hmgc1 (Collection)

Project:

HHS

Project (Entity type)

Dcc Asset:

datapackage.zip

Processed File (Entity type)

Dcc:

HMP

DCC (Entity type)

Has Time Series Data:false

Description:Clustered gene index: This collection contains a non-redundant catalog of bacterial genes by body site. This was done by clustering the HMP gene indices (gene predictions from the 690 samples that passed QC, refer "hmgi1" collection), using the same identity parameter used by the Metahit project to cluster their human intestinal tract data (Qin et al, 2010. Nature, 464:59). Genes were compared at a 95% identity cut-off and those overlapping were considered redundant and removed. The non-redundant gene set contains a total of 15,006,602 genes across all 15 body sites. Attention: the gene counts available here differ from what was originally reported in the publication. This is due to the fact that samples that did not pass our assembly QC had not been removed prior to initial clustering. Clustering has been rerun and the data is now accurate. Gene clusters were annotated for carbohydrate-active enzymes, using the CAZy database. This annotation is available here, as a gff3 file.

Abbreviation:hmgc1

Results found

Linked to

	Label	Description
	hmgc1 stool Collection (Entity type)	This collection contains a non-redundant catalog of bacterial genes from stool samples. This was don...
	hmgc1 anterior nares Collection (Entity type)	This collection contains a non-redundant catalog of bacterial genes from anterior_nares samples. Thi...
	hmgc1 subgingival plaque Collection (Entity type)	This collection contains a non-redundant catalog of bacterial genes from subgingival_plaque samples....
	hmgc1 buccal mucosa Collection (Entity type)	This collection contains a non-redundant catalog of bacterial genes from buccal_mucosa samples. This...
	hmgc1 attached keratinized gingiva Collection (Entity type)	This collection contains a non-redundant catalog of bacterial genes from attached_keratinized_gingiv...
	hmgc1 tongue dorsum Collection (Entity type)	This collection contains a non-redundant catalog of bacterial genes from tongue_dorsum samples. This...
	hmgc1 supragingival plaque Collection (Entity type)	This collection contains a non-redundant catalog of bacterial genes from supragingival_plaque sample...
	hmgc1 right retroauricular crease Collection (Entity type)	This collection contains a non-redundant catalog of bacterial genes from right_retroauricular_crease...
	hmgc1 vaginal introitus Collection (Entity type)	This collection contains a non-redundant catalog of bacterial genes from vaginal_introitus samples. ...
	hmgc1 saliva Collection (Entity type)	This collection contains a non-redundant catalog of bacterial genes from saliva samples. This was do...

hmgc1 stool

Collection (Entity type)

This collection contains a non-redundant catalog of bacterial genes from stool samples. This was don...

hmgc1 anterior nares

Collection (Entity type)

This collection contains a non-redundant catalog of bacterial genes from anterior_nares samples. Thi...

hmgc1 subgingival plaque

Collection (Entity type)

This collection contains a non-redundant catalog of bacterial genes from subgingival_plaque samples....

hmgc1 buccal mucosa

Collection (Entity type)

This collection contains a non-redundant catalog of bacterial genes from buccal_mucosa samples. This...

hmgc1 attached keratinized gingiva

Collection (Entity type)

This collection contains a non-redundant catalog of bacterial genes from attached_keratinized_gingiv...

hmgc1 tongue dorsum

Collection (Entity type)

This collection contains a non-redundant catalog of bacterial genes from tongue_dorsum samples. This...

hmgc1 supragingival plaque

Collection (Entity type)

This collection contains a non-redundant catalog of bacterial genes from supragingival_plaque sample...

hmgc1 right retroauricular crease

Collection (Entity type)

This collection contains a non-redundant catalog of bacterial genes from right_retroauricular_crease...

hmgc1 vaginal introitus

Collection (Entity type)

This collection contains a non-redundant catalog of bacterial genes from vaginal_introitus samples. ...

hmgc1 saliva

Collection (Entity type)

This collection contains a non-redundant catalog of bacterial genes from saliva samples. This was do...

DISPLAY PER PAGE

CFDE Workbench

Consortium

Community

Resources

@CFDE Workbench 2026

The CFDE Workbench is actively being developed and maintained by the CFDE Data Resource Center (DRC).The DRC is funded by OT2OD036435 from the Common Fund at the National Institutes of Health.

Consortium

Community

Resources

CFDE Workbench

The CFDE Workbench is actively being developed and maintained by the CFDE Data Resource Center (DRC).The DRC is funded by OT2OD036435 from the Common Fund at the National Institutes of Health.

@CFDE Workbench 2026

This repository is under review for potential modification in compliance with Administration directives.