|
||||||
|
 | |
| |
| |
| Open reading frame (ORF) annotation in the exon skipping event |
| |
| 3'-UTR located exon skipping events lost miRNA binding sites |
| |
| |
| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| |
| |
|
Gene summary for LITAF |
 Gene summary |
| Gene information | Gene symbol | LITAF | Gene ID | 9516 |
| Gene name | lipopolysaccharide induced TNF factor | |
| Synonyms | PIG7|SIMPLE|TP53I7 | |
| Cytomap | 16p13.13 | |
| Type of gene | protein-coding | |
| Description | lipopolysaccharide-induced tumor necrosis factor-alpha factorLPS-induced TNF-alpha factorlipopolysaccharide-induced TNF-alpha factorp53-induced gene 7 proteinsmall integral membrane protein of lysosome/late endosometumor protein p53 inducible protein | |
| Modification date | 20200328 | |
| UniProtAcc | ||
| Context |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
Top |
Gene structures and expression levels for LITAF |
| 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. |
 |
ENSG00000189067
| Differentially expressed gene analysis across multiple brain tissues between AD and control. |
| Tissue type | DEG direction | Base mean exp. | log2FC(AD/control) | P-value | Adj. p-value |
| Differentially expressed isoform analysis across multiple brain tissues between AD and control. |
 |
| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| PG | UP | ENST00000571277.1 | LITAF-206:protein_coding:LITAF | 1.489922e+00 | 1.197575e+00 | 7.372996e-06 | 4.011685e-04 |
| PG | UP | ENST00000571976.1 | LITAF-210:protein_coding:LITAF | 9.468762e-01 | 1.553030e+00 | 6.273407e-04 | 1.038560e-02 |
| PG | UP | ENST00000574703.5 | LITAF-214:protein_coding:LITAF | 9.103456e-01 | 1.088274e+00 | 5.101812e-03 | 4.631927e-02 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
 |
Top |
Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for LITAF |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
 |
| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_119933 | chr16 | 11549312:11549745:11553533:11553689:11556511:11556735 | 11553533:11553689 |
| exon_skip_128921 | chr16 | 11556722:11556735:11584190:11584332:11586886:11586903 | 11584190:11584332 |
| exon_skip_19742 | chr16 | 11556722:11556735:11575406:11575586:11586886:11586903 | 11575406:11575586 |
| exon_skip_201023 | chr16 | 11547999:11549745:11551707:11551804:11553533:11553689 | 11551707:11551804 |
| exon_skip_209191 | chr16 | 11549711:11549745:11551707:11551804:11553533:11553689 | 11551707:11551804 |
| exon_skip_248943 | chr16 | 11549312:11549745:11553533:11553748:11556511:11556735 | 11553533:11553748 |
| exon_skip_263199 | chr16 | 11553533:11553689:11556511:11556735:11575406:11575586 | 11556511:11556735 |
| exon_skip_26468 | chr16 | 11556722:11556735:11575406:11575586:11586886:11586919 | 11575406:11575586 |
| exon_skip_276538 | chr16 | 11556511:11556735:11575406:11575586:11586886:11586919 | 11575406:11575586 |
| exon_skip_89970 | chr16 | 11556511:11556735:11584190:11584332:11586886:11586918 | 11584190:11584332 |
| 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 |
Top |
Open reading frame (ORF) annotation in the exon skipping event for LITAF |
| 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 |
| ENST00000574763 | 11556511 | 11556735 | 3UTR-3CDS |
| ENST00000574763 | 11575406 | 11575586 | 3UTR-3UTR |
| ENST00000339430 | 11553533 | 11553689 | Frame-shift |
| ENST00000570904 | 11553533 | 11553689 | Frame-shift |
| ENST00000571688 | 11553533 | 11553689 | Frame-shift |
| ENST00000574763 | 11553533 | 11553689 | Frame-shift |
| ENST00000576036 | 11553533 | 11553689 | Frame-shift |
| ENST00000622633 | 11553533 | 11553689 | Frame-shift |
| 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 |
| ENST00000574763 | 11575406 | 11575586 | 3UTR-3UTR |
| ENST00000339430 | 11553533 | 11553689 | Frame-shift |
| ENST00000570904 | 11553533 | 11553689 | Frame-shift |
| ENST00000571688 | 11553533 | 11553689 | Frame-shift |
| ENST00000574763 | 11553533 | 11553689 | Frame-shift |
| ENST00000576036 | 11553533 | 11553689 | Frame-shift |
| ENST00000622633 | 11553533 | 11553689 | Frame-shift |
Top |
Infer the effects of exon skipping event on protein functional features for LITAF |
p-ENSG00000189067_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 |
| 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 |
| 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 |
| 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 |
Top |
3'-UTR located exon skipping events that lost miRNA binding sites in LITAF |
| 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 |
| Mayo | ENST00000574763 | 11575406 | 11575586 | hsa-miR-4677-5p | chr16:11575551-11575558 | 8mer-1a | chr16:11575551-11575574 | 170.00 | -25.01 |
| Mayo | ENST00000574763 | 11575406 | 11575586 | hsa-miR-615-5p | chr16:11575509-11575516 | 8mer-1a | chr16:11575493-11575516 | 158.00 | -31.87 |
| Mayo | ENST00000574763 | 11575406 | 11575586 | hsa-miR-1269b | chr16:11575545-11575552 | 8mer-1a | chr16:11575533-11575553 | 162.00 | -19.76 |
| Mayo | ENST00000574763 | 11575406 | 11575586 | hsa-miR-1288-3p | chr16:11575544-11575551 | 8mer-1a | chr16:11575533-11575553 | 162.00 | -19.76 |
| Mayo | ENST00000574763 | 11575406 | 11575586 | hsa-miR-1269a | chr16:11575545-11575552 | 8mer-1a | chr16:11575533-11575553 | 162.00 | -19.76 |
| Mayo | ENST00000574763 | 11575406 | 11575586 | hsa-miR-92a-2-5p | chr16:11575512-11575519 | 8mer-1a | chr16:11575507-11575528 | 146.00 | -19.61 |
| ROSMAP | ENST00000574763 | 11575406 | 11575586 | hsa-miR-4677-5p | chr16:11575551-11575558 | 8mer-1a | chr16:11575551-11575574 | 170.00 | -25.01 |
| ROSMAP | ENST00000574763 | 11575406 | 11575586 | hsa-miR-615-5p | chr16:11575509-11575516 | 8mer-1a | chr16:11575493-11575516 | 158.00 | -31.87 |
| ROSMAP | ENST00000574763 | 11575406 | 11575586 | hsa-miR-1269b | chr16:11575545-11575552 | 8mer-1a | chr16:11575533-11575553 | 162.00 | -19.76 |
| ROSMAP | ENST00000574763 | 11575406 | 11575586 | hsa-miR-1288-3p | chr16:11575544-11575551 | 8mer-1a | chr16:11575533-11575553 | 162.00 | -19.76 |
| ROSMAP | ENST00000574763 | 11575406 | 11575586 | hsa-miR-1269a | chr16:11575545-11575552 | 8mer-1a | chr16:11575533-11575553 | 162.00 | -19.76 |
| ROSMAP | ENST00000574763 | 11575406 | 11575586 | hsa-miR-92a-2-5p | chr16:11575512-11575519 | 8mer-1a | chr16:11575507-11575528 | 146.00 | -19.61 |
Top |
SNVs in the skipped exons for LITAF |
| - 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 |
Top |
AD stage-associated exon skippint events for LITAF |
| 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 |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for LITAF |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
Top |
Correlation with RNA binding proteins (RBPs) for LITAF |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
Top |
RelatedDrugs for LITAF |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
Top |
RelatedDiseases for LITAF |
| 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)
|