Metascape Gene List Analysis Report
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Bar Graph Summary
Gene Lists
User-provided gene identifiers are first converted into their corresponding H. sapiens Entrez gene IDs using the latest version of the database (last updated on 2022-04-22). If multiple identifiers correspond to the same Entrez gene ID, they will be considered as a single Entrez gene ID in downstream analyses. The gene lists are summarized in Table 1.
Table 1. Statistics of input gene lists.
Name |
Total |
Unique |
MyList |
47 |
47 |
Gene Annotation
The following are the list of annotations retrieved from the latest version of the database (last updated on 2022-04-22) (Table 2).
Table 2. Gene annotations extracted
Name |
Type |
Description |
Gene Symbol |
Description |
Primary HUGO gene symbol. |
Description |
Description |
Short description. |
Biological Process (GO) |
Function/Location |
Descriptions summarized based on gene ontology database, where up to three most informative GO terms are kept. |
Kinase Class (UniProt) |
Function/Location |
Detailed kinase classes. |
Protein Function (Protein Atlas) |
Function/Location |
Protein Function (Protein Atlas) |
Subcellular Location (Protein Atlas) |
Function/Location |
Sucellular Location (Protein Atlas) |
Drug (DrugBank) |
Genotype/Phenotype/Disease |
Drug information for the given gene as target. |
Canonical Pathways
|
Ontology |
Canonical Pathways
|
Hallmark Gene Sets
|
Ontology |
Hallmark Gene Sets
|
Pathway and Process Enrichment Analysis
For each given gene list, pathway and process enrichment analysis has been carried out with the following ontology sources: KEGG Pathway, GO Biological Processes, Reactome Gene Sets, Canonical Pathways, Cell Type Signatures, CORUM, TRRUST, DisGeNET, PaGenBase, Transcription Factor Targets, WikiPathways and COVID. All genes in the genome have been used as the enrichment background. Terms with a p-value < 0.01, a minimum count of 3, and an enrichment factor > 1.5 (the enrichment factor is the ratio between the observed counts and the counts expected by chance) are collected and grouped into clusters based on their membership similarities. More specifically, p-values are calculated based on the cumulative hypergeometric distribution
2, and q-values are calculated using the Benjamini-Hochberg procedure to account for multiple testings
3. Kappa scores
4 are used as the similarity metric when performing hierarchical clustering on the enriched terms, and sub-trees with a similarity of > 0.3 are considered a cluster. The most statistically significant term within a cluster is chosen to represent the cluster.
Table 3. Top 9 clusters with their representative enriched terms (one per cluster). "Count" is the number of genes in the user-provided lists with membership in the given ontology term. "%" is the percentage of all of the user-provided genes that are found in the given ontology term (only input genes with at least one ontology term annotation are included in the calculation). "Log10(P)" is the p-value in log base 10. "Log10(q)" is the multi-test adjusted p-value in log base 10.
GO |
Category |
Description |
Count |
% |
Log10(P) |
Log10(q) |
GO:0034645 |
GO Biological Processes |
cellular macromolecule biosynthetic process |
7 |
14.89 |
-3.83 |
0.00 |
WP4255 |
WikiPathways |
Non-small cell lung cancer |
3 |
6.38 |
-3.71 |
0.00 |
hsa05203 |
KEGG Pathway |
Viral carcinogenesis |
4 |
8.51 |
-3.54 |
0.00 |
GO:0140352 |
GO Biological Processes |
export from cell |
5 |
10.64 |
-3.26 |
0.00 |
GO:0016032 |
GO Biological Processes |
viral process |
4 |
8.51 |
-3.22 |
0.00 |
GO:0033674 |
GO Biological Processes |
positive regulation of kinase activity |
5 |
10.64 |
-3.02 |
0.00 |
hsa04145 |
KEGG Pathway |
Phagosome |
3 |
6.38 |
-2.76 |
0.00 |
GO:0016241 |
GO Biological Processes |
regulation of macroautophagy |
3 |
6.38 |
-2.72 |
0.00 |
GO:0000278 |
GO Biological Processes |
mitotic cell cycle |
5 |
10.64 |
-2.61 |
0.00 |
To further capture the relationships between the terms, a subset of enriched terms have been selected and rendered as a network plot, where terms with a similarity > 0.3 are connected by edges. We select the terms with the best p-values from each of the 20 clusters, with the constraint that there are no more than 15 terms per cluster and no more than 250 terms in total. The network is visualized using
Cytoscape5, where each node represents an enriched term and is colored first by its cluster ID (Figure 2.a) and then by its p-value (Figure 2.b). These networks can be interactively viewed in Cytoscape through the .cys files (contained in the Zip package, which also contains a publication-quality version as a PDF) or within a browser by clicking on the web icon. For clarity, term labels are only shown for one term per cluster, so it is recommended to use Cytoscape or a browser to visualize the network in order to inspect all node labels. We can also export the network into a PDF file within Cytoscape, and then edit the labels using Adobe Illustrator for publication purposes. To switch off all labels, delete the "Label" mapping under the "Style" tab within Cytoscape, and then export the network view.
Figure 2. Network of enriched terms: (a) colored by cluster ID, where nodes that share the same cluster ID are typically close to each other; (b) colored by p-value, where terms containing more genes tend to have a more significant p-value.
Protein-protein Interaction Enrichment Analysis
For each given gene list, protein-protein interaction enrichment analysis has been carried out with the following databases: STRING
6, BioGrid
7, OmniPath
8, InWeb_IM
9.Only physical interactions in STRING (physical score > 0.132) and BioGrid are used (
details). The resultant network contains the subset of proteins that form physical interactions with at least one other member in the list. If the network contains between 3 and 500 proteins, the Molecular Complex Detection (MCODE) algorithm
10 has been applied to identify densely connected network components. The MCODE networks identified for individual gene lists have been gathered and are shown in Figure 3.
Pathway and process enrichment analysis has been applied to each MCODE component independently, and the three best-scoring terms by p-value have been retained as the functional description of the corresponding components, shown in the tables underneath corresponding network plots within Figure 3.
Quality Control and Association Analysis
Gene list enrichments are identified in the following ontology categories: Cell_Type_Signatures, DisGeNET, Transcription_Factor_Targets. All genes in the genome have been used as the enrichment background. Terms with a p-value < 0.01, a minimum count of 3, and an enrichment factor > 1.5 (the enrichment factor is the ratio between the observed counts and the counts expected by chance) are collected and grouped into clusters based on their membership similarities. The top few enriched clusters (one term per cluster) are shown in the Figure 4-6. The algorithm used here is the same as that is used for pathway and process enrichment analysis.
Figure 4. Summary of enrichment analysis in Cell Type Signatures11.
|
|
GO |
Description |
Count |
% |
Log10(P) |
Log10(q) |
M40025 |
BUSSLINGER DUODENAL DIFFERENTIATING STEM CELLS |
5 |
11.00 |
-4.00 |
-0.35 |
M41652 |
TRAVAGLINI LUNG PROXIMAL BASAL CELL |
6 |
13.00 |
-3.40 |
-0.21 |
M39217 |
ZHENG CORD BLOOD C8 PUTATIVE LYMPHOID PRIMED MULTIPOTENT PROGENITOR 2 |
3 |
6.40 |
-3.30 |
-0.19 |
M39263 |
HU FETAL RETINA BLOOD |
4 |
8.50 |
-3.00 |
-0.14 |
M39125 |
AIZARANI LIVER C24 EPCAM POS BILE DUCT CELLS 3 |
3 |
6.40 |
-2.50 |
0.00 |
M41651 |
TRAVAGLINI LUNG BASAL CELL |
3 |
6.40 |
-2.50 |
0.00 |
M40026 |
BUSSLINGER DUODENAL TRANSIT AMPLIFYING CELLS |
3 |
6.40 |
-2.50 |
0.00 |
M39175 |
MURARO PANCREAS MESENCHYMAL STROMAL CELL |
5 |
11.00 |
-2.40 |
0.00 |
M41670 |
TRAVAGLINI LUNG LYMPHATIC CELL |
3 |
6.40 |
-2.40 |
0.00 |
M41749 |
RUBENSTEIN SKELETAL MUSCLE NK CELLS |
3 |
6.40 |
-2.30 |
0.00 |
M40010 |
BUSSLINGER GASTRIC ISTHMUS CELLS |
4 |
8.50 |
-2.30 |
0.00 |
M41690 |
TRAVAGLINI LUNG BASOPHIL MAST 2 CELL |
4 |
8.50 |
-2.10 |
0.00 |
M41712 |
FAN OVARY CL10 PUTATIVE EARLY ATRESIA GRANULOSA CELL |
3 |
6.40 |
-2.00 |
0.00 |
M41689 |
TRAVAGLINI LUNG BASOPHIL MAST 1 CELL |
3 |
6.40 |
-2.00 |
0.00 |
|
Figure 5. Summary of enrichment analysis in DisGeNET12.
|
|
GO |
Description |
Count |
% |
Log10(P) |
Log10(q) |
C0740392 |
Infarction, Middle Cerebral Artery |
5 |
11.00 |
-5.50 |
-0.99 |
C0266568 |
Persistent Hyperplastic Primary Vitreous |
3 |
6.40 |
-4.70 |
-0.63 |
C2062441 |
Influenza A |
7 |
15.00 |
-4.60 |
-0.63 |
C0027708 |
Nephroblastoma |
7 |
15.00 |
-4.50 |
-0.63 |
C0279583 |
Childhood T Acute Lymphoblastic Leukemia |
4 |
8.50 |
-4.40 |
-0.63 |
C0337428 |
Fibrinogen assay |
3 |
6.40 |
-4.10 |
-0.36 |
C0024301 |
Lymphoma, Follicular |
6 |
13.00 |
-4.00 |
-0.36 |
C0007193 |
Cardiomyopathy, Dilated |
6 |
13.00 |
-3.90 |
-0.35 |
C0011853 |
Diabetes Mellitus, Experimental |
6 |
13.00 |
-3.80 |
-0.34 |
C1333015 |
Childhood Kidney Wilms Tumor |
5 |
11.00 |
-3.70 |
-0.31 |
C0006413 |
Burkitt Lymphoma |
6 |
13.00 |
-3.70 |
-0.30 |
C0038273 |
Stereotypic Movement Disorder |
4 |
8.50 |
-3.60 |
-0.30 |
C0035242 |
Respiratory Tract Diseases |
4 |
8.50 |
-3.60 |
-0.30 |
C0266464 |
Polymicrogyria |
4 |
8.50 |
-3.60 |
-0.30 |
C0036205 |
Sarcoidosis, Pulmonary |
3 |
6.40 |
-3.60 |
-0.30 |
C1384583 |
Congenital absence of germinal epithelium of testes |
3 |
6.40 |
-3.50 |
-0.30 |
C0032269 |
Pneumococcal Infections |
3 |
6.40 |
-3.50 |
-0.28 |
C0008149 |
Chlamydia Infections |
3 |
6.40 |
-3.50 |
-0.26 |
C1961099 |
Precursor T-Cell Lymphoblastic Leukemia-Lymphoma |
6 |
13.00 |
-3.30 |
-0.19 |
C0578038 |
Thin lips |
3 |
6.40 |
-3.30 |
-0.18 |
|
Figure 6. Summary of enrichment analysis in Transcription Factor Targets.
|
|
GO |
Description |
Count |
% |
Log10(P) |
Log10(q) |
M29968 |
FOXE1 TARGET GENES |
7 |
15.00 |
-3.90 |
-0.35 |
M30190 |
TAF9B TARGET GENES |
6 |
13.00 |
-3.60 |
-0.30 |
M9902 |
ELF1 Q6 |
4 |
8.50 |
-3.20 |
-0.15 |
M9431 |
AP1 Q6 |
4 |
8.50 |
-3.20 |
-0.15 |
M17769 |
STAT1 02 |
4 |
8.50 |
-3.10 |
-0.15 |
M5440 |
AP1 Q4 |
4 |
8.50 |
-3.10 |
-0.15 |
M14686 |
ELK1 01 |
4 |
8.50 |
-3.10 |
-0.15 |
M30015 |
HOXC13 TARGET GENES |
3 |
6.40 |
-3.00 |
-0.15 |
M30131 |
PSMB5 TARGET GENES |
4 |
8.50 |
-2.90 |
-0.05 |
M40783 |
ZNF549 TARGET GENES |
5 |
11.00 |
-2.60 |
0.00 |
M40826 |
CIC TARGET GENES |
4 |
8.50 |
-2.40 |
0.00 |
M11345 |
AP4 Q6 |
3 |
6.40 |
-2.30 |
0.00 |
M30045 |
LCORL TARGET GENES |
4 |
8.50 |
-2.30 |
0.00 |
M12298 |
CEBP Q2 |
3 |
6.40 |
-2.20 |
0.00 |
M3037 |
E2F1 Q6 01 |
3 |
6.40 |
-2.20 |
0.00 |
M5320 |
HIF1 Q5 |
3 |
6.40 |
-2.20 |
0.00 |
M17508 |
USF2 Q6 |
3 |
6.40 |
-2.10 |
0.00 |
M2146 |
STAT1 03 |
3 |
6.40 |
-2.10 |
0.00 |
M11921 |
NFKB Q6 |
3 |
6.40 |
-2.10 |
0.00 |
M30340 |
ZNF528 TARGET GENES |
5 |
11.00 |
-2.10 |
0.00 |
|
Reference
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