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Gene: CRNKL1 |
Gene summary for CRNKL1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CRNKL1 | Gene ID | 51340 |
| Gene name | crooked neck pre-mRNA splicing factor 1 | |
| Gene Alias | CLF | |
| Cytomap | 20p11.23 | |
| Gene Type | protein-coding | GO ID | GO:0000245 | UniProtAcc | Q5JY65 |
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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 |
| 51340 | CRNKL1 | LZE4T | Human | Esophagus | ESCC | 1.02e-12 | 3.80e-01 | 0.0811 |
| 51340 | CRNKL1 | LZE5T | Human | Esophagus | ESCC | 2.01e-06 | 3.29e-01 | 0.0514 |
| 51340 | CRNKL1 | LZE7T | Human | Esophagus | ESCC | 9.43e-07 | 2.91e-01 | 0.0667 |
| 51340 | CRNKL1 | LZE24T | Human | Esophagus | ESCC | 4.32e-12 | 3.25e-01 | 0.0596 |
| 51340 | CRNKL1 | LZE6T | Human | Esophagus | ESCC | 2.44e-04 | 2.21e-01 | 0.0845 |
| 51340 | CRNKL1 | P1T-E | Human | Esophagus | ESCC | 1.09e-05 | 2.53e-01 | 0.0875 |
| 51340 | CRNKL1 | P2T-E | Human | Esophagus | ESCC | 1.56e-17 | 3.47e-01 | 0.1177 |
| 51340 | CRNKL1 | P4T-E | Human | Esophagus | ESCC | 5.20e-25 | 4.74e-01 | 0.1323 |
| 51340 | CRNKL1 | P5T-E | Human | Esophagus | ESCC | 2.84e-12 | 2.48e-01 | 0.1327 |
| 51340 | CRNKL1 | P8T-E | Human | Esophagus | ESCC | 6.76e-13 | 1.86e-01 | 0.0889 |
| 51340 | CRNKL1 | P9T-E | Human | Esophagus | ESCC | 1.33e-10 | 2.12e-01 | 0.1131 |
| 51340 | CRNKL1 | P10T-E | Human | Esophagus | ESCC | 6.27e-19 | 3.73e-01 | 0.116 |
| 51340 | CRNKL1 | P11T-E | Human | Esophagus | ESCC | 2.59e-09 | 4.18e-01 | 0.1426 |
| 51340 | CRNKL1 | P12T-E | Human | Esophagus | ESCC | 4.12e-24 | 4.58e-01 | 0.1122 |
| 51340 | CRNKL1 | P15T-E | Human | Esophagus | ESCC | 2.16e-19 | 4.07e-01 | 0.1149 |
| 51340 | CRNKL1 | P16T-E | Human | Esophagus | ESCC | 4.13e-24 | 3.70e-01 | 0.1153 |
| 51340 | CRNKL1 | P17T-E | Human | Esophagus | ESCC | 3.17e-07 | 3.69e-01 | 0.1278 |
| 51340 | CRNKL1 | P20T-E | Human | Esophagus | ESCC | 1.31e-21 | 4.23e-01 | 0.1124 |
| 51340 | CRNKL1 | P21T-E | Human | Esophagus | ESCC | 1.75e-28 | 5.11e-01 | 0.1617 |
| 51340 | CRNKL1 | P22T-E | Human | Esophagus | ESCC | 1.73e-14 | 1.62e-01 | 0.1236 |
| Page: 1 2 3 4 5 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ |
| ∗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:0022613111 | Esophagus | ESCC | ribonucleoprotein complex biogenesis | 365/8552 | 463/18723 | 1.74e-49 | 1.11e-45 | 365 |
| GO:0008380111 | Esophagus | ESCC | RNA splicing | 336/8552 | 434/18723 | 1.74e-42 | 3.67e-39 | 336 |
| GO:0000375111 | Esophagus | ESCC | RNA splicing, via transesterification reactions | 248/8552 | 324/18723 | 3.05e-30 | 1.49e-27 | 248 |
| GO:0000377111 | Esophagus | ESCC | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 244/8552 | 320/18723 | 2.52e-29 | 1.07e-26 | 244 |
| GO:0000398111 | Esophagus | ESCC | mRNA splicing, via spliceosome | 244/8552 | 320/18723 | 2.52e-29 | 1.07e-26 | 244 |
| GO:0071826111 | Esophagus | ESCC | ribonucleoprotein complex subunit organization | 166/8552 | 227/18723 | 2.94e-17 | 2.42e-15 | 166 |
| GO:0022618111 | Esophagus | ESCC | ribonucleoprotein complex assembly | 159/8552 | 220/18723 | 8.19e-16 | 5.71e-14 | 159 |
| GO:000024514 | Esophagus | ESCC | spliceosomal complex assembly | 48/8552 | 79/18723 | 4.93e-03 | 1.89e-02 | 48 |
| GO:000838012 | Liver | Cirrhotic | RNA splicing | 229/4634 | 434/18723 | 9.13e-37 | 2.86e-33 | 229 |
| GO:002261312 | Liver | Cirrhotic | ribonucleoprotein complex biogenesis | 231/4634 | 463/18723 | 3.28e-32 | 6.86e-29 | 231 |
| GO:000037512 | Liver | Cirrhotic | RNA splicing, via transesterification reactions | 175/4634 | 324/18723 | 5.95e-30 | 7.47e-27 | 175 |
| GO:000037712 | Liver | Cirrhotic | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 172/4634 | 320/18723 | 4.02e-29 | 3.60e-26 | 172 |
| GO:000039812 | Liver | Cirrhotic | mRNA splicing, via spliceosome | 172/4634 | 320/18723 | 4.02e-29 | 3.60e-26 | 172 |
| GO:007182612 | Liver | Cirrhotic | ribonucleoprotein complex subunit organization | 115/4634 | 227/18723 | 2.67e-17 | 3.63e-15 | 115 |
| GO:002261812 | Liver | Cirrhotic | ribonucleoprotein complex assembly | 112/4634 | 220/18723 | 4.35e-17 | 5.81e-15 | 112 |
| GO:00002454 | Liver | Cirrhotic | spliceosomal complex assembly | 34/4634 | 79/18723 | 2.78e-04 | 2.46e-03 | 34 |
| GO:002261322 | Liver | HCC | ribonucleoprotein complex biogenesis | 355/7958 | 463/18723 | 7.76e-52 | 4.92e-48 | 355 |
| GO:000838022 | Liver | HCC | RNA splicing | 313/7958 | 434/18723 | 1.36e-36 | 1.73e-33 | 313 |
| GO:000037522 | Liver | HCC | RNA splicing, via transesterification reactions | 228/7958 | 324/18723 | 1.47e-24 | 4.06e-22 | 228 |
| GO:000037722 | Liver | HCC | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 224/7958 | 320/18723 | 1.16e-23 | 2.62e-21 | 224 |
| Page: 1 2 3 |
| Enriched KEGG pathways. |
| 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 |
| 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 |
| 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 |
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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 |
| CRNKL1 | SNV | Missense_Mutation | novel | c.413N>T | p.Ser138Leu | p.S138L | Q9BZJ0 | protein_coding | tolerated_low_confidence(0.08) | benign(0) | TCGA-3C-AALI-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Poly E | Complete Response |
| CRNKL1 | SNV | Missense_Mutation | novel | c.1728N>T | p.Trp576Cys | p.W576C | Q9BZJ0 | protein_coding | deleterious(0.01) | benign(0.445) | TCGA-A8-A07O-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | CR | |
| CRNKL1 | SNV | Missense_Mutation | c.434N>G | p.Phe145Cys | p.F145C | Q9BZJ0 | protein_coding | deleterious_low_confidence(0) | benign(0.174) | TCGA-AN-A0FY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| CRNKL1 | SNV | Missense_Mutation | c.2113C>T | p.Arg705Trp | p.R705W | Q9BZJ0 | protein_coding | deleterious(0.01) | probably_damaging(0.973) | TCGA-AO-A128-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| CRNKL1 | SNV | Missense_Mutation | novel | c.1225N>A | p.Glu409Lys | p.E409K | Q9BZJ0 | protein_coding | tolerated(0.08) | benign(0.146) | TCGA-BH-A0B6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| CRNKL1 | SNV | Missense_Mutation | c.1156G>C | p.Glu386Gln | p.E386Q | Q9BZJ0 | protein_coding | deleterious(0.01) | possibly_damaging(0.808) | TCGA-D8-A1J8-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | nolvadex | SD | |
| CRNKL1 | SNV | Missense_Mutation | c.334N>T | p.Ala112Ser | p.A112S | Q9BZJ0 | protein_coding | deleterious_low_confidence(0.01) | benign(0) | TCGA-D8-A1JP-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | |
| CRNKL1 | SNV | Missense_Mutation | c.63N>T | p.Lys21Asn | p.K21N | Q9BZJ0 | protein_coding | deleterious_low_confidence(0) | benign(0) | TCGA-D8-A1XC-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD | |
| CRNKL1 | SNV | Missense_Mutation | c.646N>A | p.Asp216Asn | p.D216N | Q9BZJ0 | protein_coding | deleterious(0.03) | benign(0.411) | TCGA-D8-A27G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| CRNKL1 | SNV | Missense_Mutation | rs762926211 | c.409N>C | p.Val137Leu | p.V137L | Q9BZJ0 | protein_coding | tolerated_low_confidence(0.38) | benign(0) | TCGA-E2-A1LA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | arimidex | SD |
| Page: 1 2 3 4 5 6 7 8 |
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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 |
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