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Subset Cv CpG O/E file to just stress response genes #623

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sr320 opened this issue Mar 20, 2019 · 14 comments
Closed

Subset Cv CpG O/E file to just stress response genes #623

sr320 opened this issue Mar 20, 2019 · 14 comments
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@sr320

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@sr320 sr320 commented Mar 20, 2019

Here is file with GO information
https://d.pr/f/TVZROq

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@kaitlynrm kaitlynrm commented Mar 20, 2019

I merged the original data with the GO information and made this file containing just stress response genes. There are 2,733 genes here compared to 38,929 in the original data.

For the plots below:

  • Samples/populations are on the x axis
  • Cpg O/E values are on the y-axis
  • y-axes are labelled with what statistic was used
  • points represent all of the CpG O/E values for the genes

Note that both graphs below will have the same number of points because the points are the samples/populations, and there are always 90 samples. The number of values represented underneath the points, e.g., the genes, is what changes between the "all samples" and "stress response" plots.


all-v-stress
All genes= left column
Stress genes= right column


Below are two faceted plots with either all genes or just stress genes.

basicstats
All genes plot.


stress-basicstats
Stress response plot. Only genes that merged to stress response in the GO information file are represented here.


I can easily put genes on the x-axis instead of samples. I just wasn't sure what would be more valuable. If the samples represent the same treatment, population, or replicates then I think genes on the x axis makes more sense. However, if the question is what differences are occurring between samples/populations/etc. than samples on the x-axis would probably make more sense.

Samples/populations should be on the x axis because there are over 39k genes (or in the case of stress response ~3k) and that would be illegible.

Edit: Misunderstood what values were represented in the original dataset- corrected explanations.

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@sr320 sr320 commented Mar 20, 2019

Can you give me a list of stress genes where I could pick one and you could plot the CpG O/E for that for all 91 samples?

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@kaitlynrm kaitlynrm commented Mar 20, 2019

I just want to clarify- are rows or columns samples?
genes-or-samples

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@sr320 sr320 commented Mar 20, 2019

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@kaitlynrm kaitlynrm commented Mar 20, 2019

So the rows are genes? When making the graphs I assumed that the columns were genes and rows were sample because the columns were names of genes, but I can update the description.

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@sr320 sr320 commented Mar 20, 2019

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@sr320 sr320 commented Mar 25, 2019

How about a swarm plot of CpG OE of all stress response genes for all samples

https://paulvanderlaken.com/2019/01/25/visualization-innovation-waffleplots-and-swarmplots-aka-beeplots/

@sr320 sr320 added the high priority label Mar 25, 2019
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@kaitlynrm kaitlynrm commented Mar 25, 2019

This is on stress genes.

I used three graphs to distinguish differences between the population: density, box and swarm plots

Density plots

density
faceted-density

Box plot

box


Swarm plot

swarm


Box and Swarm plot together

swarm_box

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@sr320 sr320 commented Mar 25, 2019

Could you also plot on with these GO ID

GO:0100044	negative regulation of cellular hyperosmotic salinity response by transcription from RNA polymerase II promoter
GO:0042538	hyperosmotic salinity response
GO:0042539	hypotonic salinity response
GO:1900464	negative regulation of cellular hyperosmotic salinity response by negative regulation of transcription from RNA polymerase II promoter
GO:1900069	regulation of cellular hyperosmotic salinity response
GO:1900070	negative regulation of cellular hyperosmotic salinity response
GO:0071477	cellular hypotonic salinity response
GO:0071475	cellular hyperosmotic salinity response
GO:1902074	response to salt
GO:1902075	cellular response to salt
GO:0009651	response to salt stress
GO:1901000	regulation of response to salt stress
GO:1901002	positive regulation of response to salt stress
GO:1901001	negative regulation of response to salt stress
GO:1901200	negative regulation of calcium ion transport into cytosol involved in cellular response to salt stress
GO:1901196	positive regulation of calcium-mediated signaling involved in cellular response to salt stress
GO:1901199	positive regulation of calcium ion transport into cytosol involved in cellular response to salt stress
GO:0071472	cellular response to salt stress
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@sr320 sr320 commented Mar 25, 2019

And separately these GO IDs

GO:0070415	trehalose metabolism in response to cold stress
GO:0070414	trehalose metabolism in response to heat stress
GO:0090441	trehalose biosynthesis in response to heat stress
GO:0090442	trehalose catabolism in response to heat stress
GO:0061408	positive regulation of transcription from RNA polymerase II promoter in response to heat stress
GO:1990845	adaptive thermogenesis
GO:0031990	mRNA export from nucleus in response to heat stress
GO:0043620	regulation of DNA-templated transcription in response to stress
GO:0043555	regulation of translation in response to stress
GO:1990611	regulation of cytoplasmic translational initiation in response to stress
GO:1990497	regulation of cytoplasmic translation in response to stress
GO:0034605	cellular response to heat
GO:0070417	cellular response to cold
GO:0006950	response to stress
GO:0036003	positive regulation of transcription from RNA polymerase II promoter in response to stress
GO:0043618	regulation of transcription from RNA polymerase II promoter in response to stress
GO:0080134	regulation of response to stress
GO:0080135	regulation of cellular response to stress
GO:0097201	negative regulation of transcription from RNA polymerase II promoter in response to stress
GO:0033554	cellular response to stress
GO:0033555	multicellular organismal response to stress
GO:0009271	phage shock
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@sr320 sr320 commented Mar 25, 2019

and

GO:0045087	innate immune response
GO:0061760	antifungal innate immune response
GO:0045088	regulation of innate immune response
GO:0002218	activation of innate immune response
GO:0002227	innate immune response in mucosa
GO:1905036	positive regulation of antifungal innate immune response
GO:1905035	negative regulation of antifungal innate immune response
GO:1905034	regulation of antifungal innate immune response
GO:0035420	MAPK cascade involved in innate immune response
GO:0045824	negative regulation of innate immune response
GO:0045089	positive regulation of innate immune response
GO:0002758	innate immune response-activating signal transduction
GO:0002766	innate immune response-inhibiting signal transduction
GO:0090714	innate immunity memory response
GO:0035419	activation of MAPK activity involved in innate immune response
GO:0035423	inactivation of MAPK activity involved in innate immune response
GO:0035422	activation of MAPKKK activity involved in innate immune response
GO:0035421	activation of MAPKK activity involved in innate immune response
GO:0046735	passive induction of host innate immune response by virus
GO:0046738	active induction of innate immune response in host by virus
GO:0038075	MAP kinase activity involved in innate immune response
GO:0039503	suppression by virus of host innate immune response
GO:0052170	negative regulation by symbiont of host innate immune response
GO:0052166	positive regulation by symbiont of host innate immune response
GO:0052167	modulation by symbiont of host innate immune response
GO:0052390	induction by symbiont of host innate immune response
GO:0052305	positive regulation of innate immune response in other organism
GO:0052309	negative regulation of innate immune response in other organism
GO:0002220	innate immune response activating cell surface receptor signaling pathway
GO:0038078	MAP kinase phosphatase activity involved in regulation of innate immune response
GO:0052157	modulation by symbiont of microbe-associated molecular pattern-induced host innate immune response
GO:0052169	pathogen-associated molecular pattern dependent modulation by symbiont of host innate immune response
GO:0052033	pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response
GO:0052034	negative regulation by symbiont of microbe-associated molecular pattern-induced host innate immune response
GO:0052382	induction by organism of innate immune response in other organism involved in symbiotic interaction
GO:0052306	modulation by organism of innate immune response in other organism involved in symbiotic interaction
GO:0052308	pathogen-associated molecular pattern dependent modulation by organism of innate immune response in other organism involved in symbiotic interaction
GO:0052258	negative regulation by organism of pathogen-associated molecular pattern-induced innate immune response of other organism involved in symbiotic interaction
GO:0052257	pathogen-associated molecular pattern dependent induction by organism of innate immune response of other organism involved in symbiotic interaction
GO:0052296	modulation by organism of microbe-associated molecular pattern-induced innate immune response in other organism involved in symbiotic interaction
GO:0035663	Toll-like receptor 2 binding
GO:0035662	Toll-like receptor 4 binding
GO:0090644	age-related resistance
GO:0035325	Toll-like receptor binding
GO:0039699	viral mRNA cap methylation
GO:0046696	lipopolysaccharide receptor complex
GO:0002224	toll-like receptor signaling pathway
GO:0039539	suppression by virus of host MDA-5 signaling pathway
GO:0039538	suppression by virus of host RIG-I signaling pathway
GO:0039537	suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway
GO:0039560	suppression by virus of host IRF9 activity
GO:1990231	STING complex
GO:0002755	MyD88-dependent toll-like receptor signaling pathway
GO:0002756	MyD88-independent toll-like receptor signaling pathway
GO:0035669	TRAM-dependent toll-like receptor 4 signaling pathway
GO:0035668	TRAM-dependent toll-like receptor signaling pathway
GO:0035667	TRIF-dependent toll-like receptor 4 signaling pathway
GO:0035666	TRIF-dependent toll-like receptor signaling pathway
GO:0035661	MyD88-dependent toll-like receptor 2 signaling pathway
GO:0035660	MyD88-dependent toll-like receptor 4 signaling pathway
GO:0035665	TIRAP-dependent toll-like receptor 4 signaling pathway
GO:0035664	TIRAP-dependent toll-like receptor signaling pathway
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@kaitlynrm kaitlynrm commented Mar 25, 2019

Osmotic Stress (List 1):

list1-swarmbox

Temperature Stress (List 2):

list2-swarmbox

Immune Response (List 3):

list3-swarmbox

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@kaitlynrm kaitlynrm commented Mar 25, 2019

Swarm and Box plot together of Averages (rather than on sums as in the first box/swarm/density plots for stress response genes)

swarm_box

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