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Gene: PRPF4 |
Gene summary for PRPF4 |
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Gene information | Species | Human | Gene symbol | PRPF4 | Gene ID | 9128 |
Gene name | pre-mRNA processing factor 4 | |
Gene Alias | HPRP4 | |
Cytomap | 9q32 | |
Gene Type | protein-coding | GO ID | GO:0000375 | UniProtAcc | O43172 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
9128 | PRPF4 | LZE2T | Human | Esophagus | ESCC | 6.88e-04 | 2.61e-01 | 0.082 |
9128 | PRPF4 | LZE4T | Human | Esophagus | ESCC | 9.84e-12 | 4.21e-01 | 0.0811 |
9128 | PRPF4 | LZE7T | Human | Esophagus | ESCC | 2.28e-08 | 4.77e-01 | 0.0667 |
9128 | PRPF4 | LZE8T | Human | Esophagus | ESCC | 1.71e-07 | 9.92e-02 | 0.067 |
9128 | PRPF4 | LZE20T | Human | Esophagus | ESCC | 4.18e-07 | 2.79e-01 | 0.0662 |
9128 | PRPF4 | LZE24T | Human | Esophagus | ESCC | 9.97e-10 | 2.35e-01 | 0.0596 |
9128 | PRPF4 | LZE21T | Human | Esophagus | ESCC | 3.33e-05 | 2.21e-01 | 0.0655 |
9128 | PRPF4 | P1T-E | Human | Esophagus | ESCC | 1.37e-12 | 3.30e-01 | 0.0875 |
9128 | PRPF4 | P2T-E | Human | Esophagus | ESCC | 1.61e-34 | 6.05e-01 | 0.1177 |
9128 | PRPF4 | P4T-E | Human | Esophagus | ESCC | 1.72e-21 | 4.89e-01 | 0.1323 |
9128 | PRPF4 | P5T-E | Human | Esophagus | ESCC | 5.92e-25 | 5.61e-01 | 0.1327 |
9128 | PRPF4 | P8T-E | Human | Esophagus | ESCC | 1.93e-12 | 1.43e-01 | 0.0889 |
9128 | PRPF4 | P9T-E | Human | Esophagus | ESCC | 1.35e-11 | 3.29e-01 | 0.1131 |
9128 | PRPF4 | P10T-E | Human | Esophagus | ESCC | 4.77e-36 | 7.65e-01 | 0.116 |
9128 | PRPF4 | P11T-E | Human | Esophagus | ESCC | 3.11e-03 | 3.52e-01 | 0.1426 |
9128 | PRPF4 | P12T-E | Human | Esophagus | ESCC | 2.41e-24 | 6.94e-01 | 0.1122 |
9128 | PRPF4 | P15T-E | Human | Esophagus | ESCC | 3.30e-31 | 1.04e+00 | 0.1149 |
9128 | PRPF4 | P16T-E | Human | Esophagus | ESCC | 1.51e-18 | 2.89e-01 | 0.1153 |
9128 | PRPF4 | P17T-E | Human | Esophagus | ESCC | 2.64e-02 | 3.28e-01 | 0.1278 |
9128 | PRPF4 | P20T-E | Human | Esophagus | ESCC | 2.99e-09 | 1.78e-01 | 0.1124 |
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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:000091019 | Thyroid | PTC | cytokinesis | 82/5968 | 173/18723 | 1.37e-05 | 1.47e-04 | 82 |
GO:00324655 | Thyroid | PTC | regulation of cytokinesis | 40/5968 | 92/18723 | 1.26e-02 | 4.92e-02 | 40 |
GO:000838034 | Thyroid | ATC | RNA splicing | 270/6293 | 434/18723 | 7.50e-35 | 1.19e-31 | 270 |
GO:000037534 | Thyroid | ATC | RNA splicing, via transesterification reactions | 200/6293 | 324/18723 | 1.75e-25 | 7.39e-23 | 200 |
GO:000037734 | Thyroid | ATC | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 197/6293 | 320/18723 | 6.54e-25 | 2.18e-22 | 197 |
GO:000039834 | Thyroid | ATC | mRNA splicing, via spliceosome | 197/6293 | 320/18723 | 6.54e-25 | 2.18e-22 | 197 |
GO:002260429 | Thyroid | ATC | regulation of cell morphogenesis | 171/6293 | 309/18723 | 2.36e-15 | 1.70e-13 | 171 |
GO:000836026 | Thyroid | ATC | regulation of cell shape | 91/6293 | 154/18723 | 7.33e-11 | 2.31e-09 | 91 |
GO:0000910110 | Thyroid | ATC | cytokinesis | 93/6293 | 173/18723 | 3.59e-08 | 6.67e-07 | 93 |
GO:003246511 | Thyroid | ATC | regulation of cytokinesis | 47/6293 | 92/18723 | 3.95e-04 | 2.39e-03 | 47 |
GO:00513027 | Thyroid | ATC | regulation of cell division | 80/6293 | 177/18723 | 8.54e-04 | 4.68e-03 | 80 |
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Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0304027 | Esophagus | ESCC | Spliceosome | 128/4205 | 217/8465 | 3.31e-03 | 8.79e-03 | 4.50e-03 | 128 |
hsa0304037 | Esophagus | ESCC | Spliceosome | 128/4205 | 217/8465 | 3.31e-03 | 8.79e-03 | 4.50e-03 | 128 |
hsa0304022 | Liver | HCC | Spliceosome | 122/4020 | 217/8465 | 5.55e-03 | 1.60e-02 | 8.91e-03 | 122 |
hsa0304032 | Liver | HCC | Spliceosome | 122/4020 | 217/8465 | 5.55e-03 | 1.60e-02 | 8.91e-03 | 122 |
hsa0304016 | Oral cavity | OSCC | Spliceosome | 123/3704 | 217/8465 | 7.21e-05 | 2.74e-04 | 1.40e-04 | 123 |
hsa0304017 | Oral cavity | OSCC | Spliceosome | 123/3704 | 217/8465 | 7.21e-05 | 2.74e-04 | 1.40e-04 | 123 |
hsa0304026 | Oral cavity | LP | Spliceosome | 106/2418 | 217/8465 | 1.30e-10 | 2.40e-09 | 1.55e-09 | 106 |
hsa0304036 | Oral cavity | LP | Spliceosome | 106/2418 | 217/8465 | 1.30e-10 | 2.40e-09 | 1.55e-09 | 106 |
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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 |
PRPF4 | SNV | Missense_Mutation | c.1270N>C | p.Thr424Pro | p.T424P | O43172 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AR-A256-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | PD | |
PRPF4 | SNV | Missense_Mutation | novel | c.250N>T | p.Ala84Ser | p.A84S | O43172 | protein_coding | tolerated(0.66) | benign(0.017) | TCGA-D8-A1X5-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | tamoxiphen | SD |
PRPF4 | SNV | Missense_Mutation | c.1542G>C | p.Arg514Ser | p.R514S | O43172 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-D8-A1XL-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine+cyclophosphamide+tamoxifen | SD | |
PRPF4 | insertion | Nonsense_Mutation | novel | c.1433_1434insAGTGGAGGAAGAAAGAAGGTAACAGA | p.His479ValfsTer7 | p.H479Vfs*7 | O43172 | protein_coding | TCGA-A8-A083-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
PRPF4 | SNV | Missense_Mutation | rs575911571 | c.899N>T | p.Ala300Val | p.A300V | O43172 | protein_coding | deleterious(0.01) | possibly_damaging(0.849) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
PRPF4 | SNV | Missense_Mutation | novel | c.1043N>A | p.Arg348His | p.R348H | O43172 | protein_coding | deleterious(0.04) | probably_damaging(1) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
PRPF4 | SNV | Missense_Mutation | c.206C>T | p.Ser69Phe | p.S69F | O43172 | protein_coding | deleterious(0.05) | possibly_damaging(0.472) | TCGA-FU-A5XV-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD | |
PRPF4 | SNV | Missense_Mutation | c.391G>C | p.Glu131Gln | p.E131Q | O43172 | protein_coding | tolerated(0.06) | possibly_damaging(0.903) | TCGA-Q1-A73O-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
PRPF4 | SNV | Missense_Mutation | c.809G>A | p.Arg270Gln | p.R270Q | O43172 | protein_coding | tolerated(0.05) | possibly_damaging(0.462) | TCGA-Q1-A73O-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
PRPF4 | SNV | Missense_Mutation | rs373783471 | c.980N>T | p.Ala327Val | p.A327V | O43172 | protein_coding | deleterious(0.01) | possibly_damaging(0.714) | TCGA-VS-A9UI-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD |
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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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