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Gene: HNRNPF |
Gene summary for HNRNPF |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | HNRNPF | Gene ID | 3185 |
| Gene name | heterogeneous nuclear ribonucleoprotein F | |
| Gene Alias | HNRPF | |
| Cytomap | 10q11.21 | |
| Gene Type | protein-coding | GO ID | GO:0000375 | UniProtAcc | A0A024R7T3 |
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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 |
| 3185 | HNRNPF | GSM4909282 | Human | Breast | IDC | 3.76e-05 | 3.35e-01 | -0.0288 |
| 3185 | HNRNPF | GSM4909285 | Human | Breast | IDC | 3.04e-12 | 4.23e-01 | 0.21 |
| 3185 | HNRNPF | GSM4909286 | Human | Breast | IDC | 9.55e-03 | 2.88e-02 | 0.1081 |
| 3185 | HNRNPF | GSM4909290 | Human | Breast | IDC | 4.12e-05 | 3.69e-01 | 0.2096 |
| 3185 | HNRNPF | GSM4909293 | Human | Breast | IDC | 2.59e-02 | -6.10e-02 | 0.1581 |
| 3185 | HNRNPF | GSM4909294 | Human | Breast | IDC | 1.01e-05 | 4.92e-02 | 0.2022 |
| 3185 | HNRNPF | GSM4909296 | Human | Breast | IDC | 3.52e-15 | -2.90e-01 | 0.1524 |
| 3185 | HNRNPF | GSM4909297 | Human | Breast | IDC | 1.31e-19 | 1.48e-02 | 0.1517 |
| 3185 | HNRNPF | GSM4909301 | Human | Breast | IDC | 6.06e-03 | -1.75e-01 | 0.1577 |
| 3185 | HNRNPF | GSM4909309 | Human | Breast | IDC | 1.10e-04 | -3.42e-01 | 0.0483 |
| 3185 | HNRNPF | GSM4909311 | Human | Breast | IDC | 2.11e-37 | -3.27e-01 | 0.1534 |
| 3185 | HNRNPF | GSM4909312 | Human | Breast | IDC | 1.49e-22 | 2.36e-01 | 0.1552 |
| 3185 | HNRNPF | GSM4909318 | Human | Breast | IDC | 2.44e-03 | 3.69e-01 | 0.2031 |
| 3185 | HNRNPF | GSM4909319 | Human | Breast | IDC | 1.01e-48 | -4.49e-01 | 0.1563 |
| 3185 | HNRNPF | GSM4909320 | Human | Breast | IDC | 1.59e-09 | -5.93e-01 | 0.1575 |
| 3185 | HNRNPF | GSM4909321 | Human | Breast | IDC | 7.56e-19 | -8.83e-02 | 0.1559 |
| 3185 | HNRNPF | brca1 | Human | Breast | Precancer | 5.62e-03 | 2.75e-01 | -0.0338 |
| 3185 | HNRNPF | brca2 | Human | Breast | Precancer | 8.48e-05 | 3.46e-01 | -0.024 |
| 3185 | HNRNPF | brca3 | Human | Breast | Precancer | 5.62e-04 | 3.26e-01 | -0.0263 |
| 3185 | HNRNPF | brca10 | Human | Breast | Precancer | 1.24e-11 | -5.02e-01 | -0.0029 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| 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 | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| 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:00083809 | Breast | Precancer | RNA splicing | 65/1080 | 434/18723 | 1.27e-12 | 2.53e-10 | 65 |
| GO:00434849 | Breast | Precancer | regulation of RNA splicing | 34/1080 | 148/18723 | 2.66e-12 | 4.75e-10 | 34 |
| GO:00003759 | Breast | Precancer | RNA splicing, via transesterification reactions | 52/1080 | 324/18723 | 1.74e-11 | 2.22e-09 | 52 |
| GO:00003779 | Breast | Precancer | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 51/1080 | 320/18723 | 3.55e-11 | 4.04e-09 | 51 |
| GO:00003989 | Breast | Precancer | mRNA splicing, via spliceosome | 51/1080 | 320/18723 | 3.55e-11 | 4.04e-09 | 51 |
| GO:000838014 | Breast | IDC | RNA splicing | 73/1434 | 434/18723 | 1.27e-10 | 1.57e-08 | 73 |
| GO:004348414 | Breast | IDC | regulation of RNA splicing | 36/1434 | 148/18723 | 3.32e-10 | 3.77e-08 | 36 |
| GO:000037514 | Breast | IDC | RNA splicing, via transesterification reactions | 58/1434 | 324/18723 | 9.44e-10 | 9.58e-08 | 58 |
| GO:000037714 | Breast | IDC | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 57/1434 | 320/18723 | 1.60e-09 | 1.49e-07 | 57 |
| GO:000039814 | Breast | IDC | mRNA splicing, via spliceosome | 57/1434 | 320/18723 | 1.60e-09 | 1.49e-07 | 57 |
| 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:0008380 | Colorectum | AD | RNA splicing | 169/3918 | 434/18723 | 3.59e-18 | 2.04e-15 | 169 |
| GO:0000377 | Colorectum | AD | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 130/3918 | 320/18723 | 5.88e-16 | 2.16e-13 | 130 |
| GO:0000398 | Colorectum | AD | mRNA splicing, via spliceosome | 130/3918 | 320/18723 | 5.88e-16 | 2.16e-13 | 130 |
| GO:0000375 | Colorectum | AD | RNA splicing, via transesterification reactions | 131/3918 | 324/18723 | 7.11e-16 | 2.22e-13 | 131 |
| GO:0043484 | Colorectum | AD | regulation of RNA splicing | 70/3918 | 148/18723 | 6.47e-13 | 1.16e-10 | 70 |
| Page: 1 2 3 4 5 6 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| Page: 1 |
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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. |
| Page: 1 |
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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 |
| HNRNPF | SNV | Missense_Mutation | novel | c.958G>C | p.Glu320Gln | p.E320Q | P52597 | protein_coding | tolerated(0.17) | benign(0.301) | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD |
| HNRNPF | SNV | Missense_Mutation | rs780029236 | c.316N>A | p.Asp106Asn | p.D106N | P52597 | protein_coding | tolerated(0.11) | benign(0.037) | TCGA-E2-A14R-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | PD |
| HNRNPF | SNV | Missense_Mutation | novel | c.706N>C | p.Tyr236His | p.Y236H | P52597 | protein_coding | tolerated(0.15) | benign(0.104) | TCGA-E9-A54X-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| HNRNPF | SNV | Missense_Mutation | novel | c.162N>A | p.Ser54Arg | p.S54R | P52597 | protein_coding | deleterious(0.02) | probably_damaging(0.998) | TCGA-VS-A9U6-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PD |
| HNRNPF | SNV | Missense_Mutation | c.390N>A | p.Phe130Leu | p.F130L | P52597 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
| HNRNPF | SNV | Missense_Mutation | c.528N>G | p.Ile176Met | p.I176M | P52597 | protein_coding | tolerated(0.08) | possibly_damaging(0.734) | TCGA-AA-A022-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| HNRNPF | SNV | Missense_Mutation | c.337N>A | p.Val113Met | p.V113M | P52597 | protein_coding | deleterious(0) | probably_damaging(0.986) | TCGA-AA-A02K-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | folinic | PD | |
| HNRNPF | SNV | Missense_Mutation | c.295N>T | p.His99Tyr | p.H99Y | P52597 | protein_coding | deleterious(0.01) | possibly_damaging(0.465) | TCGA-F4-6461-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | |
| HNRNPF | SNV | Missense_Mutation | c.1096G>T | p.Gly366Trp | p.G366W | P52597 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-G4-6299-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Ancillary | leucovorin | SD | |
| HNRNPF | SNV | Missense_Mutation | c.889C>T | p.Pro297Ser | p.P297S | P52597 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-QG-A5Z2-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 |
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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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