What is the exact meaning of Lineage？

[Siteng999]

Hello

I am very confused about the following question, can you tell me the exact meaning of Lineage?

I have performed five experimental conditions (Original, T1, T2, T3, T4) on the same cell tissue, for example root hair. I specified Original as "start.clus" and T1-T4 as "end.clus". I got 4 Lineages with the names Lineage1: Original T1; Lineage2: Original T2; Lineage3: Original T3; Lineage4: Original T4. Can I assume that Lineage1 represents the specific branch in the T1 condition? But I found that Lineage1 also contains cells in other conditions(T2-T4).

Can the comparison between Lineage1 and Lineage2 using tradeSeq represent the comparison between T1 and T2?

If my thinking above is wrong. Should I construct only one Lineage for all five experimental conditions?

I would appreciate any advice you can give!

siteng

[kstreet13]

Hi @Siteng999,

I think you are confusing the terms "lineage" and "condition". There are five experimental conditions, but that does not mean that you should expect 4 lineages (and you almost certainly shouldn't be using the conditions as if they were cell clusters). We use the term "lineage" to mean a single path from a progenitor cell type to a terminal cell type. The number of different terminal cell types is the number of lineages, but it has almost nothing to do with how many experimental conditions are present. I don't know how many lineages would be appropriate for your data, but that has more to do with the biology of the cell system you're studying than with the number of experimental conditions.

Hope this helps clear some things up! Kelly

[Siteng999]

Hello kstreet13

Thank you very much for your reply.

I may need to add some more to the above question. In this experiment I want to obtain the hub-genes of a single tissue cell (e.g. root hair) in response to stimulus specificity. The experimental conditions are sampled in a temporal order under two stimuli. Thus I want to look at single tissues under different time treatments as different states of differentiation. By comparing the differences between the two stimuli at the same sampling time point, I hope to obtain some key signals. Can I solve the above problem when I compare the "lineage" obtained by specifying "start.clus" and "end.clus"?

Sincerely， siteng

[Siteng999]

Sorry！

Now,I have a clear understanding of the above issues. I will close this issue. Thanks again for your enthusiastic response!

siteng