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Gene: CSF1R |
Gene summary for CSF1R |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CSF1R | Gene ID | 1436 |
| Gene name | colony stimulating factor 1 receptor | |
| Gene Alias | BANDDOS | |
| Cytomap | 5q32 | |
| Gene Type | protein-coding | GO ID | GO:0000165 | UniProtAcc | P07333 |
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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 |
| 1436 | CSF1R | HTA11_3410_2000001011 | Human | Colorectum | AD | 6.15e-14 | 3.59e-01 | 0.0155 |
| 1436 | CSF1R | HTA11_2487_2000001011 | Human | Colorectum | SER | 8.42e-14 | 5.73e-01 | -0.1808 |
| 1436 | CSF1R | HTA11_2951_2000001011 | Human | Colorectum | AD | 2.54e-22 | 1.30e+00 | 0.0216 |
| 1436 | CSF1R | HTA11_1938_2000001011 | Human | Colorectum | AD | 4.06e-23 | 8.81e-01 | -0.0811 |
| 1436 | CSF1R | HTA11_78_2000001011 | Human | Colorectum | AD | 9.19e-35 | 1.07e+00 | -0.1088 |
| 1436 | CSF1R | HTA11_347_2000001011 | Human | Colorectum | AD | 4.57e-42 | 1.12e+00 | -0.1954 |
| 1436 | CSF1R | HTA11_411_2000001011 | Human | Colorectum | SER | 1.52e-07 | 1.12e+00 | -0.2602 |
| 1436 | CSF1R | HTA11_2112_2000001011 | Human | Colorectum | SER | 2.95e-03 | 4.43e-01 | -0.2196 |
| 1436 | CSF1R | HTA11_3361_2000001011 | Human | Colorectum | AD | 1.01e-06 | 5.80e-01 | -0.1207 |
| 1436 | CSF1R | HTA11_83_2000001011 | Human | Colorectum | SER | 2.25e-31 | 1.16e+00 | -0.1526 |
| 1436 | CSF1R | HTA11_696_2000001011 | Human | Colorectum | AD | 1.17e-41 | 7.62e-01 | -0.1464 |
| 1436 | CSF1R | HTA11_866_2000001011 | Human | Colorectum | AD | 6.25e-19 | 4.37e-01 | -0.1001 |
| 1436 | CSF1R | HTA11_1391_2000001011 | Human | Colorectum | AD | 1.12e-37 | 1.08e+00 | -0.059 |
| 1436 | CSF1R | HTA11_2992_2000001011 | Human | Colorectum | SER | 1.80e-20 | 1.07e+00 | -0.1706 |
| 1436 | CSF1R | HTA11_5212_2000001011 | Human | Colorectum | AD | 4.90e-09 | 6.10e-01 | -0.2061 |
| 1436 | CSF1R | HTA11_5216_2000001011 | Human | Colorectum | SER | 2.22e-17 | 1.24e+00 | -0.1462 |
| 1436 | CSF1R | HTA11_546_2000001011 | Human | Colorectum | AD | 2.10e-18 | 9.08e-01 | -0.0842 |
| 1436 | CSF1R | HTA11_9341_2000001011 | Human | Colorectum | SER | 4.33e-04 | 6.22e-01 | -0.00410000000000005 |
| 1436 | CSF1R | HTA11_7862_2000001011 | Human | Colorectum | AD | 2.24e-21 | 8.81e-01 | -0.0179 |
| 1436 | CSF1R | HTA11_866_3004761011 | Human | Colorectum | AD | 4.54e-46 | 1.12e+00 | 0.096 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 |
| ∗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:0032970 | Colorectum | AD | regulation of actin filament-based process | 142/3918 | 397/18723 | 4.05e-12 | 5.90e-10 | 142 |
| GO:0048732 | Colorectum | AD | gland development | 149/3918 | 436/18723 | 6.07e-11 | 6.33e-09 | 149 |
| GO:0032956 | Colorectum | AD | regulation of actin cytoskeleton organization | 127/3918 | 358/18723 | 1.03e-10 | 1.04e-08 | 127 |
| GO:0045216 | Colorectum | AD | cell-cell junction organization | 80/3918 | 200/18723 | 5.57e-10 | 4.58e-08 | 80 |
| GO:0022604 | Colorectum | AD | regulation of cell morphogenesis | 109/3918 | 309/18723 | 3.08e-09 | 2.07e-07 | 109 |
| GO:0030099 | Colorectum | AD | myeloid cell differentiation | 119/3918 | 381/18723 | 1.24e-06 | 4.01e-05 | 119 |
| GO:0030879 | Colorectum | AD | mammary gland development | 53/3918 | 137/18723 | 1.46e-06 | 4.58e-05 | 53 |
| GO:0008360 | Colorectum | AD | regulation of cell shape | 56/3918 | 154/18723 | 7.01e-06 | 1.73e-04 | 56 |
| GO:0046777 | Colorectum | AD | protein autophosphorylation | 74/3918 | 227/18723 | 2.48e-05 | 4.76e-04 | 74 |
| GO:0031532 | Colorectum | AD | actin cytoskeleton reorganization | 41/3918 | 107/18723 | 2.81e-05 | 5.28e-04 | 41 |
| GO:0061180 | Colorectum | AD | mammary gland epithelium development | 28/3918 | 67/18723 | 8.74e-05 | 1.35e-03 | 28 |
| GO:0060249 | Colorectum | AD | anatomical structure homeostasis | 94/3918 | 314/18723 | 9.37e-05 | 1.42e-03 | 94 |
| GO:0043954 | Colorectum | AD | cellular component maintenance | 26/3918 | 61/18723 | 1.04e-04 | 1.56e-03 | 26 |
| GO:0033674 | Colorectum | AD | positive regulation of kinase activity | 131/3918 | 467/18723 | 1.28e-04 | 1.85e-03 | 131 |
| GO:0022612 | Colorectum | AD | gland morphogenesis | 42/3918 | 118/18723 | 1.62e-04 | 2.23e-03 | 42 |
| GO:0001894 | Colorectum | AD | tissue homeostasis | 81/3918 | 268/18723 | 1.96e-04 | 2.62e-03 | 81 |
| GO:0030224 | Colorectum | AD | monocyte differentiation | 17/3918 | 36/18723 | 3.79e-04 | 4.36e-03 | 17 |
| GO:0060562 | Colorectum | AD | epithelial tube morphogenesis | 93/3918 | 325/18723 | 5.65e-04 | 6.00e-03 | 93 |
| GO:0045860 | Colorectum | AD | positive regulation of protein kinase activity | 107/3918 | 386/18723 | 8.01e-04 | 7.92e-03 | 107 |
| GO:0060443 | Colorectum | AD | mammary gland morphogenesis | 18/3918 | 43/18723 | 1.51e-03 | 1.27e-02 | 18 |
| Page: 1 2 3 4 5 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa04015 | Colorectum | AD | Rap1 signaling pathway | 71/2092 | 210/8465 | 1.72e-03 | 9.68e-03 | 6.18e-03 | 71 |
| hsa040151 | Colorectum | AD | Rap1 signaling pathway | 71/2092 | 210/8465 | 1.72e-03 | 9.68e-03 | 6.18e-03 | 71 |
| hsa040152 | Colorectum | SER | Rap1 signaling pathway | 54/1580 | 210/8465 | 6.55e-03 | 3.68e-02 | 2.67e-02 | 54 |
| hsa040153 | Colorectum | SER | Rap1 signaling pathway | 54/1580 | 210/8465 | 6.55e-03 | 3.68e-02 | 2.67e-02 | 54 |
| hsa040154 | Colorectum | MSS | Rap1 signaling pathway | 66/1875 | 210/8465 | 1.03e-03 | 5.94e-03 | 3.64e-03 | 66 |
| hsa040155 | Colorectum | MSS | Rap1 signaling pathway | 66/1875 | 210/8465 | 1.03e-03 | 5.94e-03 | 3.64e-03 | 66 |
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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 |
| CSF1 | CSF1R | CSF1_CSF1R | CSF | Breast | DCIS |
| CSF1 | CSF1R | CSF1_CSF1R | CSF | Cervix | ADJ |
| IL34 | CSF1R | IL34_CSF1R | CSF | Cervix | CC |
| CSF1 | CSF1R | CSF1_CSF1R | CSF | Cervix | CC |
| CSF1 | CSF1R | CSF1_CSF1R | CSF | Cervix | Precancer |
| IL34 | CSF1R | IL34_CSF1R | CSF | CRC | AD |
| CSF1 | CSF1R | CSF1_CSF1R | CSF | CRC | AD |
| CSF1 | CSF1R | CSF1_CSF1R | CSF | CRC | ADJ |
| CSF1 | CSF1R | CSF1_CSF1R | CSF | CRC | MSI-H |
| CSF1 | CSF1R | CSF1_CSF1R | CSF | CRC | SER |
| CSF1 | CSF1R | CSF1_CSF1R | CSF | Endometrium | ADJ |
| CSF1 | CSF1R | CSF1_CSF1R | CSF | Endometrium | AEH |
| CSF1 | CSF1R | CSF1_CSF1R | CSF | Endometrium | EEC |
| CSF1 | CSF1R | CSF1_CSF1R | CSF | Endometrium | Healthy |
| CSF1 | CSF1R | CSF1_CSF1R | CSF | HNSCC | ADJ |
| IL34 | CSF1R | IL34_CSF1R | CSF | HNSCC | Healthy |
| IL34 | CSF1R | IL34_CSF1R | CSF | HNSCC | OSCC |
| CSF1 | CSF1R | CSF1_CSF1R | CSF | HNSCC | OSCC |
| IL34 | CSF1R | IL34_CSF1R | CSF | HNSCC | Precancer |
| CSF1 | CSF1R | CSF1_CSF1R | CSF | HNSCC | Precancer |
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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 |
| CSF1R | SNV | Missense_Mutation | c.1423N>C | p.Glu475Gln | p.E475Q | P07333 | protein_coding | tolerated(0.61) | benign(0.021) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| CSF1R | SNV | Missense_Mutation | c.403G>C | p.Glu135Gln | p.E135Q | P07333 | protein_coding | tolerated(0.39) | benign(0.007) | TCGA-D8-A1J9-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| CSF1R | insertion | Nonsense_Mutation | novel | c.209_210insATGAATGATCAGCCTCTCTGAGCTTCCTT | p.Ser70ArgfsTer2 | p.S70Rfs*2 | P07333 | protein_coding | TCGA-A2-A04Y-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
| CSF1R | insertion | Frame_Shift_Ins | novel | c.154_155insTGCTAGCACAGGAGGTGGTCGTGTTC | p.Gly52ValfsTer69 | p.G52Vfs*69 | P07333 | protein_coding | TCGA-A8-A07G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | 5-fluorouracil | CR | ||
| CSF1R | deletion | Frame_Shift_Del | novel | c.330delN | p.Leu111Ter | p.L111* | P07333 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | ||
| CSF1R | SNV | Missense_Mutation | novel | c.2009A>G | p.Asp670Gly | p.D670G | P07333 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| CSF1R | SNV | Missense_Mutation | novel | c.1679G>A | p.Ser560Asn | p.S560N | P07333 | protein_coding | tolerated(1) | benign(0) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| CSF1R | SNV | Missense_Mutation | novel | c.235A>G | p.Thr79Ala | p.T79A | P07333 | protein_coding | deleterious(0.01) | probably_damaging(0.927) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| CSF1R | SNV | Missense_Mutation | c.916N>C | p.Glu306Gln | p.E306Q | P07333 | protein_coding | tolerated(0.43) | benign(0.157) | TCGA-C5-A1BK-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| CSF1R | SNV | Missense_Mutation | c.1092N>A | p.Phe364Leu | p.F364L | P07333 | protein_coding | tolerated(0.09) | benign(0.021) | TCGA-IR-A3LK-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | PD |
| Page: 1 2 3 4 5 6 7 8 9 10 |
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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 |
| 1436 | CSF1R | CLINICALLY ACTIONABLE, KINASE, TYROSINE KINASE, CELL SURFACE, DRUGGABLE GENOME | inhibitor | 178102292 | CEDIRANIB | |
| 1436 | CSF1R | CLINICALLY ACTIONABLE, KINASE, TYROSINE KINASE, CELL SURFACE, DRUGGABLE GENOME | AMG 820 | |||
| 1436 | CSF1R | CLINICALLY ACTIONABLE, KINASE, TYROSINE KINASE, CELL SURFACE, DRUGGABLE GENOME | inhibitor | CHEMBL1567 | SUNITINIB MALATE | |
| 1436 | CSF1R | CLINICALLY ACTIONABLE, KINASE, TYROSINE KINASE, CELL SURFACE, DRUGGABLE GENOME | inhibitor | 178102317 | CHEMBL1908396 | |
| 1436 | CSF1R | CLINICALLY ACTIONABLE, KINASE, TYROSINE KINASE, CELL SURFACE, DRUGGABLE GENOME | DOVITINIB | DOVITINIB | 28759044 | |
| 1436 | CSF1R | CLINICALLY ACTIONABLE, KINASE, TYROSINE KINASE, CELL SURFACE, DRUGGABLE GENOME | AST-487 | AST-487 | ||
| 1436 | CSF1R | CLINICALLY ACTIONABLE, KINASE, TYROSINE KINASE, CELL SURFACE, DRUGGABLE GENOME | DCC-3014 | |||
| 1436 | CSF1R | CLINICALLY ACTIONABLE, KINASE, TYROSINE KINASE, CELL SURFACE, DRUGGABLE GENOME | inhibitor | DASATINIB | DASATINIB | |
| 1436 | CSF1R | CLINICALLY ACTIONABLE, KINASE, TYROSINE KINASE, CELL SURFACE, DRUGGABLE GENOME | GW843682X | GW843682X | ||
| 1436 | CSF1R | CLINICALLY ACTIONABLE, KINASE, TYROSINE KINASE, CELL SURFACE, DRUGGABLE GENOME | antibody | 315661194 |
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