# goseq for Top over−represented & under-represented GO terms plot

**URL:** <https://help.galaxyproject.org/t/goseq-for-top-over-represented-under-represented-go-terms-plot/14059>\
**Category:** Uncategorized\
**Tags:** transcriptomics, goseq, goenrichment\
**Created:** [December 3, 2024, 8:47pm UTC](https://help.galaxyproject.org/t/goseq-for-top-over-represented-under-represented-go-terms-plot/14059 "2024-12-03T20:47:18Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![olha\_strilbytska](https://avatars.discourse-cdn.com/v4/letter/o/b9e5f3/32.png) [@olha\_strilbytska](https://help.galaxyproject.org/u/olha_strilbytska)\
**Post date:** [December 3, 2024, 8:47pm UTC](https://help.galaxyproject.org/t/goseq-for-top-over-represented-under-represented-go-terms-plot/14059/1 "2024-12-03T20:47:18Z")

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Hi there! I’ve performed goseq for Top over−represented categories. And It’s fine according to “Ranked category list - Wallenius method” column 8 - “p\_adjust\_over\_represented”. But I has signifficantly changed categories in column 9 (“p\_adjust\_under\_represented”) which are not plotted (no option).  
My questions:

1. how to get plot of Top under-represented GO terms?
2. “over\_represented” means upregulated and “under-represented” - downregulated?

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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [December 4, 2024, 6:25pm UTC](https://help.galaxyproject.org/t/goseq-for-top-over-represented-under-represented-go-terms-plot/14059/2 "2024-12-04T18:25:32Z")

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Hi @olha_strilbytska

We have several tutorials with examples for **goseq**. Find these on the tool form – scroll down to the Help section to find the links. I am including the **GOEnrichment** tool, too.

* * *

- Single Cell / [GO Enrichment Analysis on Single-Cell RNA-Seq Data](https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/GO-enrichment/tutorial.html)
- Transcriptomics / [GO Enrichment Analysis](https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/goenrichment/tutorial.html)
- Transcriptomics / [Pathway analysis with the MINERVA Platform](https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/minerva-pathways/tutorial.html)
- Transcriptomics / [Reference-based RNA-Seq data analysis](https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html)
- Transcriptomics / [3: RNA-seq genes to pathways](https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-genes-to-pathways/tutorial.html)

* * *

Start with the last tutorial in the list, and you will find the answers to your questions with more nuance than I can reproduce here. In short: goseq is just one tool, and there are others you can try.

Up and Down regulation isn’t straightforward because these data can have biases. These tools are helping to normalize the expression results _in the presence of those biases_, and each does that a bit differently.

Example: goseq considers transcript _length_. That’s why you are supplying the length data at runtime – the primary up/down input file does not include that data point yet.

Hope this helps 🙂

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**Author:** ![olha\_strilbytska](https://avatars.discourse-cdn.com/v4/letter/o/b9e5f3/32.png) [@olha\_strilbytska](https://help.galaxyproject.org/u/olha_strilbytska)\
**Post date:** [December 13, 2024, 10:25am UTC](https://help.galaxyproject.org/t/goseq-for-top-over-represented-under-represented-go-terms-plot/14059/3 "2024-12-13T10:25:01Z")

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Hi @jennaj

Thank you for these recommendations! I would hope in goseq there will appear an option to visualise underrepresented terms in the feature