Question: About low temperature insect transcriptome KEGG passway results
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gravatar for Kurban
3.7 years ago by
Kurban170
china/Urumqi/xinjiang academy of animal scinces
Kurban170 wrote:

Hello every one we have used a overwintering insect species as a treatment group and laboratory reared counterpart as a control (normal photoperiod and 30℃) conducted RNA-seq, each group has a 3 biological replicates, and the sample is not a model species. After we finished the DEGs analysis we did the KEGG passway enrichment analysis to most up regulated genes in the experiment. But after the analysis we realized that most of the enriched passways related to the human disease and cancers. The result shown as below:

Term Database ID Input number Background number P-Value

Malaria KEGG PATHWAY ko05144 10 43 1.83E-06

ECM-receptor interaction KEGG PATHWAY ko04512 18 191 2.70E-05

Leukocyte transendothelial migration KEGG PATHWAY ko04670 13 146 0.000559142

Focal adhesion KEGG PATHWAY ko04510 25 426 0.00105033

Pathways in cancer KEGG PATHWAY ko05200 25 456 0.002503296

PI3K-Akt signaling pathway KEGG PATHWAY ko04151 26 496 0.003662382

Amoebiasis KEGG PATHWAY ko05146 12 163 0.003935047

Hippo signaling pathway - fly KEGG PATHWAY ko04391 11 145 0.004579537

Estrogen signaling pathway KEGG PATHWAY ko04915 17 288 0.005862042

Arrhythmogenic right ventricular cardiomyopathy (ARVC) KEGG PATHWAY ko05412 10 132 0.006754881

Proteoglycans in cancer KEGG PATHWAY ko05205 23 448 0.007551182

Complement and coagulation cascades KEGG PATHWAY ko04610 7 75 0.00809103

Hypertrophic cardiomyopathy (HCM) KEGG PATHWAY ko05410 10 137 0.008537237

Dilated cardiomyopathy KEGG PATHWAY ko05414 10 145 0.012112799

Platelet activation KEGG PATHWAY ko04611 13 215 0.012404795

Transcriptional misregulation in cancer KEGG PATHWAY ko05202 10 166 0.026779391

MicroRNAs in cancer KEGG PATHWAY ko05206 12 218 0.029204877

Tight junction KEGG PATHWAY ko04530 12 218 0.029204877

Regulation of actin cytoskeleton KEGG PATHWAY ko04810 15 299 0.032055192

Toxoplasmosis KEGG PATHWAY ko05145 13 259 0.043595147

Hippo signaling pathway KEGG PATHWAY ko04390 11 207 0.043746375

MAPK signaling pathway KEGG PATHWAY ko04010 16 341 0.044860622

Small cell lung cancer KEGG PATHWAY ko05222 8 133 0.044958569

Cardiac muscle contraction KEGG PATHWAY ko04260 9 159 0.047184137

Antigen processing and presentation KEGG PATHWAY ko04612 13 264 0.049090165

from the result we could it see much enriched pathways related to overwintering, diapause, metabolism cryoprotectants and chitin metabolism. why this result? now we are confused to how to interpret the result here. please give me some suggestions!

ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by Kurban170
1

Maybe you should explain more about your experiment. For example, how did you annotate your genes? How did you do the enrichment? Which tool? What are the p-values? Are they corrected for multiple testing?

It is true that the pathways are biased towards human diseases and cancer, that's because most research is done on humans.

ADD REPLYlink written 3.7 years ago by Benn7.9k

Do you know if relevant pathways even exist in KEGG ? Also to consider is to which model organisms you map your species genes. Human genes are probably the most annotated but as you found out most of these annotations are disease-biased. Also as far as I know humans don't generally do diapause so I think it highly unlikely that by using human genes, you'll find anything diapause-related. I would suggest instead to use model organisms such as C. elegans and/or Drosophila that do have diapause and to use GO annotations.

ADD REPLYlink written 3.7 years ago by Jean-Karim Heriche21k
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