Ötzi the Iceman
The glacier mummy Ötzi is Europe’s oldest known natural human mummy. It is the preserved body of a man that lived 5,300 years ago. The mummy was found in September 1991 in the Ötztal Alps near the border between Austria and Italy by two mountaineers. Since its discovery the corpse has been extensively examined and has been main focus in various studies  .
In a recently published study  scientists examined the proteome of two distinct brain samples. One of these samples contained a dark spot that is assumed to be coagulated blood from an injury to brain or head. Amongst other methods the researchers performed an enrichment analysis based on the obtained proteins using the first version of GeneTrail . This analysis indeed revealed a significant accumulation of proteins related to stress response and wound healing, which might reinforce the assumption about the brain injury. Additionally, many proteins were identified that are known to be highly abundant or even exclusively expressed in the brain tissue.
In this use case we analyze the proteomics data, that was obtained from the brain of Ötzi the Iceman . We used GeneTrail 2 to perform an ORA enrichment analogously to the one performed in the paper. As a reference set we used all human proteins that are annotated in the UniProt database . We try to verify all results of the paper and to complement them by using futher databases GeneTrail2 provides in addition to the former version.
In this use case we want to analyze a unordered set of proteins, i.e. all proteins that could be detected in the mass spectrometry of the two brain samples. As we have no information about the extend of regulation for each protein, an Over-Representation Analysis (ORA) has to be performed. This approach is based on the hypergeometric distribution and can be used to test if our set of proteins is significantly more or less present in a biological category than expected by chance.
- Test set: Unordered list of proteins (mass spectrometry (MS))
- Reference set: All proteins (Uniprot)
- Algorithm: Over-representation analysis (ORA)
- P-value adjustment method: Benjamini-Hochberg
The following slideshow depicts the different analysis steps of the GeneTrail2 workflow (expert mode).
In this section, we describe our findings and compare them to the results of Keller et. al .
In their paper the scientists described an enrichment of neurological disorders, like Alzheimers, Huntingtons, and Parkinsons diseases, which indicated that the found proteins are related to neurological functions. In our analysis we find the same categories to be significantly enriched.
Confirming this observation, we additionally found categories that are involved in the neuronal system and the release of several neurotransmitters, like Acetylcholine, Dopamine, Norepinephrine, or Serotonin.
Stress response and wound healing
Furthermore, the researchers found proteins that are related to stress response and wound healing. In our analysis we achieved similar results. We observe an enrichment in the regulation of response to oxidative stress, the regulation of wound healing and regulation of blood coagulation. These insights reinforce the assumption about the brain injury.
In addition to the results of the paper, we find categories that might indicate a hypothermia of the body. We detect an enriched cellular response to heat stress and regulation of HSF-1-mediated heat shock response, which are known to be expressed by stress induced by exposure to cold temperatures . We also see an enrichment of oxidative phosphorylation that has been reported in the brain during the initial period of a hypothermia . To complement these findings even more, we see a regulation of the heart rate and heart contraction which are also known symptoms of a hypothermia .
In summary, all results show that GeneTrail 2 is well equipped to analyze proteomics data. We were able to confirm the observations of Keller et al.  and to reinforce their assumptions. Additionally, we found several categories that seem to indicate a hypothermia.
- Vom Leben und Sterben des Ötztaler Gletschermannes: Neue medizinische und archäologische Erkenntnisse Germania Zabern
- The man in the ice Hachette UK
- Paleoproteomic study of the Iceman’s brain tissue Cellular and Molecular Life Sciences Springer
- GeneTrail—advanced gene set enrichment analysis Nucleic acids research Oxford Univ Press (View online)
- Activities at the universal protein resource (UniProt) Nucleic acids research Oxford Univ Press
- Characterization and regulation of cold-induced heat shock protein expression in mouse brown adipose tissue American Journal of Physiology-Regulatory, Integrative and Comparative Physiology Am Physiological Soc
- [Oxidative phosphorylation in the brain and liver of warm-blooded animals during hypothermy and the initial period of self-warming] Voprosy meditsinskoi khimii
- Accidental hypothermia New England Journal of Medicine Mass Medical Soc