# Potential Pathway that could aid you

**URL:** <https://help.c-moor.org/t/potential-pathway-that-could-aid-you/308>\
**Category:** Uncategorized\
**Created:** [July 19, 2022, 5:42pm UTC](https://help.c-moor.org/t/potential-pathway-that-could-aid-you/308 "2022-07-19T17:42:08Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![yanitrevino](https://avatars.discourse-cdn.com/v4/letter/y/8baadc/32.png) [@yanitrevino](https://help.c-moor.org/u/yanitrevino)\
**Post date:** [July 19, 2022, 5:42pm UTC](https://help.c-moor.org/t/potential-pathway-that-could-aid-you/308/1 "2022-07-19T17:42:08Z")

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@Mark_Sandwich  
There’s pretty much 2 pathways for Wnt signaling: canonical(beta catenin dependent) and non-canonical(beta catenin independent). Since you already have a co-reation between your two Wnt’s you could possibly find what sort of pathway they’re involved in just by finding their co-expression with beta catenin, because if there is high co-expression between beta catenin between the 2 Wnt’s and beta catenin, that might suggest dependency.  
Here’s code you could use to see if there is co-relation between Wnt and one of beta-catenin’s:  
wnt7b and ctnnb1 co-relation:  
wnt7b and ctnnb1 co-relation score

```auto
# Create a variable with your favorite gene
my_favorite_gene <- c("ENSMUSG00000022382","ENSMUSG00000006932")

# Create a variable with you 
of.interest <- c(top.hvgs[1:200], my_favorite_gene)

# Subset dataset to just the celltypes you are interested in
sce_subset <- sce[,sce$celltype %in% c("ExE ectoderm")]

cor.pairs <- correlatePairs(x = sce_subset, subset.row = of.interest)
cor.pairs %>% as_tibble() %>% filter(gene1 %in% my_favorite_gene, gene2 %in% my_favorite_gene)
# A tibble: 1 × 5

```

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**Author:** ![Mark\_Sandwich](https://avatars.discourse-cdn.com/v4/letter/m/cab0a1/32.png) [@Mark\_Sandwich](https://help.c-moor.org/u/Mark_Sandwich)\
**Post date:** [July 20, 2022, 1:11am UTC](https://help.c-moor.org/t/potential-pathway-that-could-aid-you/308/2 "2022-07-20T01:11:45Z")

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Hi Yani, thank you for the code. I’ll look into whether the results can support my presentation.

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**Author:** ![Mark\_Sandwich](https://avatars.discourse-cdn.com/v4/letter/m/cab0a1/32.png) [@Mark\_Sandwich](https://help.c-moor.org/u/Mark_Sandwich)\
**Post date:** [July 21, 2022, 4:39am UTC](https://help.c-moor.org/t/potential-pathway-that-could-aid-you/308/3 "2022-07-21T04:39:41Z")

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This might be a big favor to ask for but I was wondering if you could run some lines of code in your R-Studio because mine crashed and I can’t get any expression out of genes Wnt1 and Wnt10b. Whenever I run any code with them I get zero expression like in these graphs.

 ![image](https://canada1.discourse-cdn.com/flex027/uploads/c_moor/original/1X/0cbf4d372352037350d024b16ce28ecaa8c7a89a.png)  
 ![image](https://canada1.discourse-cdn.com/flex027/uploads/c_moor/original/1X/e2ab78cc801e701bbb9f5bedd4525c0007d7d2aa.png)  
I’m still able to get expressions out of Wnt10a somehow. I also made another container in SciServer and still got nothing.

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<div class="post-metadata">

**Author:** ![Mark\_Sandwich](https://avatars.discourse-cdn.com/v4/letter/m/cab0a1/32.png) [@Mark\_Sandwich](https://help.c-moor.org/u/Mark_Sandwich)\
**Post date:** [July 21, 2022, 5:47am UTC](https://help.c-moor.org/t/potential-pathway-that-could-aid-you/308/4 "2022-07-21T05:47:08Z")

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Hi never mind, Shamoun pointed out I loaded the wrong dataset somehow.

I’m still not sure how I can use the code you provided in my presentation but I still appreciate the help.