Outputs
The cellmaps_hierarchyeval tool produces several output files within the specified directory. These files are the results of the enrichment analysis, as well as, logs and essential metadata.
Enriched Hierarchy and Parent Network
The enriched hierarchy and parent network are provided in CX2 format:
hierarchy.cx2:This is the enriched hierarchy network file that integrates the results of the enrichment analysis into the hierarchy, formatted in CX2.
Example of annotated node in the hierarchy (“HCX::members” value was removed for readability):
{
"id": 226,
"v": {
"CD_MemberList": "LRRFIP2 CNN3 SEPTIN5 TNNC1 SEPTIN7 FAM216A GPX8 PRKRIP1 ACTN4 SPRYD3 LSM6 CDC42EP4 SPECC1L BZW2 FRMD1 HTRA1 SZT2 BBOX1 BRICD5 MYH9 PDRG1 TPM3 RAI14 LIMCH1 CTPS1 SIPA1L1 SEPTIN9 NEXN APPL1 LUZP1 WASHC3 PPP1R12A SEPTIN3 SEPTIN10 GABRA3 TAX1BP3 NCOA5 GSN MAP2 ATP6V1H DMWD",
"CD_MemberList_Size": 41,
"CD_MemberList_LogSize": 5.358,
"CD_AnnotatedMembers": "",
"CD_AnnotatedMembers_Size": 0,
"CD_AnnotatedMembers_Overlap": 0.0,
"CD_AnnotatedMembers_Pvalue": 0.0,
"HiDeF_persistence": 81,
"CD_CommunityName": "C5044",
"CD_Labeled": true,
"HCX::isRoot": false,
"HCX::members": [],
"CORUM_terms": "",
"CORUM_FDRs": "",
"CORUM_jaccard_indexes": "",
"CORUM_overlap_genes": "",
"GO_CC_terms": "GO:0031105|GO:0005940|GO:0032156",
"GO_CC_descriptions": "septin complex|septin ring|septin cytoskeleton",
"GO_CC_FDRs": "3.150973655449002e-07|3.150973655449002e-07|6.709368907329383e-07",
"GO_CC_jaccard_indexes": "0.11904761904761904|0.11904761904761904|0.11627906976744186",
"GO_CC_overlap_genes": "SEPTIN5,SEPTIN3,SEPTIN10,SEPTIN9,SEPTIN7|SEPTIN5,SEPTIN3,SEPTIN10,SEPTIN9,SEPTIN7|SEPTIN5,SEPTIN3,SEPTIN10,SEPTIN9,SEPTIN7",
"HPA_terms": "Actin filaments",
"HPA_FDRs": "6.450286324867403e-58",
"HPA_jaccard_indexes": "0.375",
"HPA_overlap_genes": "TPM3,BRICD5,CTPS1,SEPTIN5,SEPTIN3,GPX8,MYH9,SEPTIN10,CNN3,LUZP1,BBOX1,SPECC1L,PRKRIP1,LSM6,SEPTIN7,PPP1R12A,BZW2,LRRFIP2,LIMCH1,FRMD1,CDC42EP4,DMWD,NCOA5,PDRG1,FAM216A,SIPA1L1,NEXN,SZT2,TNNC1,SPRYD3,ATP6V1H,SEPTIN9,GSN,RAI14,ACTN4,TAX1BP3",
"n": "C5044",
"r": "C5044"
}
}
hierarchy_parent.cx2:The reference parent network from which the hierarchy was generated, formatted in CX2. Copy from input.
Node Attributes
The attributes for each node within the enriched hierarchy:
hierarchy_node_attributes.tsv:A TSV file containing attributes for each node, which includes information such as enriched terms, their descriptions, and related statistical data.
name represents CD_MemberList CD_MemberList_Size CD_MemberList_LogSize CD_AnnotatedMembers CD_AnnotatedMembers_Size CD_AnnotatedMembers_Overlap CD_AnnotatedMembers_Pvalue HiDeF_persistence CD_CommunityName CD_Labeled HCX::isRoot HCX::members CORUM_terms CORUM_FDRs CORUM_jaccard_indexes CORUM_overlap_genes GO_CC_terms GO_CC_descriptions GO_CC_FDRs GO_CC_jaccard_indexes GO_CC_overlap_genes HPA_terms HPA_FDRs HPA_jaccard_indexes HPA_overlap_genes
C5044 C5044 LRRFIP2 CNN3 SEPTIN5 TNNC1 SEPTIN7 FAM216A GPX8 PRKRIP1 ACTN4 SPRYD3 LSM6 CDC42EP4 SPECC1L BZW2 FRMD1 HTRA1 SZT2 BBOX1 BRICD5 MYH9 PDRG1 TPM3 RAI14 LIMCH1 CTPS1 SIPA1L1 SEPTIN9 NEXN APPL1 LUZP1 WASHC3 PPP1R12A SEPTIN3 SEPTIN10 GABRA3 TAX1BP3 NCOA5 GSN MAP2 ATP6V1H DMWD 41 5.358 0 0 0 81 C5044 TRUE FALSE [4002, 92, 4446, 3572, 36, 2324, 4131, 3546, 1008, 294, 3722, 4786, 1923, 4241, 4756, 2307, 4804, 4970, 2326, 35, 1009, 4110, 633, 4169, 2733, 4858, 4775, 4963, 2368, 287, 1215, 4440, 3016, 2986, 4927, 290, 3566, 632, 1033, 289, 4262] GO:0031105|GO:0005940|GO:0032156 septin complex|septin ring|septin cytoskeleton 3.150973655449002e-07|3.150973655449002e-07|6.709368907329383e-07 0.11904761904761904|0.11904761904761904|0.11627906976744186 SEPTIN5,SEPTIN3,SEPTIN10,SEPTIN9,SEPTIN7|SEPTIN5,SEPTIN3,SEPTIN10,SEPTIN9,SEPTIN7|SEPTIN5,SEPTIN3,SEPTIN10,SEPTIN9,SEPTIN7 Actin filaments 6.45E-58 0.375 TPM3,BRICD5,CTPS1,SEPTIN5,SEPTIN3,GPX8,MYH9,SEPTIN10,CNN3,LUZP1,BBOX1,SPECC1L,PRKRIP1,LSM6,SEPTIN7,PPP1R12A,BZW2,LRRFIP2,LIMCH1,FRMD1,CDC42EP4,DMWD,NCOA5,PDRG1,FAM216A,SIPA1L1,NEXN,SZT2,TNNC1,SPRYD3,ATP6V1H,SEPTIN9,GSN,RAI14,ACTN4,TAX1BP3
C5285 C5285 NAA15 NAA16 NAA50 HYPK 4 2 0 0 0 19 C5285 TRUE FALSE [2258, 2257, 2565, 4598] GO:0031415|GO:0031414 NatA complex|N-terminal protein acetyltransferase complex 1.943122029855394e-07|2.2862713150320575e-06 0.6|0.3333333333333333 NAA15,NAA16,NAA50|NAA15,NAA16,NAA50
Logs and Metadata
error.log:Contains error messages and exceptions that might have occurred during execution.
output.log:Provides detailed logs about the steps performed and their outcomes.
ro-crate-metadata.json:Metadata in RO-Crate format, a community effort to establish a lightweight approach to packaging research data with their metadata.
It contains general information about the data i.a. ID, Type, Name, Description, contextual definitions, Software detail, as well as datasets details of each individual part of the data.
For example, the metadata for the content of hierarchy.cx provides unique id, context, type, url, name, keywords, etc. The url can be used to view the hierarchy in Cytoscape Web.
{ "@id": "00000000-0000-0000-0000-000000000000:dataset::4.hierarchy", "@context": { "@vocab": "https://schema.org/", "evi": "https://w3id.org/EVI#" }, "metadataType": "https://w3id.org/EVI#Dataset", "url": "https://idekerlab.ndexbio.org/cytoscape/network/aaaaaaaa-aaaa-aaaa-aaaa-aaaaaaaaaaaa", "name": "Output Dataset", "keywords": [ "CM4AI", "Example", "interactome", "ppi", "network", "CX2", "file", "hierarchy", "network", "HCX" ], "description": "CM4AI Example Example input dataset AP-MS edgelist download|IF microscopy merged embedding AP-MS edgelist download|IF microscopy Example input dataset hierarchy model Hierarchy network file", "author": "cellmaps_generate_hierarchy", "datePublished": "2023-09-21", "version": "0.1.0a11", "associatedPublication": null, "additionalDocumentation": null, "format": "HCX", "schema": {}, "generatedBy": [], "derivedFrom": [], "usedBy": [], "contentUrl": "path/hierarchy.hcx" }
Additionally, it contains Computation Details, name, description, Run By etc.