Pathway Analysis

Poochon developed a novel pathway analysis tool called PROMICPATH. The PROMICPATH provides both 42 common pathways analysis services (available for human and mouse samples) and customized pathway analysis services. To ensure the integrity and reliability the PROMICPATH uses 10 groups of 400 housekeeping proteins to evaluate the completeness and variability of a proteome profile. An example of output of PROMICPATH analysis is illustrated below.

PA-101: Pathway Analysis

This service package is for 42 common cellular and signaling pathways analysis as well as evaluation of the completeness and variability of a proteome profile using Poochon PROMICPATH pathway analysis tools.

Price: $1000/pair of datasets

Turnaround time: 15 to 20 business days or less.

Service Description

Introduction of PROMICPATH:

Biological information flow from the DNA/genome to protein/proteome automatically regulates cell living status in response to internal or external signals. The genome encoding the proteome is relative static while the proteome is much more dynamic which allow the protein orchestrate all biological processes precisely, ranging from central metabolism to cell structure, maintenance, and replication. It is speculated that all biological processes (on/off) are regulated and operated by the dynamics of proteins such as modifications and changes in abundance. The regulation of different cellular functions has been categorized into a number of pathways, such as the Wnt signaling pathway and the TGF signaling pathway. In each pathway, the components are generally named according to their function, including ligands, receptors, activating regulators, inhibitory regulators, and effectors. To measure the activation strength of a pathway, the protein molecules that belong to ligands, receptors, activating regulators, or inhibitory regulators were grouped as the pathway protein ontology chain (POC), and their relative abundances (ppm) were summed. Based on the summed abundance of each POC, the activation strength or activation status of a pathway could be compared between two proteome profiles. Based on these scientific assumptions Poochon developed a novel pathway tool called PROMICPATH. The PROMICPATH provides both 42 common pathways analysis services (available for human and mouse samples) and customized pathway analysis services.

Deliverables

  • A list of identified proteins with relative abundance
  • All identified peptides sequences for each proteins
  • Common pathway analysis results
  • Method description

Suitable Sample Type

  • MS raw files

42 common pathways are listed:

  1. Housekeeping Proteins and Complexes
  2. Cell cycle checkpoint
  3. Apoptosis evaluation
  4. Chromatin Modification
  5. DNA replication and Repair
  6. Transcriptional Regulation
  7. Translation
  8. Folding-sorting-degradation
  9. Extracellular Matrix – Matrisome
  10. Cellular Community
  11. Cell motility-Regulation of actin cytoskeleton
  12. PI3K/AKT
  13. RAS
  14. Notch
  15. Hedgehog
  16. MAPK
  17. STAT/JAK
  18. TGF
  19. WNT
  20. HIPPO
  21. NF-kappa pathway
  22. GPCR signaling pathway
  23. p53 Pathway
  24. Calcium Signaling
  25. Nucleotide Metabolism
  26. Amino Acid metabolism
  27. Carbohydrate metabolism
  28. Lipid metabolism
  29. Energy Metabolism
  30. Transport and catabolism
  31. Warburg Effect
  32. Excretory system
  33. Digestive system
  34. Heat Shock Protein Pathway
  35. Necroptosis-pathway
  36. Angiogenesis
  37. Epithelial Mesenchymal Transition (EMT)
  38. Signaling pathways regulating pluripotency of stem cells
  39. Autophagy Regulation
  40. Ubiquitination
  41. ER-related pathway
  42. Free Radicals

Price: Contact us for a quote!