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ImMSigDb

ImMSigDb is a NoSQL document-oriented database created using Cloud Firestore Intro to Firestore or wiki of this git repo .

We maintain three lists for data management:

• Served: Data currently up in Firestore, versioned. This data set will be bi-annually updated.
• Staged: Data awaiting cleaning before being uploaded.
• Enstaged: Data waiting to be staged, which may need extraction.

All data after the enstaged phase is versioned control with assigned model categories (pathways, gene sets).

Served in Current Data Release

V 0.0.0: Eight resources updated.

Click on the link to learn about the served datasets in current data release!

• LI BTMs
• Chaussabel BTMs
• CELL MARKER DB (Immune cells only)
• Monaco et al 2019
• IRIS Cell markers
• Villani et al,2018
• DICE Schmiedel et.al
• XCell

Staged

• Cell Pedia
• InnateDB models

Enstaged

• Etienne Becht-2016
• Gabriela Bindea--Immunity-2013
• Nature immunology review John Wherry, U penn, immunotherapy gene set

Suggested

• Diego Calderon--Landscape of stimulation-responsive chromatin across diverse human immune cells--Nature Genetics--2019
• Biola M. Javierre--Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters--2016
• Noa Novershtern-Densely interconnected transcriptional circuits control cell states in human hematopoiesis--2012 Cell
• Human Cell Atlas
• scRNA seq---Pipeline (GitHub--pipeline--working) ---prediction --data sets ---- using GRN inference algorithms

** Check scrNA seq Data here ** https://www.ebi.ac.uk/gxa/sc/experiments

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Ontologies to discuss

• CellPedia--https://stemcellinformatics.org has taxonomy and markers data

• Cell Ontology--https://bioportal.bioontology.org/ontologies/CL

  This ontology is not organism specific it covers cell types from prokaryotes to mammals.

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