This will be a very minimal analysis until we get some replicates.
I am using mm38_95.
## My load_biomart_annotations() function defaults to human, so that will be quick.
mm_annot <- load_biomart_annotations(species="mmusculus")
## The biomart annotations file already exists, loading from it.
mm_annot <- mm_annot[["annotation"]]
mm_annot[["txid"]] <- paste0(mm_annot[["ensembl_transcript_id"]], ".", mm_annot[["version"]])
rownames(mm_annot) <- make.names(mm_annot[["ensembl_gene_id"]], unique=TRUE)
tx_gene_map <- mm_annot[, c("txid", "ensembl_gene_id")]
So, I now have 2 data frames of parasite annotations and 1 human.
I am going to write a quick sample sheet in the current working directory called ‘all_samples.xlsx’ and put the names of the count tables in it.
Here I combine the metadata, count data, and annotations.
It is worth noting that the gene IDs from htseq-count probably do not match the annotations retrieved because they are likely exon-based rather than gene based. This is not really a problem, but don’t forget it!
mm38_salmon <- sm(create_expt("sample_sheets/all_samples.xlsx", tx_gene_map=tx_gene_map,
gene_info=mm_annot, file_column="salmonfile"))
mmtx_annot <- mm_annot
rownames(mmtx_annot) <- mm_annot[["txid"]]
mm38_saltx <- sm(create_expt("sample_sheets/all_samples.xlsx",
gene_info=mmtx_annot, file_column="salmonfile"))
hisat_annot <- mm_annot
rownames(hisat_annot) <- paste0("gene.", rownames(hisat_annot))
mm38_hisat <- create_expt("sample_sheets/all_samples.xlsx",
gene_info=hisat_annot)
## Reading the sample metadata.
## The sample definitions comprises: 8 rows(samples) and 8 columns(metadata fields).
## Reading count tables.
## Reading count tables with read.table().
## /mnt/sshfs/cbcbsub/fs/cbcb-lab/nelsayed/scratch/atb/rnaseq/mmusculus_iprgc_2019/preprocessing/iprgc_01/outputs/hisat2_mm38_95/r1_trimmed.count.xz contains 25788 rows.
## /mnt/sshfs/cbcbsub/fs/cbcb-lab/nelsayed/scratch/atb/rnaseq/mmusculus_iprgc_2019/preprocessing/iprgc_02/outputs/hisat2_mm38_95/r1_trimmed.count.xz contains 25788 rows and merges to 25788 rows.
## /mnt/sshfs/cbcbsub/fs/cbcb-lab/nelsayed/scratch/atb/rnaseq/mmusculus_iprgc_2019/preprocessing/iprgc_03/outputs/hisat2_mm38_95/r1_trimmed.count.xz contains 25788 rows and merges to 25788 rows.
## /mnt/sshfs/cbcbsub/fs/cbcb-lab/nelsayed/scratch/atb/rnaseq/mmusculus_iprgc_2019/preprocessing/iprgc_04/outputs/hisat2_mm38_95/r1_trimmed.count.xz contains 25788 rows and merges to 25788 rows.
## /mnt/sshfs/cbcbsub/fs/cbcb-lab/nelsayed/scratch/atb/rnaseq/mmusculus_iprgc_2019/preprocessing/iprgc_05/outputs/hisat2_mm38_95/r1_trimmed.count.xz contains 25788 rows and merges to 25788 rows.
## /mnt/sshfs/cbcbsub/fs/cbcb-lab/nelsayed/scratch/atb/rnaseq/mmusculus_iprgc_2019/preprocessing/iprgc_06/outputs/hisat2_mm38_95/r1_trimmed.count.xz contains 25788 rows and merges to 25788 rows.
## /mnt/sshfs/cbcbsub/fs/cbcb-lab/nelsayed/scratch/atb/rnaseq/mmusculus_iprgc_2019/preprocessing/iprgc_07/outputs/hisat2_mm38_95/r1_trimmed.count.xz contains 25788 rows and merges to 25788 rows.
## /mnt/sshfs/cbcbsub/fs/cbcb-lab/nelsayed/scratch/atb/rnaseq/mmusculus_iprgc_2019/preprocessing/iprgc_08/outputs/hisat2_mm38_95/r1_trimmed.count.xz contains 25788 rows and merges to 25788 rows.
## Finished reading count tables.
## Matched 25554 annotations and counts.
## Bringing together the count matrix and gene information.
## Some annotations were lost in merging, setting them to 'undefined'.
## The final expressionset has 25783 rows and 8 columns.
In this block I will calculate all the diagnostic plots, but not show them. I will show them next with a little annotation.
I will leave the output for the first of each invocation and silence it for the second.
mm38_norm_sa <- normalize_expt(mm38_salmon, norm="quant", convert="cpm",
transform="log2", filter=TRUE)
## This function will replace the expt$expressionset slot with:
## log2(cpm(quant(cbcb(data))))
## It will save copies of each step along the way
## in expt$normalized with the corresponding libsizes. Keep libsizes in mind
## when invoking limma. The appropriate libsize is non-log(cpm(normalized)).
## This is most likely kept at:
## 'new_expt$normalized$intermediate_counts$normalization$libsizes'
## A copy of this may also be found at:
## new_expt$best_libsize
## Not correcting the count-data for batch effects. If batch is
## included in EdgerR/limma's model, then this is probably wise; but in extreme
## batch effects this is a good parameter to play with.
## Step 1: performing count filter with option: cbcb
## Removing 2794 low-count genes (3970 remaining).
## Step 2: normalizing the data with quant.
## Step 3: converting the data with cpm.
## Step 4: transforming the data with log2.
## transform_counts: Found 1105 values equal to 0, adding 1 to the matrix.
## Step 5: not doing batch correction.
mm38_norm_hi <- normalize_expt(mm38_hisat, norm="quant", convert="cpm",
transform="log2", filter=TRUE)
## This function will replace the expt$expressionset slot with:
## log2(cpm(quant(cbcb(data))))
## It will save copies of each step along the way
## in expt$normalized with the corresponding libsizes. Keep libsizes in mind
## when invoking limma. The appropriate libsize is non-log(cpm(normalized)).
## This is most likely kept at:
## 'new_expt$normalized$intermediate_counts$normalization$libsizes'
## A copy of this may also be found at:
## new_expt$best_libsize
## Not correcting the count-data for batch effects. If batch is
## included in EdgerR/limma's model, then this is probably wise; but in extreme
## batch effects this is a good parameter to play with.
## Step 1: performing count filter with option: cbcb
## Removing 12233 low-count genes (13550 remaining).
## Step 2: normalizing the data with quant.
## Step 3: converting the data with cpm.
## Step 4: transforming the data with log2.
## transform_counts: Found 19 values equal to 0, adding 1 to the matrix.
## Step 5: not doing batch correction.
The only interesting DE I see in this is to compare the retinas to the dlgns. I can treat them as replicates and compare.
These differential expression analyses are EXPLICITLY NOT what you care about. However, they are useful for two purposes:
When we receive full replicate sets, this cheater method of encapsulating the data will not longer be required.
mm_sa <- set_expt_conditions(mm38_salmon, fact="celltype")
mm_norm_sa <- sm(normalize_expt(mm_sa, convert="rpkm", transform="log2", column="cds_length"))
plot_pca(mm_norm_sa)$plot
## This function will replace the expt$expressionset slot with:
## log2(cpm(quant(cbcb(data))))
## It will save copies of each step along the way
## in expt$normalized with the corresponding libsizes. Keep libsizes in mind
## when invoking limma. The appropriate libsize is non-log(cpm(normalized)).
## This is most likely kept at:
## 'new_expt$normalized$intermediate_counts$normalization$libsizes'
## A copy of this may also be found at:
## new_expt$best_libsize
## Not correcting the count-data for batch effects. If batch is
## included in EdgerR/limma's model, then this is probably wise; but in extreme
## batch effects this is a good parameter to play with.
## Step 1: performing count filter with option: cbcb
## Removing 2794 low-count genes (3970 remaining).
## Step 2: normalizing the data with quant.
## Step 3: converting the data with cpm.
## Step 4: transforming the data with log2.
## transform_counts: Found 1105 values equal to 0, adding 1 to the matrix.
## Step 5: not doing batch correction.
## Plotting a PCA before surrogates/batch inclusion.
## Not putting labels on the plot.
## Assuming no batch in model for testing pca.
## Not putting labels on the plot.
## Finished running DE analyses, collecting outputs.
## Comparing analyses.
Until we get full replicates, I will do simple subtractions.
In an attempt to keep some clarity in the terms used, I want to define them now. There are three contexts in which we will consider the data:
The individual sample type. When considering individual samples, I will use three terms in this and only this context: wild-type (wt), het, and mut.
The individual translatome. These are defines as something / baseline. I will exclusively call the wt samples ‘baseline’ when speaking in this context. I will exclusively state ‘normal’ when referring to het / wt samples, and I will state ‘ko’ when referring to mut / wt samples in the translatome context.
Translatome vs. translatome. Whenever comparing translatomes, I will use the names as in #2 and always put the numerator first when writing the name of a comparison.
The most complex example of the above nomenclature is:
“normko_retdlgn is defined as normret_vs_normdlgn - koret_vs_kodlgn”
This states we are examining at the translatome context: (norm(retina translatome) - norm(dlgn translatome)) - (ko(retina translatome) - ko(dlgn translatome))
Which in turn is synonymous to the following at the sample context: ((rethet - retwt) - (dlgnhet - dlgnwt)) - ((retko - retwt) - (dlgnko - dlgnwt))
Now let us associate the various variable names with the appropriate samples:
dlgnwt <- "iprgc_01"
retwt <- "iprgc_02"
scnwt <- "iprgc_03"
dlgnhet <- "iprgc_04"
rethet <- "iprgc_05"
scnhet <- NULL ## Does not yet exist.
dlgnmut <- "iprgc_06"
retmut <- "iprgc_07"
scnmut <- "iprgc_08"
Give these variable names, now lets associate columns of the expression data with them. These are at the sample context, so the appropriate names are: ‘wt’, ‘het’, and ‘mut’. In each case I will prefix the genotype with the tissue type: ‘ret’, ‘dlgn’, and ‘scn’. Thus ‘retwt’ refers to the sample used to calculate the translatome retina baseline; in contrast ‘dlgnmut’ is the sample which provides the dlgn knockout.
## Sample context
mm38_norm <- mm_norm_sa
dlgnwt <- exprs(mm38_norm)[, dlgnwt]
retwt <- exprs(mm38_norm)[, retwt]
scnwt <- exprs(mm38_norm)[, scnwt]
dlgnhet <- exprs(mm38_norm)[, dlgnhet]
rethet <- exprs(mm38_norm)[, rethet]
dlgnmut <- exprs(mm38_norm)[, dlgnmut]
retmut <- exprs(mm38_norm)[, retmut]
scnmut <- exprs(mm38_norm)[, scnmut]
Each of the above 8 variables provides 1 column of information. We have 3 baseline comparisons available to us. In each of these we compare one wt sample to another.
## Baseline comparisons
wt_dlgnret <- dlgnwt - retwt
wt_scnret <- scnwt - retwt
wt_dlgnscn <- dlgnwt - scnwt
Simultaneously, we have 5 available translatomes. This are provided by comparing each het or mut to the associated wt. These will therefore receive names: ‘norm’ and ‘ko’ instead of ‘het’ and ‘mut’.
## Translatome context
normret <- rethet - retwt
koret <- retmut - retwt
koscn <- scnmut - scnwt
normdlgn <- dlgnhet - dlgnwt
kodlgn <- dlgnmut - dlgnwt
Given these translatomes, there are a few contrasts of likely interest. These are performed by comparing the relevant translatomes.
Will will split these into 4 separate categories: het vs het, ko vs ko, ko vs het, and ratio vs ratio.
Finally, note that we are being explicitly redundant in these definitions. I am making variable names for both the a/b ratio and the b/a ratio. Thus we have some redundantly redundant (haha) flexibility when deciding on what we want to plot.
## ko vs ko
koret_vs_kodlgn <- koret - kodlgn
kodlgn_vs_koret <- kodlgn - koret
koret_vs_koscn <- koret - koscn
koscn_vs_koret <- koscn - koret
kodlgn_vs_koscn <- kodlgn - koscn
koscn_vs_kodlgn <- koscn - kodlgn
On the other hand, I am assuming we always want the normals as denominators and kos as numerators.
Finally, here is the ratio of ratios example I printed above:
I named it ‘normko_retdlgn’ in an attempt to make clear that it is actually: (normret/normdlgn)/(koret/kodlgn)
or stated differently: “norm divided by ko for ret divided by dlgn.”
My matrix of data will now contain 1 column for each of the above 27 samples/comparisons.
pair_mtrx <- cbind(
## Individual samples
dlgnwt, retwt, scnwt, dlgnhet, rethet, dlgnmut, retmut, scnmut,
## Baseline comparisons
wt_dlgnret, wt_scnret, wt_dlgnscn,
## Baseline subtractions
normdlgn, normret, kodlgn, koret, koscn,
## het_vs_het, of which there is only 1 because we do not have hetscn
normdlgn_vs_normret, normret_vs_normdlgn,
## ko_vs_ko, of which we have 3
koret_vs_kodlgn, kodlgn_vs_koret,
koret_vs_koscn, koscn_vs_koret,
kodlgn_vs_koscn, koscn_vs_kodlgn,
## ko_vs_het, 3 including one getting around missing hetscn
koret_vs_normret, kodlgn_vs_normdlgn,
## ratio of ratios
normko_retdlgn)
I am not sure if we will use these indexes, but I am writing these out as subsets of genes to look at. These indexes are stating that, given a cutoff (0), we want to look at only the genes which have higher x / baseline values than the cutoff.
## Queries about gene subsets.
## These are all in the context of translatomes.
cutoff <- 0
ret_kept_idx <- normret > cutoff & koret > cutoff
scn_kept_idx <- koscn > cutoff
dlgn_kept_idx <- normdlgn > cutoff & kodlgn > cutoff
ret_dlgn_kept_idx <- ret_kept_idx & dlgn_kept_idx
ret_scn_kept_idx <- ret_kept_idx & scn_kept_idx
dlgn_scn_kept_idx <- dlgn_kept_idx & scn_kept_idx
##normdlgn_vs_normret[!ret_dlgn_kept_idx] <- NA
##normret_vs_normdlgn[!ret_dlgn_kept_idx] <- NA
##koret_vs_kodlgn[!ret_dlgn_kept_idx] <- NA
##kodlgn_vs_koret[!ret_dlgn_kept_idx] <- NA
##koret_vs_koscn[!ret_scn_kept_idx] <- NA
##koscn_vs_koret[!ret_scn_kept_idx] <- NA
##kodlgn_vs_koscn[!dlgn_scn_kept_idx] <- NA
##koscn_vs_kodlgn[!dlgn_scn_kept_idx] <- NA
##koret_vs_normret[!ret_kept_idx] <- NA
##kodlgn_vs_normdlgn[!dlgn_kept_idx] <- NA
##normko_retdlgn <- normko_retdlgn[!ret_dlgn_kept_idx] <- NA
I will use my function combine_de_tables() to add this information to my existing annotation data along with the results from the statistically valid comparison of the three tissue types.
## Put retina baseline on y axis as black, retina het on x axis as black.
## Then recolor a subset of these as red, the reds are when normret > 0
library(ggplot2)
plotted <- as.data.frame(pair_mtrx[, c("rethet", "retwt")])
red_idx <- normret > 0
plotted[, "color"] <- ifelse(red_idx, "red", "black")
plotted[["label"]] <- rownames(plotted)
ret_hetwt <- ggplot(
plotted,
aes_string(x="rethet", y="retwt", label="label", color="color")) +
geom_point(alpha=0.5) +
scale_color_manual(values=c("black", "red"))
ret_hetwt
## Warning: Removed 37 rows containing missing values (geom_point).
plotted <- as.data.frame(pair_mtrx[, c("retmut", "retwt")])
plotted[["label"]] <- rownames(plotted)
plotted[["color"]] <- "black"
ret_mutwt <- ggplot(
plotted,
aes_string(x="retmut", y="retwt", label="label", color="color")) +
geom_point(alpha=0.5) +
scale_color_manual(values=c("black", "red"))
ret_mutwt
## Warning: Removed 37 rows containing missing values (geom_point).
plotted <- as.data.frame(pair_mtrx[, c("dlgnhet", "dlgnwt")])
plotted[["label"]] <- rownames(plotted)
plotted[["color"]] <- "black"
dlgn_hetwt <- ggplot(
plotted,
aes_string(x="dlgnhet", y="dlgnwt", label="label", color="color")) +
geom_point(alpha=0.5) +
scale_color_manual(values=c("black", "red"))
dlgn_hetwt
## Warning: Removed 37 rows containing missing values (geom_point).
plotted <- as.data.frame(pair_mtrx[, c("dlgnmut", "dlgnwt")])
plotted[["label"]] <- rownames(plotted)
plotted[["color"]] <- "black"
dlgn_mutwt <- ggplot(
plotted,
aes_string(x="dlgnmut", y="dlgnwt", label="label", color="color")) +
geom_point(alpha=0.5) +
scale_color_manual(values=c("black", "red"))
dlgn_mutwt
## Warning: Removed 37 rows containing missing values (geom_point).
plotted <- as.data.frame(pair_mtrx[, c("scnmut", "scnwt")])
plotted[["label"]] <- rownames(plotted)
plotted[["color"]] <- "black"
scn_mutwt <- ggplot(
plotted,
aes_string(x="scnmut", y="scnwt", label="label", color="color")) +
geom_point(alpha=0.5) +
scale_color_manual(values=c("black", "red"))
scn_mutwt
## Warning: Removed 37 rows containing missing values (geom_point).
## x-axis: normdlgn_vs_normret or normret_vs_normdlgn,
## ^^^^
## y-axis: dlgnwt-retwt (baseline dlgn - baseline retina)
plotted <- as.data.frame(pair_mtrx[, c("normdlgn_vs_normret", "wt_dlgnret")])
red_idx <- normret > 0
## Note that this order is opposite of above.
plotted[, "color"] <- ifelse(red_idx, "black", "red")
plotted[["label"]] <- rownames(plotted)
axon_trans_ret_target <- ggplot(
plotted,
aes_string(x="normdlgn_vs_normret", y="wt_dlgnret", label="label", color="color")) +
geom_point(alpha=0.5) +
scale_color_manual(values=c("black", "red"))
axon_trans_ret_target
## Warning: Removed 37 rows containing missing values (geom_point).
plotted <- as.data.frame(pair_mtrx[, c("normret", "normdlgn")])
plotted[["label"]] <- rownames(plotted)
plotted[["color"]] <- "black"
normret_normdlgn <- ggplot(
plotted,
aes_string(x="normret", y="normdlgn", label="label", color="color")) +
geom_point(alpha=0.5) +
scale_color_manual(values=c("black", "red"))
normret_normdlgn
## Warning: Removed 37 rows containing missing values (geom_point).
plotted <- as.data.frame(pair_mtrx[, c("koret", "kodlgn")])
plotted[["label"]] <- rownames(plotted)
plotted[["color"]] <- "black"
koret_kodlgn <- ggplot(
plotted,
aes_string(x="koret", y="kodlgn", label="label", color="color")) +
geom_point(alpha=0.5) +
scale_color_manual(values=c("black", "red"))
koret_kodlgn
koret_kodlgn_clicky <- ggplotly_url(
koret_kodlgn, "koret_kodlgn.html", title="KO retina translatome vs KO dlgn translatome.",
url_data="http://useast.ensembl.org/Mus_musculus/Gene/Summary?g={ids}")
``
## KO Retina vs KO SCN
## Error: attempt to use zero-length variable name
plotted <- as.data.frame(pair_mtrx[, c("koret", "koscn")])
plotted[["label"]] <- rownames(plotted)
plotted[["color"]] <- "black"
koret_koscn <- ggplot(
plotted,
aes_string(x="koret", y="koscn", label="label", color="color")) +
geom_point(alpha=0.5) +
scale_color_manual(values=c("black", "red"))
koret_koscn
## Warning: Removed 37 rows containing missing values (geom_point).
plotted <- as.data.frame(pair_mtrx[, c("normdlgn", "kodlgn")])
plotted[["label"]] <- rownames(plotted)
plotted[["color"]] <- "black"
normdlgn_kodlgn <- ggplot(
plotted,
aes_string(x="normdlgn", y="kodlgn", label="label", color="color")) +
geom_point(alpha=0.5) +
scale_color_manual(values=c("black", "red"))
normdlgn_kodlgn
## Warning: Removed 37 rows containing missing values (geom_point).
plotted <- as.data.frame(pair_mtrx[, c("normret", "koret")])
plotted[["label"]] <- rownames(plotted)
plotted[["color"]] <- "black"
normret_koret <- ggplot(
plotted,
aes_string(x="normret", y="koret", label="label", color="color")) +
geom_point(alpha=0.5) +
scale_color_manual(values=c("black", "red"))
normret_koret
## Warning: Removed 37 rows containing missing values (geom_point).
plotted <- as.data.frame(pair_mtrx[, c("normret_vs_normdlgn", "koret_vs_kodlgn")])
plotted[["label"]] <- rownames(plotted)
plotted[["color"]] <- "black"
normal_ko_axon_translatome <- ggplot(
plotted,
aes_string(x="normret_vs_normdlgn", y="koret_vs_kodlgn", label="label", color="color")) +
geom_point(alpha=0.5) +
scale_color_manual(values=c("black", "red"))
normal_ko_axon_translatome
## Warning: Removed 37 rows containing missing values (geom_point).
translatome_plotter <- function(pair_mtrx, x_axis="koret", y_axis="koscn", lfc=NULL, fc=NULL, linewidth=1.5,
up_color="red", down_color="#098534", line_color="#fcba03", alpha=0.5,
x_limit=c(-7, 7), y_limit=c(-7, 7)) {
if (is.null(fc) & is.null(lfc)) {
message("No fc/lfc was provided, defaulting to 10 fold.")
lfc <- log2(10)
} else if (is.null(lfc)) {
lfc <- log2(fc)
}
plotted <- as.data.frame(pair_mtrx[, c(x_axis, y_axis)])
na_idx <- is.na(plotted)
plotted[na_idx] <- 0
up_idx <- plotted[, y_axis] - plotted[, x_axis] >= lfc
down_idx <- plotted[, y_axis] - plotted[, x_axis] <= (lfc * -1)
up_genes <- rownames(plotted)[up_idx]
down_genes <- rownames(plotted)[down_idx]
## Note that this order is opposite of above.
plotted[["color"]] <- "black"
plotted[up_idx, "color"] <- up_color
plotted[down_idx, "color"] <- down_color
plotted[["color"]] <- as.factor(plotted[["color"]])
levels(plotted[["color"]]) <- c("black", up_color, down_color)
plt <- ggplot2::ggplot(plotted, aes_string(x=x_axis,
y=y_axis,
color="color")) +
geom_abline(size=1.1, slope=1, intercept=lfc, color="orange") +
geom_abline(size=1.1, slope=1, intercept=(-1 * lfc), color="orange") +
scale_x_continuous(limits=c(x_limit)) +
scale_y_continuous(limits=c(y_limit)) +
geom_point(alpha=alpha) +
scale_color_manual(values=c(down_color, "black", up_color))
retlist <- list(
"mtrx" = plotted,
"ups" = up_genes,
"downs" = down_genes,
"plot" = plt)
return(retlist)
}
First plot: KO scn translatome on y axis vs. KO retina translatome on x axis.
## No fc/lfc was provided, defaulting to 10 fold.
## Warning: Removed 1 rows containing missing values (geom_point).
scnko_wrt_retko_up_go <- simple_gprofiler(sig_genes=scnko_wrt_retko_translatome$ups,
species="mmusculus")
## Performing gProfiler GO search of 70 genes against mmusculus.
## GO search found 0 hits.
## Performing gProfiler KEGG search of 70 genes against mmusculus.
## KEGG search found 0 hits.
## Performing gProfiler REAC search of 70 genes against mmusculus.
## REAC search found 0 hits.
## Performing gProfiler MI search of 70 genes against mmusculus.
## MI search found 0 hits.
## Performing gProfiler TF search of 70 genes against mmusculus.
## TF search found 0 hits.
## Performing gProfiler CORUM search of 70 genes against mmusculus.
## CORUM search found 0 hits.
## Performing gProfiler HP search of 70 genes against mmusculus.
## HP search found 0 hits.
scnko_wrt_retko_down_go <- simple_gprofiler(sig_genes=scnko_wrt_retko_translatome$downs,
species="mmusculus")
## Performing gProfiler GO search of 42 genes against mmusculus.
## GO search found 2 hits.
## Performing gProfiler KEGG search of 42 genes against mmusculus.
## KEGG search found 1 hits.
## Performing gProfiler REAC search of 42 genes against mmusculus.
## REAC search found 0 hits.
## Performing gProfiler MI search of 42 genes against mmusculus.
## MI search found 0 hits.
## Performing gProfiler TF search of 42 genes against mmusculus.
## TF search found 10 hits.
## Performing gProfiler CORUM search of 42 genes against mmusculus.
## CORUM search found 1 hits.
## Performing gProfiler HP search of 42 genes against mmusculus.
## HP search found 0 hits.
## query.number significant p.value term.size query.size overlap.size precision
## 1 1 TRUE 0.0202 40 3 2 0.667
## 2 1 TRUE 0.0128 32 3 2 0.667
## recall term.id domain subgraph.number term.name
## 1 0.050 GO:0035136 BP 1 forelimb morphogenesis
## 2 0.062 GO:0035115 BP 1 embryonic forelimb morphogenesis
## relative.depth intersection
## 1 1 ENSMUSG00000013584,ENSMUSG00000021469
## 2 2 ENSMUSG00000013584,ENSMUSG00000021469
## query.number significant p.value term.size query.size overlap.size precision
## 1 1 TRUE 0.0334 71 11 2 0.182
## recall term.id domain subgraph.number term.name relative.depth
## 1 0.028 KEGG:04115 keg 1 p53 signaling pathway 1
## intersection
## 1 ENSMUSG00000024521,ENSMUSG00000032009
## query.number significant p.value term.size query.size overlap.size precision
## 1 1 TRUE 0.0249 1 16 1 0.062
## recall term.id domain subgraph.number term.name
## 1 1 CORUM:6829 cor 1 Klotho-Kdr-Trpc1 complex
## relative.depth intersection
## 1 1 ENSMUSG00000058488
dlgnnorm_wrt_retnorm_translatome <- translatome_plotter(pair_mtrx,
x_axis="normret", y_axis="normdlgn")
## No fc/lfc was provided, defaulting to 10 fold.
## Warning: Removed 1 rows containing missing values (geom_point).
dlgnnorm_wrt_retnorm_up_go <- simple_gprofiler(sig_genes=dlgnnorm_wrt_retnorm_translatome$ups,
species="mmusculus")
## Performing gProfiler GO search of 59 genes against mmusculus.
## GO search found 3 hits.
## Performing gProfiler KEGG search of 59 genes against mmusculus.
## KEGG search found 0 hits.
## Performing gProfiler REAC search of 59 genes against mmusculus.
## REAC search found 2 hits.
## Performing gProfiler MI search of 59 genes against mmusculus.
## MI search found 0 hits.
## Performing gProfiler TF search of 59 genes against mmusculus.
## TF search found 0 hits.
## Performing gProfiler CORUM search of 59 genes against mmusculus.
## CORUM search found 1 hits.
## Performing gProfiler HP search of 59 genes against mmusculus.
## HP search found 0 hits.
dlgnnorm_wrt_retnorm_down_go <- simple_gprofiler(sig_genes=dlgnnorm_wrt_retnorm_translatome$downs,
species="mmusculus")
## Performing gProfiler GO search of 69 genes against mmusculus.
## GO search found 14 hits.
## Performing gProfiler KEGG search of 69 genes against mmusculus.
## KEGG search found 1 hits.
## Performing gProfiler REAC search of 69 genes against mmusculus.
## REAC search found 3 hits.
## Performing gProfiler MI search of 69 genes against mmusculus.
## MI search found 0 hits.
## Performing gProfiler TF search of 69 genes against mmusculus.
## TF search found 4 hits.
## Performing gProfiler CORUM search of 69 genes against mmusculus.
## CORUM search found 1 hits.
## Performing gProfiler HP search of 69 genes against mmusculus.
## HP search found 47 hits.
## query.number significant p.value term.size query.size overlap.size
## 1 1 TRUE 2.11e-02 366 45 7
## 2 1 TRUE 1.97e-02 362 45 7
## 3 1 TRUE 1.97e-02 362 45 7
## 4 1 TRUE 2.65e-08 142 45 9
## 5 1 TRUE 2.04e-08 138 45 9
## 6 1 TRUE 1.39e-02 115 23 4
## 7 1 TRUE 1.34e-02 114 23 4
## 8 1 TRUE 3.77e-04 47 23 4
## 9 1 TRUE 1.67e-02 36 23 3
## 10 1 TRUE 1.32e-03 148 45 6
## 11 1 TRUE 1.39e-02 126 45 5
## 12 1 TRUE 3.64e-03 96 45 5
## 13 1 TRUE 3.45e-03 95 45 5
## 14 1 TRUE 8.05e-04 71 45 5
## precision recall term.id domain subgraph.number
## 1 0.156 0.019 GO:0048880 BP 1
## 2 0.156 0.019 GO:0150063 BP 1
## 3 0.156 0.019 GO:0001654 BP 1
## 4 0.200 0.063 GO:0050953 BP 3
## 5 0.200 0.065 GO:0007601 BP 3
## 6 0.174 0.035 GO:0009581 BP 2
## 7 0.174 0.035 GO:0009582 BP 2
## 8 0.174 0.085 GO:0009583 BP 2
## 9 0.130 0.083 GO:0009584 BP 2
## 10 0.133 0.041 GO:0060041 BP 5
## 11 0.111 0.040 GO:0097730 CC 4
## 12 0.111 0.052 GO:0097731 CC 4
## 13 0.111 0.053 GO:0097733 CC 4
## 14 0.111 0.070 GO:0001750 CC 4
## term.name relative.depth
## 1 sensory system development 1
## 2 visual system development 2
## 3 eye development 1
## 4 sensory perception of light stimulus 1
## 5 visual perception 2
## 6 detection of external stimulus 1
## 7 detection of abiotic stimulus 1
## 8 detection of light stimulus 2
## 9 detection of visible light 3
## 10 retina development in camera-type eye 1
## 11 non-motile cilium 1
## 12 9+0 non-motile cilium 2
## 13 photoreceptor cell cilium 1
## 14 photoreceptor outer segment 1
## intersection
## 1 ENSMUSG00000021099,ENSMUSG00000023978,ENSMUSG00000029491,ENSMUSG00000031293,ENSMUSG00000037446,ENSMUSG00000048015,ENSMUSG00000071648
## 2 ENSMUSG00000021099,ENSMUSG00000023978,ENSMUSG00000029491,ENSMUSG00000031293,ENSMUSG00000037446,ENSMUSG00000048015,ENSMUSG00000071648
## 3 ENSMUSG00000021099,ENSMUSG00000023978,ENSMUSG00000029491,ENSMUSG00000031293,ENSMUSG00000037446,ENSMUSG00000048015,ENSMUSG00000071648
## 4 ENSMUSG00000021804,ENSMUSG00000023978,ENSMUSG00000025386,ENSMUSG00000029491,ENSMUSG00000031293,ENSMUSG00000037446,ENSMUSG00000041534,ENSMUSG00000053773,ENSMUSG00000071648
## 5 ENSMUSG00000021804,ENSMUSG00000023978,ENSMUSG00000025386,ENSMUSG00000029491,ENSMUSG00000031293,ENSMUSG00000037446,ENSMUSG00000041534,ENSMUSG00000053773,ENSMUSG00000071648
## 6 ENSMUSG00000021804,ENSMUSG00000029491,ENSMUSG00000031293,ENSMUSG00000037446
## 7 ENSMUSG00000021804,ENSMUSG00000029491,ENSMUSG00000031293,ENSMUSG00000037446
## 8 ENSMUSG00000021804,ENSMUSG00000029491,ENSMUSG00000031293,ENSMUSG00000037446
## 9 ENSMUSG00000021804,ENSMUSG00000031293,ENSMUSG00000037446
## 10 ENSMUSG00000023978,ENSMUSG00000029491,ENSMUSG00000031293,ENSMUSG00000037446,ENSMUSG00000048015,ENSMUSG00000071648
## 11 ENSMUSG00000023978,ENSMUSG00000028777,ENSMUSG00000029491,ENSMUSG00000037446,ENSMUSG00000071648
## 12 ENSMUSG00000023978,ENSMUSG00000028777,ENSMUSG00000029491,ENSMUSG00000037446,ENSMUSG00000071648
## 13 ENSMUSG00000023978,ENSMUSG00000028777,ENSMUSG00000029491,ENSMUSG00000037446,ENSMUSG00000071648
## 14 ENSMUSG00000023978,ENSMUSG00000028777,ENSMUSG00000029491,ENSMUSG00000037446,ENSMUSG00000071648
## No fc/lfc was provided, defaulting to 10 fold.
dlgnko_wrt_retko_up_go <- simple_gprofiler(sig_genes=dlgnko_wrt_retko_translatome$ups,
species="mmusculus")
## Performing gProfiler GO search of 78 genes against mmusculus.
## GO search found 2 hits.
## Performing gProfiler KEGG search of 78 genes against mmusculus.
## KEGG search found 3 hits.
## Performing gProfiler REAC search of 78 genes against mmusculus.
## REAC search found 2 hits.
## Performing gProfiler MI search of 78 genes against mmusculus.
## MI search found 0 hits.
## Performing gProfiler TF search of 78 genes against mmusculus.
## TF search found 2 hits.
## Performing gProfiler CORUM search of 78 genes against mmusculus.
## CORUM search found 2 hits.
## Performing gProfiler HP search of 78 genes against mmusculus.
## HP search found 0 hits.
## query.number significant p.value term.size query.size overlap.size precision
## 1 1 TRUE 0.033300 88 12 3 0.25
## 2 1 TRUE 0.000871 3 8 2 0.25
## recall term.id domain subgraph.number term.name
## 1 0.034 GO:1903008 BP 2 organelle disassembly
## 2 0.667 GO:0031493 MF 1 nucleosomal histone binding
## relative.depth intersection
## 1 1 ENSMUSG00000000628,ENSMUSG00000021115,ENSMUSG00000022789
## 2 1 ENSMUSG00000001228,ENSMUSG00000021115
## query.number significant p.value term.size query.size overlap.size precision
## 1 1 TRUE 0.0352 5 2 1 0.500
## 2 1 TRUE 0.0403 33 21 2 0.095
## 3 1 TRUE 0.0454 35 21 2 0.095
## recall term.id domain subgraph.number
## 1 0.200 KEGG:00524 keg 2
## 2 0.061 KEGG:00052 keg 3
## 3 0.057 KEGG:00051 keg 1
## term.name relative.depth
## 1 Neomycin, kanamycin and gentamicin biosynthesis 1
## 2 Galactose metabolism 1
## 3 Fructose and mannose metabolism 1
## intersection
## 1 ENSMUSG00000000628
## 2 ENSMUSG00000000628,ENSMUSG00000029762
## 3 ENSMUSG00000000628,ENSMUSG00000029762
## query.number significant p.value term.size query.size overlap.size precision
## 1 1 TRUE 0.0328 54 49 3 0.061
## 2 1 TRUE 0.0293 52 49 3 0.061
## recall term.id domain subgraph.number
## 1 0.056 REAC:R-MMU-6806667 rea 1
## 2 0.058 REAC:R-MMU-975634 rea 1
## term.name relative.depth
## 1 Metabolism of fat-soluble vitamins 1
## 2 Retinoid metabolism and transport 1
## intersection
## 1 ENSMUSG00000028003,ENSMUSG00000029762,ENSMUSG00000055653
## 2 ENSMUSG00000028003,ENSMUSG00000029762,ENSMUSG00000055653
dlgnko_wrt_retko_down_go <- simple_gprofiler(sig_genes=dlgnko_wrt_retko_translatome$downs,
species="mmusculus")
## Performing gProfiler GO search of 51 genes against mmusculus.
## GO search found 4 hits.
## Performing gProfiler KEGG search of 51 genes against mmusculus.
## KEGG search found 9 hits.
## Performing gProfiler REAC search of 51 genes against mmusculus.
## REAC search found 2 hits.
## Performing gProfiler MI search of 51 genes against mmusculus.
## MI search found 0 hits.
## Performing gProfiler TF search of 51 genes against mmusculus.
## TF search found 0 hits.
## Performing gProfiler CORUM search of 51 genes against mmusculus.
## CORUM search found 0 hits.
## Performing gProfiler HP search of 51 genes against mmusculus.
## HP search found 0 hits.
## query.number significant p.value term.size query.size overlap.size precision
## 1 1 TRUE 0.04480 319 12 4 0.333
## 2 1 TRUE 0.01250 194 14 4 0.286
## 3 1 TRUE 0.00675 166 14 4 0.286
## 4 1 TRUE 0.00161 116 14 4 0.286
## recall term.id domain subgraph.number
## 1 0.013 GO:0071496 BP 1
## 2 0.021 GO:0007249 BP 2
## 3 0.024 GO:0043122 BP 2
## 4 0.034 GO:0043123 BP 2
## term.name relative.depth
## 1 cellular response to external stimulus 1
## 2 I-kappaB kinase/NF-kappaB signaling 1
## 3 regulation of I-kappaB kinase/NF-kappaB signaling 1
## 4 positive regulation of I-kappaB kinase/NF-kappaB signaling 1
## intersection
## 1 ENSMUSG00000026029,ENSMUSG00000026989,ENSMUSG00000027398,ENSMUSG00000032009
## 2 ENSMUSG00000026029,ENSMUSG00000027398,ENSMUSG00000032496,ENSMUSG00000035186
## 3 ENSMUSG00000026029,ENSMUSG00000027398,ENSMUSG00000032496,ENSMUSG00000035186
## 4 ENSMUSG00000026029,ENSMUSG00000027398,ENSMUSG00000032496,ENSMUSG00000035186
## query.number significant p.value term.size query.size overlap.size precision
## 1 1 TRUE 0.000369 99 10 3 0.300
## 2 1 TRUE 0.017500 61 10 2 0.200
## 3 1 TRUE 0.006040 251 10 3 0.300
## 4 1 TRUE 0.028600 78 10 2 0.200
## 5 1 TRUE 0.015200 57 10 2 0.200
## 6 1 TRUE 0.002690 94 24 3 0.125
## 7 1 TRUE 0.048800 102 10 2 0.200
## 8 1 TRUE 0.039200 71 12 2 0.167
## 9 1 TRUE 0.049800 103 10 2 0.200
## recall term.id domain subgraph.number
## 1 0.030 KEGG:04620 keg 9
## 2 0.033 KEGG:04623 keg 3
## 3 0.012 KEGG:05163 keg 4
## 4 0.026 KEGG:05132 keg 8
## 5 0.035 KEGG:05134 keg 6
## 6 0.032 KEGG:04657 keg 5
## 7 0.020 KEGG:05142 keg 1
## 8 0.028 KEGG:04115 keg 2
## 9 0.019 KEGG:04064 keg 7
## term.name relative.depth
## 1 Toll-like receptor signaling pathway 1
## 2 Cytosolic DNA-sensing pathway 1
## 3 Human cytomegalovirus infection 1
## 4 Salmonella infection 1
## 5 Legionellosis 1
## 6 IL-17 signaling pathway 1
## 7 Chagas disease (American trypanosomiasis) 1
## 8 p53 signaling pathway 1
## 9 NF-kappa B signaling pathway 1
## intersection
## 1 ENSMUSG00000018930,ENSMUSG00000026029,ENSMUSG00000027398
## 2 ENSMUSG00000018930,ENSMUSG00000027398
## 3 ENSMUSG00000018930,ENSMUSG00000026029,ENSMUSG00000027398
## 4 ENSMUSG00000018930,ENSMUSG00000027398
## 5 ENSMUSG00000026029,ENSMUSG00000027398
## 6 ENSMUSG00000026029,ENSMUSG00000027398,ENSMUSG00000056054
## 7 ENSMUSG00000026029,ENSMUSG00000027398
## 8 ENSMUSG00000026029,ENSMUSG00000032009
## 9 ENSMUSG00000018930,ENSMUSG00000027398
## query.number significant p.value term.size query.size overlap.size precision
## 1 1 TRUE 0.000516 3 24 2 0.083
## 2 1 TRUE 0.000172 4 10 2 0.200
## recall term.id domain subgraph.number
## 1 0.667 REAC:R-MMU-6799990 rea 1
## 2 0.500 REAC:R-MMU-5660668 rea 2
## term.name relative.depth
## 1 Metal sequestration by antimicrobial proteins 1
## 2 CLEC7A/inflammasome pathway 1
## intersection
## 1 ENSMUSG00000032496,ENSMUSG00000056054
## 2 ENSMUSG00000026029,ENSMUSG00000027398
dlgnnorm_wrt_dlgnko_translatome <- translatome_plotter(pair_mtrx,
x_axis="normdlgn",
y_axis="kodlgn")
## No fc/lfc was provided, defaulting to 10 fold.
dlgnnorm_wrt_dlgnko_up_go <- simple_gprofiler(sig_genes=dlgnnorm_wrt_dlgnko_translatome$ups,
species="mmusculus")
## Performing gProfiler GO search of 14 genes against mmusculus.
## GO search found 0 hits.
## Performing gProfiler KEGG search of 14 genes against mmusculus.
## KEGG search found 0 hits.
## Performing gProfiler REAC search of 14 genes against mmusculus.
## REAC search found 1 hits.
## Performing gProfiler MI search of 14 genes against mmusculus.
## MI search found 0 hits.
## Performing gProfiler TF search of 14 genes against mmusculus.
## TF search found 0 hits.
## Performing gProfiler CORUM search of 14 genes against mmusculus.
## CORUM search found 0 hits.
## Performing gProfiler HP search of 14 genes against mmusculus.
## HP search found 0 hits.
dlgnnorm_wrt_dlgnko_down_go <- simple_gprofiler(sig_genes=dlgnnorm_wrt_dlgnko_translatome$downs,
species="mmusculus")
## Performing gProfiler GO search of 17 genes against mmusculus.
## GO search found 3 hits.
## Performing gProfiler KEGG search of 17 genes against mmusculus.
## KEGG search found 0 hits.
## Performing gProfiler REAC search of 17 genes against mmusculus.
## REAC search found 0 hits.
## Performing gProfiler MI search of 17 genes against mmusculus.
## MI search found 0 hits.
## Performing gProfiler TF search of 17 genes against mmusculus.
## TF search found 0 hits.
## Performing gProfiler CORUM search of 17 genes against mmusculus.
## CORUM search found 1 hits.
## Performing gProfiler HP search of 17 genes against mmusculus.
## HP search found 0 hits.
## query.number significant p.value term.size query.size overlap.size precision
## 1 1 TRUE 0.01190 154 6 3 0.5
## 2 1 TRUE 0.01800 29 4 2 0.5
## 3 1 TRUE 0.00932 21 4 2 0.5
## recall term.id domain subgraph.number term.name
## 1 0.019 GO:0045471 BP 1 response to ethanol
## 2 0.069 GO:0070717 MF 2 poly-purine tract binding
## 3 0.095 GO:0008143 MF 2 poly(A) binding
## relative.depth intersection
## 1 1 ENSMUSG00000021609,ENSMUSG00000026029,ENSMUSG00000037727
## 2 1 ENSMUSG00000021012,ENSMUSG00000023025
## 3 2 ENSMUSG00000021012,ENSMUSG00000023025
## No fc/lfc was provided, defaulting to 10 fold.
## Warning: Removed 1 rows containing missing values (geom_point).
dlgnko_wrt_scnko_up_go <- simple_gprofiler(sig_genes=dlgnko_wrt_scnko_translatome$ups,
species="mmusculus")
## Performing gProfiler GO search of 69 genes against mmusculus.
## GO search found 18 hits.
## Performing gProfiler KEGG search of 69 genes against mmusculus.
## KEGG search found 1 hits.
## Performing gProfiler REAC search of 69 genes against mmusculus.
## REAC search found 1 hits.
## Performing gProfiler MI search of 69 genes against mmusculus.
## MI search found 0 hits.
## Performing gProfiler TF search of 69 genes against mmusculus.
## TF search found 0 hits.
## Performing gProfiler CORUM search of 69 genes against mmusculus.
## CORUM search found 1 hits.
## Performing gProfiler HP search of 69 genes against mmusculus.
## HP search found 0 hits.
## query.number significant p.value term.size query.size overlap.size
## 1 1 TRUE 0.012600 89 9 3
## 2 1 TRUE 0.007540 75 9 3
## 3 1 TRUE 0.000911 558 20 7
## 4 1 TRUE 0.009520 3235 23 13
## 5 1 TRUE 0.003780 47 40 4
## 6 1 TRUE 0.018600 3444 26 14
## 7 1 TRUE 0.003890 295 16 5
## 8 1 TRUE 0.009500 1329 23 9
## 9 1 TRUE 0.012100 588 18 6
## 10 1 TRUE 0.011900 587 18 6
## 11 1 TRUE 0.011700 585 18 6
## 12 1 TRUE 0.011700 585 18 6
## 13 1 TRUE 0.004730 443 20 6
## 14 1 TRUE 0.008770 3212 23 13
## 15 1 TRUE 0.007800 3773 23 14
## 16 1 TRUE 0.000434 500 20 7
## 17 1 TRUE 0.016900 1689 20 9
## 18 1 TRUE 0.000293 472 20 7
## precision recall term.id domain subgraph.number
## 1 0.333 0.034 GO:0015844 BP 1
## 2 0.333 0.040 GO:0051937 BP 1
## 3 0.350 0.013 GO:0010469 BP 7
## 4 0.565 0.004 GO:0023051 BP 4
## 5 0.100 0.085 GO:0009583 BP 9
## 6 0.538 0.004 GO:0065008 BP 5
## 7 0.312 0.017 GO:0001505 BP 5
## 8 0.391 0.007 GO:0007267 BP 6
## 9 0.333 0.010 GO:0099536 BP 6
## 10 0.333 0.010 GO:0099537 BP 6
## 11 0.333 0.010 GO:0098916 BP 6
## 12 0.333 0.010 GO:0007268 BP 6
## 13 0.300 0.014 GO:0023061 BP 6
## 14 0.565 0.004 GO:0010646 BP 2
## 15 0.609 0.004 GO:0048583 BP 8
## 16 0.350 0.014 GO:0030545 MF 3
## 17 0.450 0.005 GO:0005102 MF 3
## 18 0.350 0.015 GO:0048018 MF 3
## term.name relative.depth
## 1 monoamine transport 1
## 2 catecholamine transport 2
## 3 regulation of signaling receptor activity 1
## 4 regulation of signaling 1
## 5 detection of light stimulus 1
## 6 regulation of biological quality 1
## 7 regulation of neurotransmitter levels 2
## 8 cell-cell signaling 1
## 9 synaptic signaling 2
## 10 trans-synaptic signaling 3
## 11 anterograde trans-synaptic signaling 4
## 12 chemical synaptic transmission 5
## 13 signal release 2
## 14 regulation of cell communication 1
## 15 regulation of response to stimulus 1
## 16 receptor regulator activity 1
## 17 signaling receptor binding 1
## 18 receptor ligand activity 2
## intersection
## 1 ENSMUSG00000021609,ENSMUSG00000021647,ENSMUSG00000023064
## 2 ENSMUSG00000021609,ENSMUSG00000021647,ENSMUSG00000023064
## 3 ENSMUSG00000018930,ENSMUSG00000021647,ENSMUSG00000023078,ENSMUSG00000024784,ENSMUSG00000027398,ENSMUSG00000028963,ENSMUSG00000029304
## 4 ENSMUSG00000018930,ENSMUSG00000021647,ENSMUSG00000023064,ENSMUSG00000023078,ENSMUSG00000024519,ENSMUSG00000024784,ENSMUSG00000025610,ENSMUSG00000026029,ENSMUSG00000027398,ENSMUSG00000028963,ENSMUSG00000029304,ENSMUSG00000031293,ENSMUSG00000035451
## 5 ENSMUSG00000029491,ENSMUSG00000031293,ENSMUSG00000037446,ENSMUSG00000056043
## 6 ENSMUSG00000006764,ENSMUSG00000018930,ENSMUSG00000021012,ENSMUSG00000021609,ENSMUSG00000021647,ENSMUSG00000023064,ENSMUSG00000023078,ENSMUSG00000024519,ENSMUSG00000027398,ENSMUSG00000028963,ENSMUSG00000029304,ENSMUSG00000029491,ENSMUSG00000035451,ENSMUSG00000037446
## 7 ENSMUSG00000006764,ENSMUSG00000021609,ENSMUSG00000023064,ENSMUSG00000024519,ENSMUSG00000027398
## 8 ENSMUSG00000021609,ENSMUSG00000021647,ENSMUSG00000023064,ENSMUSG00000023078,ENSMUSG00000024519,ENSMUSG00000027398,ENSMUSG00000028963,ENSMUSG00000029304,ENSMUSG00000035451
## 9 ENSMUSG00000021609,ENSMUSG00000021647,ENSMUSG00000023064,ENSMUSG00000024519,ENSMUSG00000027398,ENSMUSG00000028963
## 10 ENSMUSG00000021609,ENSMUSG00000021647,ENSMUSG00000023064,ENSMUSG00000024519,ENSMUSG00000027398,ENSMUSG00000028963
## 11 ENSMUSG00000021609,ENSMUSG00000021647,ENSMUSG00000023064,ENSMUSG00000024519,ENSMUSG00000027398,ENSMUSG00000028963
## 12 ENSMUSG00000021609,ENSMUSG00000021647,ENSMUSG00000023064,ENSMUSG00000024519,ENSMUSG00000027398,ENSMUSG00000028963
## 13 ENSMUSG00000021647,ENSMUSG00000023064,ENSMUSG00000024519,ENSMUSG00000027398,ENSMUSG00000028963,ENSMUSG00000029304
## 14 ENSMUSG00000018930,ENSMUSG00000021647,ENSMUSG00000023064,ENSMUSG00000023078,ENSMUSG00000024519,ENSMUSG00000024784,ENSMUSG00000025610,ENSMUSG00000026029,ENSMUSG00000027398,ENSMUSG00000028963,ENSMUSG00000029304,ENSMUSG00000031293,ENSMUSG00000035451
## 15 ENSMUSG00000018930,ENSMUSG00000021609,ENSMUSG00000021647,ENSMUSG00000022661,ENSMUSG00000023064,ENSMUSG00000023078,ENSMUSG00000024784,ENSMUSG00000025610,ENSMUSG00000026029,ENSMUSG00000027398,ENSMUSG00000028963,ENSMUSG00000029304,ENSMUSG00000031293,ENSMUSG00000035451
## 16 ENSMUSG00000018930,ENSMUSG00000021647,ENSMUSG00000023078,ENSMUSG00000024784,ENSMUSG00000027398,ENSMUSG00000028963,ENSMUSG00000029304
## 17 ENSMUSG00000018930,ENSMUSG00000021609,ENSMUSG00000021647,ENSMUSG00000023078,ENSMUSG00000024784,ENSMUSG00000026029,ENSMUSG00000027398,ENSMUSG00000028963,ENSMUSG00000029304
## 18 ENSMUSG00000018930,ENSMUSG00000021647,ENSMUSG00000023078,ENSMUSG00000024784,ENSMUSG00000027398,ENSMUSG00000028963,ENSMUSG00000029304
dlgnko_wrt_scnko_down_go <- simple_gprofiler(sig_genes=dlgnko_wrt_scnko_translatome$downs,
species="mmusculus")
## Performing gProfiler GO search of 67 genes against mmusculus.
## GO search found 2 hits.
## Performing gProfiler KEGG search of 67 genes against mmusculus.
## KEGG search found 0 hits.
## Performing gProfiler REAC search of 67 genes against mmusculus.
## REAC search found 1 hits.
## Performing gProfiler MI search of 67 genes against mmusculus.
## MI search found 0 hits.
## Performing gProfiler TF search of 67 genes against mmusculus.
## TF search found 0 hits.
## Performing gProfiler CORUM search of 67 genes against mmusculus.
## CORUM search found 3 hits.
## Performing gProfiler HP search of 67 genes against mmusculus.
## HP search found 0 hits.
## query.number significant p.value term.size query.size overlap.size precision
## 1 1 TRUE 0.0205 8 13 2 0.154
## 2 1 TRUE 0.0108 27 27 3 0.111
## recall term.id domain subgraph.number term.name
## 1 0.250 GO:0001758 MF 2 retinal dehydrogenase activity
## 2 0.111 GO:0005520 MF 1 insulin-like growth factor binding
## relative.depth intersection
## 1 1 ENSMUSG00000013584,ENSMUSG00000029762
## 2 1 ENSMUSG00000035551,ENSMUSG00000037362,ENSMUSG00000042379
As I understand it, there is some interest in an ontology search using the ratio of ratios.
## [1] 1877
## [1] 476
ror_gprofiler_up <- simple_gprofiler(
sig_genes=ror_up, species="mmusculus",
excel=glue::glue("excel/{rundate}mm_ror_gpfoiler_up-v{ver}.xlsx"))
## Performing gProfiler GO search of 1877 genes against mmusculus.
## GO search found 271 hits.
## Performing gProfiler KEGG search of 1877 genes against mmusculus.
## KEGG search found 8 hits.
## Performing gProfiler REAC search of 1877 genes against mmusculus.
## REAC search found 11 hits.
## Performing gProfiler MI search of 1877 genes against mmusculus.
## MI search found 0 hits.
## Performing gProfiler TF search of 1877 genes against mmusculus.
## TF search found 376 hits.
## Performing gProfiler CORUM search of 1877 genes against mmusculus.
## CORUM search found 1 hits.
## Performing gProfiler HP search of 1877 genes against mmusculus.
## HP search found 5 hits.
## Writing data to: excel/20200116mm_ror_gpfoiler_up-v20200114.xlsx.
## Finished writing data.
## Warning: Removed 1 rows containing missing values (geom_col).
ror_gprofiler_down <- simple_gprofiler(
sig_genes=ror_down, species="mmusculus",
excel=glue::glue("excel/{rundate}mm_ror_gpfoiler_down-v{ver}.xlsx"))
## Performing gProfiler GO search of 476 genes against mmusculus.
## GO search found 82 hits.
## Performing gProfiler KEGG search of 476 genes against mmusculus.
## KEGG search found 7 hits.
## Performing gProfiler REAC search of 476 genes against mmusculus.
## REAC search found 2 hits.
## Performing gProfiler MI search of 476 genes against mmusculus.
## MI search found 0 hits.
## Performing gProfiler TF search of 476 genes against mmusculus.
## TF search found 6 hits.
## Performing gProfiler CORUM search of 476 genes against mmusculus.
## CORUM search found 0 hits.
## Performing gProfiler HP search of 476 genes against mmusculus.
## HP search found 0 hits.
## Writing data to: excel/20200116mm_ror_gpfoiler_down-v20200114.xlsx.
## Finished writing data.