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Gene: PUF60 |
Gene summary for PUF60 |
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Gene information | Species | Human | Gene symbol | PUF60 | Gene ID | 22827 |
Gene name | poly(U) binding splicing factor 60 | |
Gene Alias | FIR | |
Cytomap | 8q24.3 | |
Gene Type | protein-coding | GO ID | GO:0000245 | UniProtAcc | Q9UHX1 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
22827 | PUF60 | GSM4909285 | Human | Breast | IDC | 1.02e-23 | 5.23e-01 | 0.21 |
22827 | PUF60 | GSM4909287 | Human | Breast | IDC | 2.43e-02 | 2.82e-01 | 0.2057 |
22827 | PUF60 | GSM4909294 | Human | Breast | IDC | 1.19e-03 | 2.90e-01 | 0.2022 |
22827 | PUF60 | GSM4909296 | Human | Breast | IDC | 4.24e-07 | -1.04e-01 | 0.1524 |
22827 | PUF60 | GSM4909297 | Human | Breast | IDC | 9.15e-08 | -2.81e-02 | 0.1517 |
22827 | PUF60 | GSM4909304 | Human | Breast | IDC | 2.92e-04 | 3.12e-01 | 0.1636 |
22827 | PUF60 | GSM4909305 | Human | Breast | IDC | 6.82e-03 | 3.05e-01 | 0.0436 |
22827 | PUF60 | GSM4909306 | Human | Breast | IDC | 1.06e-05 | 3.45e-01 | 0.1564 |
22827 | PUF60 | GSM4909309 | Human | Breast | IDC | 2.53e-02 | 2.00e-01 | 0.0483 |
22827 | PUF60 | GSM4909311 | Human | Breast | IDC | 6.78e-24 | 7.52e-02 | 0.1534 |
22827 | PUF60 | GSM4909312 | Human | Breast | IDC | 7.60e-17 | 2.78e-01 | 0.1552 |
22827 | PUF60 | GSM4909317 | Human | Breast | IDC | 2.14e-25 | 6.47e-01 | 0.1355 |
22827 | PUF60 | GSM4909318 | Human | Breast | IDC | 1.22e-08 | 6.72e-01 | 0.2031 |
22827 | PUF60 | GSM4909319 | Human | Breast | IDC | 1.02e-34 | 1.55e-01 | 0.1563 |
22827 | PUF60 | GSM4909321 | Human | Breast | IDC | 4.49e-11 | 1.95e-02 | 0.1559 |
22827 | PUF60 | brca1 | Human | Breast | Precancer | 3.71e-08 | 3.90e-01 | -0.0338 |
22827 | PUF60 | brca2 | Human | Breast | Precancer | 5.41e-13 | 3.65e-01 | -0.024 |
22827 | PUF60 | brca3 | Human | Breast | Precancer | 2.54e-02 | 2.98e-01 | -0.0263 |
22827 | PUF60 | NCCBC14 | Human | Breast | DCIS | 7.18e-04 | 1.12e-01 | 0.2021 |
22827 | PUF60 | NCCBC5 | Human | Breast | DCIS | 2.84e-04 | 1.04e-01 | 0.2046 |
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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:000039814 | Breast | IDC | mRNA splicing, via spliceosome | 57/1434 | 320/18723 | 1.60e-09 | 1.49e-07 | 57 |
GO:004802414 | Breast | IDC | regulation of mRNA splicing, via spliceosome | 23/1434 | 101/18723 | 1.74e-06 | 7.28e-05 | 23 |
GO:005068413 | Breast | IDC | regulation of mRNA processing | 24/1434 | 137/18723 | 1.09e-04 | 2.04e-03 | 24 |
GO:190331113 | Breast | IDC | regulation of mRNA metabolic process | 40/1434 | 288/18723 | 1.79e-04 | 3.01e-03 | 40 |
GO:000038113 | Breast | IDC | regulation of alternative mRNA splicing, via spliceosome | 13/1434 | 60/18723 | 5.09e-04 | 6.65e-03 | 13 |
GO:000038013 | Breast | IDC | alternative mRNA splicing, via spliceosome | 15/1434 | 77/18723 | 6.51e-04 | 8.04e-03 | 15 |
GO:002261324 | Breast | DCIS | ribonucleoprotein complex biogenesis | 83/1390 | 463/18723 | 3.65e-14 | 1.09e-11 | 83 |
GO:007182624 | Breast | DCIS | ribonucleoprotein complex subunit organization | 52/1390 | 227/18723 | 1.54e-13 | 3.95e-11 | 52 |
GO:002261824 | Breast | DCIS | ribonucleoprotein complex assembly | 51/1390 | 220/18723 | 1.60e-13 | 3.95e-11 | 51 |
GO:000838024 | Breast | DCIS | RNA splicing | 73/1390 | 434/18723 | 3.05e-11 | 5.08e-09 | 73 |
GO:004348424 | Breast | DCIS | regulation of RNA splicing | 36/1390 | 148/18723 | 1.40e-10 | 1.69e-08 | 36 |
GO:000037524 | Breast | DCIS | RNA splicing, via transesterification reactions | 58/1390 | 324/18723 | 2.89e-10 | 3.34e-08 | 58 |
GO:000037724 | Breast | DCIS | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 57/1390 | 320/18723 | 5.01e-10 | 5.35e-08 | 57 |
GO:000039824 | Breast | DCIS | mRNA splicing, via spliceosome | 57/1390 | 320/18723 | 5.01e-10 | 5.35e-08 | 57 |
GO:004802424 | Breast | DCIS | regulation of mRNA splicing, via spliceosome | 23/1390 | 101/18723 | 1.02e-06 | 4.04e-05 | 23 |
GO:005068423 | Breast | DCIS | regulation of mRNA processing | 24/1390 | 137/18723 | 6.71e-05 | 1.33e-03 | 24 |
GO:190331123 | Breast | DCIS | regulation of mRNA metabolic process | 40/1390 | 288/18723 | 9.26e-05 | 1.71e-03 | 40 |
GO:000038123 | Breast | DCIS | regulation of alternative mRNA splicing, via spliceosome | 13/1390 | 60/18723 | 3.78e-04 | 5.27e-03 | 13 |
GO:000038023 | Breast | DCIS | alternative mRNA splicing, via spliceosome | 15/1390 | 77/18723 | 4.70e-04 | 6.20e-03 | 15 |
GO:0008380 | Colorectum | AD | RNA splicing | 169/3918 | 434/18723 | 3.59e-18 | 2.04e-15 | 169 |
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Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa030408 | Breast | Precancer | Spliceosome | 39/684 | 217/8465 | 1.44e-06 | 2.27e-05 | 1.74e-05 | 39 |
hsa0304013 | Breast | Precancer | Spliceosome | 39/684 | 217/8465 | 1.44e-06 | 2.27e-05 | 1.74e-05 | 39 |
hsa0304023 | Breast | IDC | Spliceosome | 40/867 | 217/8465 | 1.53e-04 | 1.42e-03 | 1.06e-03 | 40 |
hsa0304033 | Breast | IDC | Spliceosome | 40/867 | 217/8465 | 1.53e-04 | 1.42e-03 | 1.06e-03 | 40 |
hsa0304043 | Breast | DCIS | Spliceosome | 40/846 | 217/8465 | 8.97e-05 | 8.52e-04 | 6.28e-04 | 40 |
hsa0304053 | Breast | DCIS | Spliceosome | 40/846 | 217/8465 | 8.97e-05 | 8.52e-04 | 6.28e-04 | 40 |
hsa03040 | Colorectum | AD | Spliceosome | 73/2092 | 217/8465 | 1.73e-03 | 9.68e-03 | 6.18e-03 | 73 |
hsa030401 | Colorectum | AD | Spliceosome | 73/2092 | 217/8465 | 1.73e-03 | 9.68e-03 | 6.18e-03 | 73 |
hsa030402 | Colorectum | MSS | Spliceosome | 66/1875 | 217/8465 | 2.58e-03 | 1.27e-02 | 7.81e-03 | 66 |
hsa030403 | Colorectum | MSS | Spliceosome | 66/1875 | 217/8465 | 2.58e-03 | 1.27e-02 | 7.81e-03 | 66 |
hsa030404 | Colorectum | MSI-H | Spliceosome | 37/797 | 217/8465 | 2.49e-04 | 3.23e-03 | 2.70e-03 | 37 |
hsa030405 | Colorectum | MSI-H | Spliceosome | 37/797 | 217/8465 | 2.49e-04 | 3.23e-03 | 2.70e-03 | 37 |
hsa0304018 | Esophagus | HGIN | Spliceosome | 79/1383 | 217/8465 | 3.22e-13 | 7.00e-12 | 5.56e-12 | 79 |
hsa0304019 | Esophagus | HGIN | Spliceosome | 79/1383 | 217/8465 | 3.22e-13 | 7.00e-12 | 5.56e-12 | 79 |
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 |
hsa030407 | Liver | Cirrhotic | Spliceosome | 102/2530 | 217/8465 | 5.69e-08 | 9.47e-07 | 5.84e-07 | 102 |
hsa0304012 | Liver | Cirrhotic | Spliceosome | 102/2530 | 217/8465 | 5.69e-08 | 9.47e-07 | 5.84e-07 | 102 |
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 |
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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 |
PUF60 | SNV | Missense_Mutation | c.1264N>A | p.Glu422Lys | p.E422K | Q9UHX1 | protein_coding | tolerated(0.2) | benign(0.424) | TCGA-D8-A27G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
PUF60 | deletion | Frame_Shift_Del | c.1278delC | p.Glu427SerfsTer8 | p.E427Sfs*8 | Q9UHX1 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | |||
PUF60 | SNV | Missense_Mutation | novel | c.1643N>G | p.Asp548Gly | p.D548G | Q9UHX1 | protein_coding | deleterious(0) | possibly_damaging(0.654) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
PUF60 | SNV | Missense_Mutation | c.178A>G | p.Thr60Ala | p.T60A | Q9UHX1 | protein_coding | deleterious(0.03) | benign(0.184) | TCGA-C5-A7CL-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Chemotherapy | cisplatin | PD | |
PUF60 | SNV | Missense_Mutation | c.567N>C | p.Gln189His | p.Q189H | Q9UHX1 | protein_coding | tolerated(0.06) | benign(0.163) | TCGA-EK-A2PG-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD | |
PUF60 | SNV | Missense_Mutation | novel | c.556N>A | p.Ala186Thr | p.A186T | Q9UHX1 | protein_coding | deleterious(0) | probably_damaging(0.988) | TCGA-AA-3872-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Unknown | Unknown | SD |
PUF60 | SNV | Missense_Mutation | c.1469N>C | p.Phe490Ser | p.F490S | Q9UHX1 | protein_coding | deleterious(0.02) | benign(0.239) | TCGA-AD-A5EJ-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
PUF60 | SNV | Missense_Mutation | c.1162N>T | p.Pro388Ser | p.P388S | Q9UHX1 | protein_coding | deleterious(0.03) | benign(0.245) | TCGA-CM-4743-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Chemotherapy | capecitabine | SD | |
PUF60 | SNV | Missense_Mutation | c.688N>A | p.Val230Met | p.V230M | Q9UHX1 | protein_coding | deleterious(0.04) | probably_damaging(0.983) | TCGA-D5-6928-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
PUF60 | SNV | Missense_Mutation | rs756023794 | c.493G>A | p.Val165Ile | p.V165I | Q9UHX1 | protein_coding | tolerated(0.44) | benign(0.031) | TCGA-G4-6320-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | oxaliplatin | 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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