From 7cfa2abf70dfba8640cb481f3c817313a2f71d7a Mon Sep 17 00:00:00 2001 From: Roy Francis Date: Mon, 6 Jan 2025 21:08:48 +0100 Subject: [PATCH] Updated DGE on chr19 list --- topics/rnaseq/lab_rnaseq.qmd | 68 ++++++++++++++++++------------------ 1 file changed, 34 insertions(+), 34 deletions(-) diff --git a/topics/rnaseq/lab_rnaseq.qmd b/topics/rnaseq/lab_rnaseq.qmd index e678cb60..7c15f8e6 100644 --- a/topics/rnaseq/lab_rnaseq.qmd +++ b/topics/rnaseq/lab_rnaseq.qmd @@ -1141,40 +1141,40 @@ For every file you open a number of panels are opened that visualise the data in To see actual reads you have to zoom in until the reads are drawn on screen. If you have a gene of interest you can also use the search box to directly go to that gene. -Here is the list of top 30 differentially expressed genes on Chr19 ordered by absolute fold change. The adjusted p value is shown as padj, the average expression of the gene is shown as baseMean. - -``` - ensembl_gene_id external_gene_name baseMean log2FoldChange padj gene_biotype -1 ENSMUSG00000117896 AA387883 59.94083 -2.7846887 1.943690e-17 lncRNA -2 ENSMUSG00000024799 Tm7sf2 947.63388 -2.0385744 1.677171e-44 protein_coding -3 ENSMUSG00000025172 Ankrd2 59.28633 1.7519899 1.261004e-08 protein_coding -4 ENSMUSG00000049134 Nrap 220.59983 1.6993887 1.067822e-08 protein_coding -5 ENSMUSG00000024935 Slc1a1 63.82987 1.6821634 1.652208e-09 protein_coding -6 ENSMUSG00000037071 Scd1 6678.59981 -1.4473717 2.961722e-14 protein_coding -7 ENSMUSG00000024665 Fads2 3269.79425 -1.4152150 3.134559e-29 protein_coding -8 ENSMUSG00000024747 Aldh1a7 65.81205 -1.3544431 1.002599e-06 protein_coding -9 ENSMUSG00000025216 Lbx1 26.03640 1.3356124 1.328372e-04 protein_coding -10 ENSMUSG00000056290 Ms4a4b 23.27050 1.3299845 5.015617e-05 protein_coding -11 ENSMUSG00000025221 Kcnip2 34.13675 -1.3165310 1.463369e-04 protein_coding -12 ENSMUSG00000032648 Pygm 1129.47092 1.2452572 2.736196e-04 protein_coding -13 ENSMUSG00000043639 Rbm20 51.36261 1.1816554 7.774718e-04 protein_coding -14 ENSMUSG00000118032 Gm50147 39.53043 -1.1797580 3.794393e-04 lncRNA -15 ENSMUSG00000036278 Macrod1 244.02353 1.0824415 4.984802e-07 protein_coding -16 ENSMUSG00000025203 Scd2 44054.03491 -1.0504733 1.874759e-11 protein_coding -17 ENSMUSG00000010663 Fads1 4074.38868 -1.0503935 1.470460e-18 protein_coding -18 ENSMUSG00000060675 Plaat3 5284.36470 -1.0462725 2.114719e-13 protein_coding -19 ENSMUSG00000016496 Cd274 35.91671 1.0175443 5.632932e-03 protein_coding -20 ENSMUSG00000024673 Ms4a1 25.80723 1.0130356 6.294275e-03 protein_coding -21 ENSMUSG00000032773 Chrm1 76.11444 0.9262597 7.665519e-04 protein_coding -22 ENSMUSG00000067279 Ppp1r3c 162.14777 0.9018589 3.672613e-04 protein_coding -23 ENSMUSG00000025013 Tll2 108.20333 -0.9012959 1.249858e-03 protein_coding -24 ENSMUSG00000006457 Actn3 1322.01659 0.8988003 1.352229e-02 protein_coding -25 ENSMUSG00000075289 Carns1 1003.91026 -0.8819988 4.982949e-10 protein_coding -26 ENSMUSG00000075010 AW112010 56.94897 0.8128744 4.027595e-02 lncRNA -27 ENSMUSG00000025227 Mfsd13a 107.55434 -0.8126676 1.107050e-03 protein_coding -28 ENSMUSG00000067242 Lgi1 506.42577 -0.7842945 2.570293e-06 protein_coding -29 ENSMUSG00000024812 Tjp2 1478.96029 -0.7627251 9.004722e-07 protein_coding -30 ENSMUSG00000047368 Abhd17b 1562.07350 -0.7625545 5.750875e-07 protein_coding +Here is the list of top 20 differentially expressed genes on Chr19 ordered by absolute fold change. The adjusted p value is shown as padj, the average expression of the gene is shown as baseMean. + +```{r} +#| eval: false +#| echo: false +readRDS("dge_r#| esults_full.rds") %>% + filter(chromosome_name == 19, padj < 0.05) %>% + arrange(-abs(log2FoldChange)) %>% + head(20) %>% + select(external_gene_name, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj) +``` + +``` + external_gene_name baseMean log2FoldChange lfcSE stat pvalue padj +1 AA387883 59.94083 -2.784689 0.2706306 -9.076824 1.117894e-19 1.943690e-17 +2 Tm7sf2 947.63388 -2.038574 0.1399445 -14.539498 6.809003e-48 1.677171e-44 +3 Ankrd2 59.28633 1.751990 0.2747018 6.323854 2.551188e-10 1.261004e-08 +4 Nrap 220.59983 1.699389 0.2680529 6.352080 2.124228e-10 1.067822e-08 +5 Slc1a1 63.82987 1.682163 0.2501657 6.651224 2.906652e-11 1.652208e-09 +6 Scd1 6678.59981 -1.447372 0.1767165 -8.190325 2.605209e-16 2.961722e-14 +7 Fads2 3269.79425 -1.415215 0.1201146 -11.779700 4.966970e-32 3.134559e-29 +8 Aldh1a7 65.81205 -1.354443 0.2413361 -5.548387 2.883175e-08 1.002599e-06 +9 Lbx1 26.03640 1.335612 0.2954499 4.503693 6.678261e-06 1.328372e-04 +10 Ms4a4b 23.27050 1.329984 0.2927615 4.729255 2.253447e-06 5.015617e-05 +11 Kcnip2 34.13675 -1.316531 0.2914951 -4.479672 7.475767e-06 1.463369e-04 +12 Pygm 1129.47092 1.245257 0.2912826 4.323631 1.534817e-05 2.736196e-04 +13 Rbm20 51.36261 1.181655 0.2927293 4.051754 5.083520e-05 7.774718e-04 +14 Gm50147 39.53043 -1.179758 0.2754761 -4.239382 2.241359e-05 3.794393e-04 +15 Macrod1 244.02353 1.082442 0.1904105 5.681007 1.339039e-08 4.984802e-07 +16 Scd2 44054.03491 -1.050473 0.1434332 -7.323814 2.410205e-13 1.874759e-11 +17 Fads1 4074.38868 -1.050393 0.1121926 -9.361514 7.860230e-21 1.470460e-18 +18 Plaat3 5284.36470 -1.046273 0.1317594 -7.940261 2.017561e-15 2.114719e-13 +19 Cd274 35.91671 1.017544 0.2938405 3.474263 5.122580e-04 5.632932e-03 +20 Ms4a1 25.80723 1.013036 0.2949268 3.437803 5.864549e-04 6.294275e-03 ``` Have a look at few of the interesting genes on Chr19 using the `external_gene_name` identifier. Look into gene **Tm7sf2** or **Ankrd2**. You might have to right-click and change option to **Squished** to see more reads.