCPD1 | LZE21T | Human | Esophagus | ESCC | 1.90e-02 | 9.05e-02 | 0.0655 |
56261 | GPCPD1 | P1T-E | Human | Esophagus | ESCC | 9.01e-08 | 9.66e-01 | 0.0875 |
56261 | GPCPD1 | P2T-E | Human | Esophagus | ESCC | 4.30e-12 | 2.09e-01 | 0.1177 |
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∗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 |
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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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GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:00605375 | Cervix | CC | muscle tissue development | 76/2311 | 403/18723 | 9.76e-05 | 1.27e-03 | 76 |
GO:00147064 | Cervix | CC | striated muscle tissue development | 72/2311 | 384/18723 | 1.76e-04 | 2.07e-03 | 72 |
GO:00075173 | Cervix | CC | muscle organ development | 58/2311 | 327/18723 | 2.73e-03 | 1.85e-02 | 58 |
GO:00075192 | Cervix | CC | skeletal muscle tissue development | 30/2311 | 155/18723 | 7.97e-03 | 4.18e-02 | 30 |
GO:00160422 | Colorectum | MSS | lipid catabolic process | 77/3467 | 320/18723 | 7.43e-03 | 4.71e-02 | 77 |
GO:00442422 | Colorectum | FAP | cellular lipid catabolic process | 49/2622 | 214/18723 | 2.87e-04 | 3.77e-03 | 49 |
GO:00160423 | Colorectum | FAP | lipid catabolic process | 65/2622 | 320/18723 | 1.13e-03 | 1.08e-02 | 65 |
GO:00066502 | Colorectum | FAP | glycerophospholipid metabolic process | 62/2622 | 306/18723 | 1.54e-03 | 1.38e-02 | 62 |
GO:00066442 | Colorectum | FAP | phospholipid metabolic process | 74/2622 | 383/18723 | 2.24e-03 | 1.83e-02 | 74 |
GO:00066503 | Colorectum | CRC | glycerophospholipid metabolic process | 55/2078 | 306/18723 | 2.10e-04 | 3.55e-03 | 55 |
GO:00066443 | Colorectum | CRC | phospholipid metabolic process | 65/2078 | 383/18723 | 3.21e-04 | 4.95e-03 | 65 |
GO:00464861 | Colorectum | CRC | glycerolipid metabolic process | 64/2078 | 392/18723 | 1.01e-03 | 1.19e-02 | 64 |
GO:00160424 | Colorectum | CRC | lipid catabolic process | 53/2078 | 320/18723 | 1.89e-03 | 1.93e-02 | 53 |
GO:0060537 | Colorectum | CRC | muscle tissue development | 63/2078 | 403/18723 | 3.17e-03 | 2.78e-02 | 63 |
GO:00442423 | Colorectum | CRC | cellular lipid catabolic process | 37/2078 | 214/18723 | 4.16e-03 | 3.40e-02 | 37 |
GO:0014706 | Colorectum | CRC | striated muscle tissue development | 59/2078 | 384/18723 | 6.11e-03 | 4.47e-02 | 59 |
GO:00605376 | Endometrium | AEH | muscle tissue development | 83/2100 | 403/18723 | 2.57e-08 | 1.50e-06 | 83 |
GO:00147065 | Endometrium | AEH | striated muscle tissue development | 75/2100 | 384/18723 | 1.06e-06 | 3.62e-05 | 75 |
GO:00075174 | Endometrium | AEH | muscle organ development | 60/2100 | 327/18723 | 8.19e-05 | 1.22e-03 | 60 |
GO:00605382 | Endometrium | AEH | skeletal muscle organ development | 30/2100 | 166/18723 | 5.64e-03 | 3.46e-02 | 30 |
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Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa05231 | Colorectum | MSS | Choline metabolism in cancer | 34/1875 | 98/8465 | 2.90e-03 | 1.39e-02 | 8.50e-03 | 34 |
hsa052311 | Colorectum | MSS | Choline metabolism in cancer | 34/1875 | 98/8465 | 2.90e-03 | 1.39e-02 | 8.50e-03 | 34 |
hsa052312 | Colorectum | FAP | Choline metabolism in cancer | 29/1404 | 98/8465 | 9.03e-04 | 5.20e-03 | 3.16e-03 | 29 |
hsa052313 | Colorectum | FAP | Choline metabolism in cancer | 29/1404 | 98/8465 | 9.03e-04 | 5.20e-03 | 3.16e-03 | 29 |
hsa052314 | Colorectum | CRC | Choline metabolism in cancer | 24/1091 | 98/8465 | 1.21e-03 | 9.84e-03 | 6.67e-03 | 24 |
hsa052315 | Colorectum | CRC | Choline metabolism in cancer | 24/1091 | 98/8465 | 1.21e-03 | 9.84e-03 | 6.67e-03 | 24 |
hsa052319 | Esophagus | ESCC | Choline metabolism in cancer | 61/4205 | 98/8465 | 7.97e-03 | 1.92e-02 | 9.84e-03 | 61 |
hsa0523114 | Esophagus | ESCC | Choline metabolism in cancer | 61/4205 | 98/8465 | 7.97e-03 | 1.92e-02 | 9.84e-03 | 61 |
hsa052316 | Liver | HCC | Choline metabolism in cancer | 57/4020 | 98/8465 | 2.14e-02 | 4.90e-02 | 2.72e-02 | 57 |
hsa0523111 | Liver | HCC | Choline metabolism in cancer | 57/4020 | 98/8465 | 2.14e-02 | 4.90e-02 | 2.72e-02 | 57 |
hsa052317 | Lung | IAC | Choline metabolism in cancer | 23/1053 | 98/8465 | 1.72e-03 | 9.66e-03 | 6.41e-03 | 23 |
hsa0523112 | Lung | IAC | Choline metabolism in cancer | 23/1053 | 98/8465 | 1.72e-03 | 9.66e-03 | 6.41e-03 | 23 |
hsa052318 | Oral cavity | EOLP | Choline metabolism in cancer | 25/1218 | 98/8465 | 2.49e-03 | 8.14e-03 | 4.80e-03 | 25 |
hsa0523113 | Oral cavity | EOLP | Choline metabolism in cancer | 25/1218 | 98/8465 | 2.49e-03 | 8.14e-03 | 4.80e-03 | 25 |
hsa0523122 | Oral cavity | NEOLP | Choline metabolism in cancer | 21/1112 | 98/8465 | 1.48e-02 | 4.68e-02 | 2.94e-02 | 21 |
hsa0523132 | Oral cavity | NEOLP | Choline metabolism in cancer | 21/1112 | 98/8465 | 1.48e-02 | 4.68e-02 | 2.94e-02 | 21 |
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Cell-cell communication analysis |
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Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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Single-cell gene regulatory network inference analysis |
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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 |
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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 |
GPCPD1 | SNV | Missense_Mutation | c.994A>G | p.Thr332Ala | p.T332A | Q9NPB8 | protein_coding | tolerated(0.39) | benign(0.001) | TCGA-E2-A14W-01 | Breast | breast invasive carcinoma | Male | >=65 | I/II | Chemotherapy | cytoxan | SD | |
GPCPD1 | insertion | Frame_Shift_Ins | novel | c.915_916insGTAAATAATA | p.Lys306ValfsTer35 | p.K306Vfs*35 | Q9NPB8 | protein_coding | TCGA-AC-A3QQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
GPCPD1 | SNV | Missense_Mutation | novel | c.280N>G | p.Leu94Val | p.L94V | Q9NPB8 | protein_coding | tolerated(0.22) | benign(0.136) | TCGA-VS-A9UB-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
GPCPD1 | SNV | Missense_Mutation | novel | c.1717C>G | p.Gln573Glu | p.Q573E | Q9NPB8 | protein_coding | tolerated(0.9) | benign(0) | TCGA-VS-A9UH-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
GPCPD1 | insertion | Frame_Shift_Ins | novel | c.462_463insA | p.Ser155IlefsTer2 | p.S155Ifs*2 | Q9NPB8 | protein_coding | TCGA-ZJ-AAXB-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | ||
GPCPD1 | SNV | Missense_Mutation | c.767N>A | p.Cys256Tyr | p.C256Y | Q9NPB8 | protein_coding | tolerated(0.66) | possibly_damaging(0.804) | TCGA-AA-3672-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
GPCPD1 | SNV | Missense_Mutation | c.447G>T | p.Lys149Asn | p.K149N | Q9NPB8 | protein_coding | tolerated(0.07) | probably_damaging(0.994) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
GPCPD1 | SNV | Missense_Mutation | c.259G>T | p.Val87Phe | p.V87F | Q9NPB8 | protein_coding | deleterious(0) | possibly_damaging(0.814) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR | |
GPCPD1 | SNV | Missense_Mutation | rs748581132 | c.662N>T | p.Thr221Met | p.T221M | Q9NPB8 | protein_coding | tolerated(0.07) | probably_damaging(0.974) | TCGA-AA-A01R-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5-fluorouracil | PD |
GPCPD1 | SNV | Missense_Mutation | c.1955N>T | p.Ser652Phe | p.S652F | Q9NPB8 | protein_coding | deleterious(0.03) | benign(0.055) | TCGA-CA-6718-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | PD |
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Related drugs of malignant transformation related genes |
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(DGIdb 4.0) |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
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