Notes on cytokines

doc/04-merge-cytokines.Rmd

@@ -35,7 +35,7 @@ sort(cytokines$SampleID)[1:10]
 ```
 
 ```{r}
-cytokines %>% 
+cytokines %>%
   filter(SampleID=="16K0007")
 ```
 
@@ -49,7 +49,7 @@ c1 = data %>%
 Oh, an error because the column names are different! Let's fix that by renaming the SampleID to subjectid
 
 ```{r}
-cytokines = cytokines %>% 
+cytokines = cytokines %>%
   rename(subjectid=SampleID)
 c1 = data %>%
   inner_join(cytokines, by="subjectid")
@@ -73,7 +73,7 @@ c1 %>%
                                    "C+21"="21",
                                   "DoD"="30"
                                    ))) %>%
-  ggplot(aes(t,IFNg,colour=phenotype)) + 
+  ggplot(aes(t,IFNg,colour=phenotype)) +
     geom_point()
 ```
 
@@ -81,8 +81,7 @@ Now let's try a linear regression
 
 
 ```{r}
-ggplot(c1,aes(phenotype,IFNg,colour=Timepoint)) + 
-    geom_point() 
-   
-```
+ggplot(c1,aes(phenotype,IFNg,colour=Timepoint)) +
+    geom_point()
 
+```

progress.org

@@ -7,9 +7,9 @@ datasets.
   + [X] Install Rstudio
   + [X] Install packages described in [[README.md]]
 
-- [-] Learning R and loading data
+- [X] Learning R and loading data
   + [X] Read 'R for Data Science'
-  + [ ] Read 'Discovering Statistics with R
+  + [X] Read 'Discovering Statistics with R
   + [X] Set current working directory in http://git.genenetwork.org/African-genetics/malaria-infect/src/branch/master/doc/02-load-data.Rmd#L13
   + [X] Read file in http://git.genenetwork.org/African-genetics/malaria-infect/src/branch/master/doc/02-load-data.Rmd#L27
   + [X] Some data attributes and simple plot in http://git.genenetwork.org/African-genetics/malaria-infect/src/branch/master/doc/02-load-data.Rmd#L62
@@ -25,7 +25,7 @@ datasets.
   + [X] Describe datasets in  http://git.genenetwork.org/African-genetics/malaria-infect/src/branch/master/doc/01-datasets.md
   + [ ] Assess new dataset with covariates
 
-- [-] Modelling
+- [-] Modeling
   + [X] Schizont/ELISA vs time to diagnosis, see https://biogems.info/KEMRI/Malaria/03-using-tidyverse.html
   + [X] Merge cytokines with covariates
   + [ ] Explore cytokines responses with groups
@@ -50,7 +50,12 @@ Francis Ndungu & Pjotr Prins
   units)
   + ELISA maps to Schizont column (log10 transformed)
   + anti-schizont antibody is measured before infection
-- lumefantrine log10 too
+- Lumefantrine log10 too. Lumefantrine is an antimalarial drug. It is
+  only used in combination with artemether. The term "co-artemether"
+  is sometimes used to describe this combination. Lumefantrine has a
+  much longer half-life compared to artemether, and is therefore
+  thought to clear any residual parasites that remain after
+  combination treatment.
 - Treg_freq – The frequency of Tregs as a proportion of CD4+ T cells
 - Treg_Ki67_FC – The fold change in the number of Tregs expressing
   Ki-67 (a proliferation marker) between C-1 and C+14
@@ -62,6 +67,8 @@ Francis Ndungu & Pjotr Prins
   cell marker)
 - Cytokine_status_cm1 – Detectable level of pro-inflammatory cytokines
   at C-1 (1 = yes, 0 = no)
+- Measured cytokines [[https://en.wikipedia.org/wiki/Interferon_type_I][IFNa]], [[https://en.wikipedia.org/wiki/Interferon_gamma][IFNg]], [[https://en.wikipedia.org/wiki/Interleukin_1_beta][IL1.b]], [[https://en.wikipedia.org/wiki/Interleukin_2][IL.2]], [[https://en.wikipedia.org/wiki/Interleukin_4][LI.4]], [[https://en.wikipedia.org/wiki/Interleukin_17][IL.17]], [[https://en.wikipedia.org/wiki/Tumor_necrosis_factor][TNFa]],
+  [[https://en.wikipedia.org/wiki/Transforming_growth_factor_beta][TGFb]], [[https://en.wikipedia.org/wiki/Interleukin_10][IL10]].
 - Screening PCR – Whether the volunteer had detectable parasitaemia at
   screening by qPCR (1 = yes, 0 = no)
 - Symptoms_DoD – (Treated group only) whether the volunteer was
@@ -71,3 +78,46 @@ Francis Ndungu & Pjotr Prins
   yes, 0 = no)
 - IL10_DoD – Whether the volunteer had detectable IL-10 at the day of
   Diagnosis (1 = yes, 0 = no)
+
+* Notes
+
+** Cytokines
+
+Cytokines are a broad and loose category of small proteins (~5–20 kDa)
+important in cell signaling. Cytokines are peptides and cannot cross
+the lipid bilayer of cells to enter the cytoplasm. A given cytokine
+may be produced by more than one type of cell. They act through
+cell surface receptors and are especially important in the immune
+system; cytokines modulate the balance between humoral and cell-based
+immune responses.
+
+For malaria the relative balance between Th1 and Th2 cytokines appears
+crucial. Th1 cytokines, interleukin-12 (IL-12) and gamma interferon
+(IFN-γ), and anti-inflammatory Th2 cytokines, IL-4 and IL-10 play a
+role.
+
+Interleukin 10 (IL-10), also known as human cytokine synthesis
+inhibitory factor (CSIF), is an anti-inflammatory cytokine. In humans,
+interleukin 10 is encoded by the IL10 gene. IL-10 downregulates the
+expression of Th1 cytokines, MHC class II antigens, and co-stimulatory
+molecules on macrophages. It also enhances B cell survival,
+proliferation, and antibody production. IL-10 can block NF-κB
+activity, and is involved in the regulation of the JAK-STAT signaling
+pathway. IL-10 counteracts the hyperactive immune response in the
+human body.
+
+* T helper cells (CD4+)
+
+The T helper cells (Th cells), also known as CD4+ cells, are a type of
+T cell that play an important role in the immune system, particularly
+in the adaptive immune system. They help the activity of other immune
+cells by releasing T cell cytokines. These cells help suppress or
+regulate immune responses.
+
+* Regulatory T cells (Tregs)
+
+The regulatory T cells (Tregs /ˈtiːrɛɡ/ or Treg cells), formerly known
+as suppressor T cells, are a subpopulation of T cells that modulate
+the immune system, maintain tolerance to self-antigens, and prevent
+autoimmune disease. Tregs are immunosuppressive and generally suppress
+or downregulate induction and proliferation of effector T cells.