Valuable_Genests.md

In zzwch/convgene: This package is designed to conveniently convert gene between human and mouse.

Valuable Gene set

• Transcription Factor

• AnimalTFDB (v3.0)

  • AnimalTFDB is a comprehensive database including classification and annotation of genome-wide transcription factors (TFs), and transcription cofactors in 97 animal genomes. The TFs are further classified into 73 families based on their DNA-binding domain (DBD) and cofactors are classified into 83 families and 6 categories.

• Surface Molecule

• Cell Surface Protein Atlas
  • A Mass Spectrometric-Derived Cell Surface Protein Atlas

• cluster of differentiation molecules

  • Gene group: CD molecules from HGNC

• Cell type markers/Feature genes

• PanglaoDB (metadata on Github) IT IS SO GREAT!

  • Cell type gene expression markers

  This is a list of gene expression markers are used to define cell types. Green rows indicate canonical markers (classical markers used to define the cell type).

  Summary: 8286 associations (178 cell types, 4679 gene symbols, 29 tissues); Last updated: 27/03/2020 10:44:00 CET

  • Ubiquitousness index

  Ubiquitousness Index (0-1). 0 indicates the gene is not expressed in any cell cluster and 1 (maximum) indicates that the gene is expressed in all cell clusters. Can be useful for spotting genes that are likely to be housekeeping genes.

  • Publications in the scientific literature (Yes, it's not markers 😂)

  This list contains 3030 papers covering various topics of single cell sequencing. It is compiled by searching for keywords in abstracts and titles using data from ftp://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/ and ftp://ftp.ncbi.nlm.nih.gov/pubmed/baseline/. It is automatically updated daily. Rows in blue indicate papers in "high impact" journals.

• Arterial

  • Dll4, Igfbp3, Unc5b, Gja4, Hey1, Mecom, Efnb2, Epas1, Vegfc, Cxcr4, Bmx, Gja5

  Note arterial genes might be of spatiotemporal heterogeneity

• Venous

  • Nr2f2, Nrp2, Aplnr

• Hematopoietic

• Endothelial

• Mescenchymal

• Cell cycle

  • G1/S
  • G2/M

• Cell-cell interaction

• Ligand & Receptor

  • [2015-NC] A draft network of ligand–receptor-mediated multicellular signalling in human

  It also gave 6 consensus classes for all genes.

• CellPhoneDB

  • CellPhoneDB is a publicly available repository of curated receptors, ligands and their interactions.

• Angiocrine/Secreted

• [2015-NC] A draft network of ligand–receptor-mediated multicellular signalling in human

• Subcategory

  • Cytokine, chemokine & growth factor
  • see MSigDB
  • Signaling (or Ligand)
  • see Ligand & Receptor
  • Extracellular Matrix (ECM)
  • see GO term

• Metabolism

• genes included in all metabolic pathways

• MSigDB genesets

The 25724 gene sets in the Molecular Signatures Database (MSigDB) are divided into 8 major collections, and several sub-collections. - H (hallmark gene sets, 50 gene sets) - C1 (positional gene sets, 299 gene sets) - C2 (curated gene sets, 5529 gene sets) - CGP (chemical and genetic perturbations, 3297 gene sets) - CP (Canonical pathways, 2232 gene sets) - CP:BIOCARTA (BioCarta gene sets, 289 gene sets) - CP:KEGG (KEGG gene sets, 186 gene sets) - CP:PID (PID gene sets, 196 gene sets) - CP:REACTOME (Reactome gene sets, 1532 gene sets) - C3 (regulatory target gene sets, 3735 gene sets) - MIR (microRNA targets, 2598 gene sets) - MIR:MIR_Legacy (Legacy microRNA targets, 221 gene sets) - MIR:MIRDB (MIRDB microRNA targets, 2377 gene sets) - TFT (All transcription factor targets, 1137 gene sets) - TFT:GTRD (GTRD transcription factor targets, 526 gene sets) - TFT:TFT_Legacy (Legacy transcription factor targets, 611 gene sets) - C4 (computational gene sets, 858 gene sets) - CGN (cancer gene neighborhoods, 427 gene sets) - CM (cancer modules, 431 gene sets) - C5 (GO gene sets, 10192 gene sets) - BP (GO biological process, 7530 gene sets) - CC (GO cellular component, 999 gene sets) - MF (GO molecular function, 1663 gene sets) - C6 (oncogenic signatures, 189 gene sets) - C7 (immunologic signatures, 4872 gene sets)

zzwch/convgene documentation built on July 11, 2021, 9:41 a.m.