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| Open reading frame (ORF) annotation in the exon skipping event |
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| 3'-UTR located exon skipping events lost miRNA binding sites |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
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Gene summary for CSF1 |
 Gene summary |
| Gene information | Gene symbol | CSF1 | Gene ID | 1435 |
| Gene name | colony stimulating factor 1 | |
| Synonyms | CSF-1|MCSF | |
| Cytomap | 1p13.3 | |
| Type of gene | protein-coding | |
| Description | macrophage colony-stimulating factor 1colony stimulating factor 1 (macrophage)lanimostimmacrophage colony stimulating factor 1 | |
| Modification date | 20200313 | |
| UniProtAcc | ||
| Context | - 28848420(Studies on Colony Stimulating Factor Receptor-1 and Ligands Colony Stimulating Factor-1 and Interleukin-34 in Alzheimer's Disease Brains and Human Microglia) |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| CSF1 | GO:0002931 | response to ischemia | 8922060 |
| CSF1 | GO:0007169 | transmembrane receptor protein tyrosine kinase signaling pathway | 19100238 |
| CSF1 | GO:0008284 | positive regulation of cell proliferation | 10652277 |
| CSF1 | GO:0010628 | positive regulation of gene expression | 1739124|10666185 |
| CSF1 | GO:0010744 | positive regulation of macrophage derived foam cell differentiation | 17244792 |
| CSF1 | GO:0010759 | positive regulation of macrophage chemotaxis | 19100238 |
| CSF1 | GO:0030316 | osteoclast differentiation | 18606301 |
| CSF1 | GO:0032270 | positive regulation of cellular protein metabolic process | 1739124 |
| CSF1 | GO:0032946 | positive regulation of mononuclear cell proliferation | 2460758 |
| CSF1 | GO:0045651 | positive regulation of macrophage differentiation | 2460758 |
| CSF1 | GO:0045672 | positive regulation of osteoclast differentiation | 15304486 |
| CSF1 | GO:1901215 | negative regulation of neuron death | 8922060 |
| CSF1 | GO:1902228 | positive regulation of macrophage colony-stimulating factor signaling pathway | 19100238 |
| CSF1 | GO:1904141 | positive regulation of microglial cell migration | 19100238 |
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Gene structures and expression levels for CSF1 |
| Skipped exons in the ROSMAP, MSBB, and Mayo based on Ensembl gene isoform structure. * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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ENSG00000184371
| Differentially expressed gene analysis across multiple brain tissues between AD and control. |
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| Tissue type | DEG direction | Base mean exp. | log2FC(AD/control) | P-value | Adj. p-value |
| PG | UP | 2.435752e+02 | 8.116817e-01 | 6.613485e-09 | 4.270543e-07 |
| Differentially expressed isoform analysis across multiple brain tissues between AD and control. |
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| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| STG | UP | ENST00000369802.7 | CSF1-204:protein_coding:CSF1 | 6.749118e+00 | 1.831686e+00 | 8.720402e-05 | 1.011234e-02 |
| PG | UP | ENST00000329608.11 | CSF1-201:protein_coding:CSF1 | 2.378651e+02 | 8.337983e-01 | 1.658305e-06 | 1.305230e-04 |
| PG | UP | ENST00000369802.7 | CSF1-204:protein_coding:CSF1 | 9.332630e+00 | 8.595539e-01 | 6.721521e-04 | 1.091865e-02 |
| PG | UP | ENST00000420111.6 | CSF1-205:protein_coding:CSF1 | 3.555323e+00 | 1.069195e+00 | 1.442658e-03 | 1.894587e-02 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for CSF1 |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
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| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_124470 | chr1 | 109910870:109911062:109914259:109914381:109915634:109915696 | 109914259:109914381 |
| exon_skip_127203 | chr1 | 109914259:109914381:109915634:109915696:109917293:109917425 | 109915634:109915696 |
| exon_skip_208161 | chr1 | 109910605:109910632:109910813:109911062:109914259:109914381 | 109910813:109911062 |
| exon_skip_281503 | chr1 | 109921847:109921994:109923166:109923711:109924060:109924190 | 109923166:109923711 |
| exon_skip_34027 | chr1 | 109910986:109911062:109914259:109914381:109915634:109915696 | 109914259:109914381 |
| exon_skip_37611 | chr1 | 109910986:109911062:109915634:109915696:109917293:109917425 | 109915634:109915696 |
| exon_skip_52365 | chr1 | 109910870:109911062:109915634:109915696:109917293:109917425 | 109915634:109915696 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
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Open reading frame (ORF) annotation in the exon skipping event for CSF1 |
| Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000329608 | 109914259 | 109914381 | In-frame |
| ENST00000369802 | 109914259 | 109914381 | In-frame |
| ENST00000329608 | 109915634 | 109915696 | In-frame |
| ENST00000369802 | 109915634 | 109915696 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000329608 | 109914259 | 109914381 | In-frame |
| ENST00000369802 | 109914259 | 109914381 | In-frame |
| ENST00000329608 | 109915634 | 109915696 | In-frame |
| ENST00000369802 | 109915634 | 109915696 | In-frame |
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Infer the effects of exon skipping event on protein functional features for CSF1 |
p-ENSG00000184371_img4.png |
| Loci of skipped exons in ROSMAP across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| ENST00000329608 | 4227 | 554 | 109914259 | 109914381 | 432 | 553 | 13 | 54 |
| ENST00000369802 | 2501 | 554 | 109914259 | 109914381 | 166 | 287 | 13 | 54 |
| ENST00000329608 | 4227 | 554 | 109915634 | 109915696 | 555 | 616 | 54 | 75 |
| ENST00000369802 | 2501 | 554 | 109915634 | 109915696 | 289 | 350 | 54 | 75 |
| Loci of skipped exons in MSBB across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| Loci of skipped exons in Mayo across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| ENST00000329608 | 4227 | 554 | 109914259 | 109914381 | 432 | 553 | 13 | 54 |
| ENST00000369802 | 2501 | 554 | 109914259 | 109914381 | 166 | 287 | 13 | 54 |
| ENST00000329608 | 4227 | 554 | 109915634 | 109915696 | 555 | 616 | 54 | 75 |
| ENST00000369802 | 2501 | 554 | 109915634 | 109915696 | 289 | 350 | 54 | 75 |
| Lost protein functional features of individual exon skipping events in ROSMAP. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| P09603 | 13 | 54 | 33 | 554 | Chain | ID=PRO_0000005857;Note=Macrophage colony-stimulating factor 1 |
| P09603 | 13 | 54 | 33 | 554 | Chain | ID=PRO_0000005857;Note=Macrophage colony-stimulating factor 1 |
| P09603 | 13 | 54 | 33 | 450 | Chain | ID=PRO_0000296231;Note=Processed macrophage colony-stimulating factor 1;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q8JZQ0 |
| P09603 | 13 | 54 | 33 | 450 | Chain | ID=PRO_0000296231;Note=Processed macrophage colony-stimulating factor 1;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q8JZQ0 |
| P09603 | 13 | 54 | 39 | 122 | Disulfide bond | Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:8422357;Dbxref=PMID:8422357 |
| P09603 | 13 | 54 | 39 | 122 | Disulfide bond | Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:8422357;Dbxref=PMID:8422357 |
| P09603 | 13 | 54 | 37 | 41 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5LXF |
| P09603 | 13 | 54 | 37 | 41 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5LXF |
| P09603 | 13 | 54 | 45 | 56 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5LXF |
| P09603 | 13 | 54 | 45 | 56 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5LXF |
| P09603 | 13 | 54 | 1 | 32 | Signal peptide | Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:3498652;Dbxref=PMID:3498652 |
| P09603 | 13 | 54 | 1 | 32 | Signal peptide | Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:3498652;Dbxref=PMID:3498652 |
| P09603 | 13 | 54 | 33 | 496 | Topological domain | Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P09603 | 13 | 54 | 33 | 496 | Topological domain | Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P09603 | 54 | 75 | 65 | 70 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5LXF |
| P09603 | 54 | 75 | 65 | 70 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5LXF |
| P09603 | 54 | 75 | 33 | 554 | Chain | ID=PRO_0000005857;Note=Macrophage colony-stimulating factor 1 |
| P09603 | 54 | 75 | 33 | 554 | Chain | ID=PRO_0000005857;Note=Macrophage colony-stimulating factor 1 |
| P09603 | 54 | 75 | 33 | 450 | Chain | ID=PRO_0000296231;Note=Processed macrophage colony-stimulating factor 1;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q8JZQ0 |
| P09603 | 54 | 75 | 33 | 450 | Chain | ID=PRO_0000296231;Note=Processed macrophage colony-stimulating factor 1;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q8JZQ0 |
| P09603 | 54 | 75 | 39 | 122 | Disulfide bond | Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:8422357;Dbxref=PMID:8422357 |
| P09603 | 54 | 75 | 39 | 122 | Disulfide bond | Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:8422357;Dbxref=PMID:8422357 |
| P09603 | 54 | 75 | 63 | 63 | Disulfide bond | Note=Interchain;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:8422357;Dbxref=PMID:8422357 |
| P09603 | 54 | 75 | 63 | 63 | Disulfide bond | Note=Interchain;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:8422357;Dbxref=PMID:8422357 |
| P09603 | 54 | 75 | 45 | 56 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5LXF |
| P09603 | 54 | 75 | 45 | 56 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5LXF |
| P09603 | 54 | 75 | 69 | 69 | Sequence conflict | Note=F->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P09603 | 54 | 75 | 69 | 69 | Sequence conflict | Note=F->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P09603 | 54 | 75 | 33 | 496 | Topological domain | Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P09603 | 54 | 75 | 33 | 496 | Topological domain | Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P09603 | 54 | 75 | 72 | 74 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5LXF |
| P09603 | 54 | 75 | 72 | 74 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5LXF |
| Lost protein functional features of individual exon skipping events in MSBB. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| Lost protein functional features of individual exon skipping events in Mayo. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| P09603 | 13 | 54 | 33 | 554 | Chain | ID=PRO_0000005857;Note=Macrophage colony-stimulating factor 1 |
| P09603 | 13 | 54 | 33 | 554 | Chain | ID=PRO_0000005857;Note=Macrophage colony-stimulating factor 1 |
| P09603 | 13 | 54 | 33 | 450 | Chain | ID=PRO_0000296231;Note=Processed macrophage colony-stimulating factor 1;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q8JZQ0 |
| P09603 | 13 | 54 | 33 | 450 | Chain | ID=PRO_0000296231;Note=Processed macrophage colony-stimulating factor 1;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q8JZQ0 |
| P09603 | 13 | 54 | 39 | 122 | Disulfide bond | Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:8422357;Dbxref=PMID:8422357 |
| P09603 | 13 | 54 | 39 | 122 | Disulfide bond | Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:8422357;Dbxref=PMID:8422357 |
| P09603 | 13 | 54 | 37 | 41 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5LXF |
| P09603 | 13 | 54 | 37 | 41 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5LXF |
| P09603 | 13 | 54 | 45 | 56 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5LXF |
| P09603 | 13 | 54 | 45 | 56 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5LXF |
| P09603 | 13 | 54 | 1 | 32 | Signal peptide | Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:3498652;Dbxref=PMID:3498652 |
| P09603 | 13 | 54 | 1 | 32 | Signal peptide | Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:3498652;Dbxref=PMID:3498652 |
| P09603 | 13 | 54 | 33 | 496 | Topological domain | Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P09603 | 13 | 54 | 33 | 496 | Topological domain | Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P09603 | 54 | 75 | 65 | 70 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5LXF |
| P09603 | 54 | 75 | 65 | 70 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5LXF |
| P09603 | 54 | 75 | 33 | 554 | Chain | ID=PRO_0000005857;Note=Macrophage colony-stimulating factor 1 |
| P09603 | 54 | 75 | 33 | 554 | Chain | ID=PRO_0000005857;Note=Macrophage colony-stimulating factor 1 |
| P09603 | 54 | 75 | 33 | 450 | Chain | ID=PRO_0000296231;Note=Processed macrophage colony-stimulating factor 1;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q8JZQ0 |
| P09603 | 54 | 75 | 33 | 450 | Chain | ID=PRO_0000296231;Note=Processed macrophage colony-stimulating factor 1;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q8JZQ0 |
| P09603 | 54 | 75 | 39 | 122 | Disulfide bond | Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:8422357;Dbxref=PMID:8422357 |
| P09603 | 54 | 75 | 39 | 122 | Disulfide bond | Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:8422357;Dbxref=PMID:8422357 |
| P09603 | 54 | 75 | 63 | 63 | Disulfide bond | Note=Interchain;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:8422357;Dbxref=PMID:8422357 |
| P09603 | 54 | 75 | 63 | 63 | Disulfide bond | Note=Interchain;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:8422357;Dbxref=PMID:8422357 |
| P09603 | 54 | 75 | 45 | 56 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5LXF |
| P09603 | 54 | 75 | 45 | 56 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5LXF |
| P09603 | 54 | 75 | 69 | 69 | Sequence conflict | Note=F->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P09603 | 54 | 75 | 69 | 69 | Sequence conflict | Note=F->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P09603 | 54 | 75 | 33 | 496 | Topological domain | Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P09603 | 54 | 75 | 33 | 496 | Topological domain | Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P09603 | 54 | 75 | 72 | 74 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5LXF |
| P09603 | 54 | 75 | 72 | 74 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5LXF |
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3'-UTR located exon skipping events that lost miRNA binding sites in CSF1 |
| 3'-UTR exon skipping evnets lost miRNA binding. |
| Tissue type | ENST | Exon skip start | Exon skip end | microRNA | Binding site by TargetScan | Binding type by TargetScan | Bdinding site by miRanda | Score of miRanda | Energy by miRanda |
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SNVs in the skipped exons for CSF1 |
| - Differential PSIs between mutated versus non-mutated samples. |
| - Depth of Coverage in the skipped exon of the mutated samples. |
| - Sashimi plot in the skipped exon of the mutated samples. |
| - Non-synonymous mutations located in the skipped exons. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| - Non-synonymous mutations located in the skipped exons in CCLE. |
| Sample | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
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AD stage-associated exon skippint events for CSF1 |
| Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR). |
| AD stage info | Cohort | Tissue | SE id | Coefficient | P-value | Chromosome | Strand | E1 start | E1 end | Skipped start | Skipped end | E2 start | E2 end |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CSF1 |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
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Correlation with RNA binding proteins (RBPs) for CSF1 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for CSF1 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for CSF1 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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