## Perform Evolutionary Transcriptomics with R

The main goal of myTAI is to take any gene age assignment table and expression dataset as input and quantify the transcriptome conservation of the studied biological process or treatment. For this purpose, myTAI combines a gene age assignment table and expression dataset and provides functionality to capture evolutionary signatures that are hidden in these transcriptomes. This approach allows to study the evolution of biological processes and to detect stages or periods of evolutionary conservation or variability.

## Getting Started

myTAI takes either a phylostratigraphic map (gene age assignment table) or a divergence stratigraphic map (sequence divergence assignment table) and an expression dataset as input and provides functions to capture and investigate evolutionary signatures that are hidden in these transcriptomes.

The three input tables: phylostratigraphic map, divergence stratigraphic map, and the expression dataset need to fulfill specific data formats when using myTAI.

The following code illustrates how an example phylostratigraphic map and divergence stratigraphic map table is structured:

# load myTAI
library(myTAI)

# load example data sets (stored in myTAI)
data(PhyloExpressionSetExample)
data(DivergenceExpressionSetExample)

# show an example phylostratigraphic map of Arabidopsis thaliana
head(PhyloExpressionSetExample[ , c("Phylostratum","GeneID")])
  Phylostratum      GeneID
1            1 at1g01040.2
2            1 at1g01050.1
3            1 at1g01070.1
4            1 at1g01080.2
5            1 at1g01090.1
6            1 at1g01120.1

In detail, a phylostratigraphic map stores the gene age assignment generated with phylostratigraphy in the first columns and the corresponding gene id in the second column.

Analogously, a divergence stratigraphic map stores the gene age assignment generated with divergence stratigraphy in the first column and the corresponding gene id in the second column:

# show an example structure of a Divergence Map
head(DivergenceExpressionSetExample[ , c("Divergence.stratum","GeneID")])
  Divergence.stratum      GeneID
1                  1 at1g01050.1
2                  1 at1g01120.1
3                  1 at1g01140.3
4                  1 at1g01170.1
5                  1 at1g01230.1
6                  1 at1g01540.2

Hence, myTAI relies on pre-computed phylostratigraphic maps and divergence stratigraphic maps. For this purpose, users can consult the following resources to generate or retrieve phylostratigraphic maps and divergence stratigraphic maps which can then be used with myTAI.

### Generate or retrieve divergence stratigraphic maps

In general, users can construct their own gene age assignment methods and are not limited to the methods listed above. After formatting the corresponding results to the phylostratigraphic map or divergence stratigraphic map specification (age assignment in the first column and gene id in the second column), users can use any function in myTAI with their custom gene age assignment table.

### Expression dataset specification

The aim of any phylotranscriptomics study is to quantify transcriptome conservation in biological processes. For this purpose, users need to provide the transcriptome dataset of their studied biological process.

In the following examples we will use a gene expression dataset covering seven stages of Arabidopsis thaliana embryo development. This data format is defined as ExpressionMatrix in the myTAI data format specification.

# gene expression set

GeneID     Zygote   Quadrant   Globular      Heart    Torpedo       Bent    Mature
1 at1g01040.2  2173.6352  1911.2001  1152.5553  1291.4224  1000.2529   962.9772 1696.4274
2 at1g01050.1  1501.0141  1817.3086  1665.3089  1564.7612  1496.3207  1114.6435 1071.6555
3 at1g01070.1  1212.7927  1233.0023   939.2000   929.6195   864.2180   877.2060  894.8189
4 at1g01080.2  1016.9203   936.3837  1181.3381  1329.4734  1392.6429  1287.9746  861.2605
5 at1g01090.1 11424.5667 16778.1685 34366.6493 39775.6405 56231.5689 66980.3673 7772.5617
6 at1g01120.1   844.0414   787.5929   859.6267   931.6180   942.8453   870.2625  792.7542

The function MatchMap() allows users to join a phylostratigraphic map with an ExpressionMatrix to obtain a joined table referred to as PhyloExpressionSet. In some cases, the GeneIDs stored in the ExpressionMatrix and in the phylostratigraphic map do not match. This is due to GeneID mappings between different databases and annotations. To map non matching GeneIDs between databases and annotations, please consult the Functional Annotation Vignette in the biomartr package. The biomartr package allows users to map GeneIDs between database annotations.

After matching a phylostratigraphic map with an ExpressionMatrix using the MatchMap() function, a standard PhyloExpressionSet is returned storing the phylostratum assignment of a given gene in the first column, the gene id of the corresponding gene in the second column, and the entire gene expression set (time series or treatments) starting with the third column. This format is crucial for all functions that are implemented in the myTAI package.

library(myTAI)

# load the example data set
data(PhyloExpressionSetExample)

# construct an example Phylostratigraphic Map
Example.PhylostratigraphicMap <- PhyloExpressionSetExample[ , 1:2]
# construct an example ExpressionMatrix
Example.ExpressionMatrix <- PhyloExpressionSetExample[ , 2:9]

# join a PhylostratigraphicMap with an ExpressionMatrix using MatchMap()
Example.PhyloExpressionSet <- MatchMap(Example.PhylostratigraphicMap, Example.ExpressionMatrix)

# look at a standard PhyloExpressionSet
head(Example.PhyloExpressionSet, 3)
Phylostratum      GeneID    Zygote  Quadrant  Globular    Heart  Torpedo     Bent   Mature
1            4 at1g01010.1  878.2158  828.2301  776.0703 753.9589 775.3377 756.2460 999.9118
2            2 at1g01020.1 1004.9710 1106.2621 1037.5141 939.0830 961.5249 871.4684 997.5953
3            3 at1g01030.1  819.4880  771.6396  810.8717 866.7780 773.7893 747.9941 785.6105

Analogous to a standard PhyloExpressionSet, a standard DivergenceExpressionSet is a data.frame storing the divergence stratum assignment of a given gene in the first column, the gene id of the corresponding gene in the second column, and the entire gene expression set (time series or treatments) starting with the third column.

The following DivergenceExpressionSet example illustrates the standard DivergenceExpressionSet data set format.

# head of an example standard DivergenceExpressionSet
head(DivergenceExpressionSetExample, 3) 
  Divergence.stratum      GeneID    Zygote  Quadrant  Globular    Heart   Torpedo      Bent    Mature
1                  1 at1g01050.1 1501.0141 1817.3086 1665.3089 1564.761 1496.3207 1114.6435 1071.6555
2                  1 at1g01120.1  844.0414  787.5929  859.6267  931.618  942.8453  870.2625  792.7542
3                  1 at1g01140.3 1041.4291  908.3929 1068.8832  967.749 1055.1901 1109.4662  825.4633


A DivergenceExpressionSet defines the joined table between a divergence stratigraphic map and a Expression Set. A DivergenceExpressionSet can be generated analogous to a PhyloExpressionSet by joining a divergence stratigraphic map with an ExpressionMatrix using the MatchMap() function. In some cases, the GeneIDs stored in the ExpressionMatrix and in the divergence stratigraphic map do not match. This is due to GeneID mappings between different databases and annotations. To map non matching GeneIDs between databases and annotations, please consult the Functional Annotation Vignette in the biomartr package.

Each function implemented in myTAI checks internally whether or not the PhyloExpressionSet or DivergenceExpressionSet standard is fulfilled.

# used by all myTAI functions to check the validity of the PhyloExpressionSet standard
is.ExpressionSet(PhyloExpressionSetExample) 
[1] TRUE


In case the PhyloExpressionSet standard is violated, the is.ExpressionSet() function will return FALSE and the corresponding function within the myTAI package will return an error message.

# used a non standard PhyloExpressionSet
head(PhyloExpressionSetExample[ , 2:5], 2)
       GeneID   Zygote Quadrant Globular
1 at1g01040.2 2173.635 1911.200 1152.555
2 at1g01050.1 1501.014 1817.309 1665.309

is.ExpressionSet(PhyloExpressionSetExample[ , 2:5]) 

Error in is.ExpressionSet(PhyloExpressionSetExample[, 2:5]) :
The present input object does not fulfill the ExpressionSet standard.


The PhyloExpressionSet and DivergenceExpressionSet formats are crucial for all functions that are implemented in the myTAI package.

Keeping these standard data formats in mind will provide users with the most important requirements to get started with the myTAI package.

Note, that within the code of each function, the argument ExpressionSet always refers to either a PhyloExpressionSet or a DivergenceExpressionSet, whereas in specialized functions some arguments are specified as PhyloExpressionSet when they take an PhyloExpressionSet as input data set, or specified as DivergenceExpressionSet when they take an DivergenceExpressionSet as input data set.

## Performing a Standard Workflow for Phylotranscriptomics Analyses

In the beginning of each phylotranscriptomics study users should investigate the distribution of PS or DS within a given PhyloExpressionSet or DivergenceExpressionSet.

For this purpose, the PlotDistribution() function was implemented:

# Display the phylostratum distribution (gene frequency distribution)
# of a PhyloExpressionSet as absolute frequency distribution
PlotDistribution( PhyloExpressionSet = PhyloExpressionSetExample,
xlab               = "Phylostratum" )

or display it as relative frequencies:

# Plot phylostrata as relative frequency distribution
PlotDistribution( PhyloExpressionSet = PhyloExpressionSetExample,
as.ratio           = TRUE,
xlab               = "Phylostratum")

Another important feature to check is whether the phylostratum assignment and divergence stratum assignment of the genes stored within the PhyloExpressionSet and DivergenceExpressionSet are correlated (linear dependent). This is important to be able to assume the linear independence of TAI and TDI measures. This step is useful, because the TAI and TDI measures aim to quantify different signatures of evolutionary conservation. Whereas the TAI measure aims to quantify evolutionary signatures based on gene origin along the tree of life, the TDI measure is based on quantifying the selection pressure acting on orthologous genes between closely related species.

For this purpose the PlotCorrelation() function was implemented:

# Visualizing the correlation between Phylostratum and Divergence-Stratum assignments
# of the intersecting set of genes that are stored within the PhyloExpressionSet
# and DivergenceExpressionSet

PlotCorrelation( PhyloExpressionSet      = PhyloExpressionSetExample,
DivergenceExpressionSet = DivergenceExpressionSetExample,
method                  = "kendall",
linearModel             = TRUE )

In this case phylostratum and divergence stratum assignments of the intersecting set of genes that are stored within the PhyloExpressionSet and DivergenceExpressionSet are weakly correlated, but can be assumed to be linear independent.

Note: The PlotCorrelation() function always takes a PhyloExpressionSet as first argument and a DivergenceExpressionSet as second argument.

### Visualizing the Transcriptome Age Index and the Transcriptome Divergence Index

Mathematically, the Transcriptome Age Index (TAI) introduced by Domazet-Loso and Tautz, 2010 represents a weighted arithmetic mean of the transcriptome age during a corresponding developmental stage s.

$$TAI_s = \sum_{i = 1}^n \frac{ps_i * e_{is}}{\sum_{i = 1}^n e_{is}}$$

where $$ps_i$$ denotes the phylostratum assignment of gene $$i$$ and $$e_{is}$$ denotes the gene expression level of gene $$i$$ at developmental time point $$s$$. A lower value of TAI describes an older transcriptome age, whereas a higher value of TAI denotes a younger transcriptome age.

Analogous to the TAI measure, the Transcriptome Divergence Index (TDI) was introduced by Quint et al., 2012 and Drost et al., 2015 as global measure of average transcriptome selection pressure where $$s$$ denotes the corresponding developmental stage.

$$TDI_s = \sum_{i = 1}^n \frac{ds_i * e_{is}}{\sum_{i = 1}^n e_{is}}$$

where $$ds_i$$ denotes the divergence stratum assignment of gene $$i$$ and $$e_{is}$$ denotes the gene expression level of gene $$i$$ at developmental time point $$s$$. A lower value of TDI describes an more conserved transcriptome (in terms of sequence dissimilarity), whereas a higher value of TDI denotes a more variable transcriptome.

## Transcriptome Age Index Analyses

Evolutionary signatures of transcriptomes can be captured by computing transcriptome indices at different measured stages of development, combining these computed values to a transcriptome index profile across the measured stages, and comparing the resulting profile with a flat line. A profile not significantly deviating from a flat line indicates the absence of significant variations of the computed transcriptome index from stage to stage. In contrast, a profile significantly deviating from a flat line indicates the presence of significant variations from stage to stage. We refer to any transcriptome index profile significantly deviating from a flat line as phylotranscriptomic pattern or evolutionary signature.

Previously, we introduced three statistical tests to quantify the significance of observed TAI or TDI patterns: Flat Line Test, Reductive Hourglass Test, and Reductive Early Conservation Test (Drost et al., 2015).

The PlotPattern() function introduced in the following sections is the main analytics function of myTAI. PlotPattern() allows users to visualize TAI or TDI patterns and internally performs the following statistical tests to assess their significance.

### Flat Line Test

The PlotPattern() function with option TestStatistic = "FlatLineTest", first computes the TAI (given a PhyloExpressionSet) or the TDI (given a DivergenceExpressionSet) profile as well as their standard deviation, and statistical significance.

# Plot the Transcriptome Age Index of a given PhyloExpressionSet
# Test Statistic : Flat Line Test (default)
PlotPattern( ExpressionSet = PhyloExpressionSetExample,
TestStatistic = "FlatLineTest,
type          = "l",
lwd           = 6,
xlab          = "Ontogeny",
ylab          = "TAI" )

The p-value (p_flt) above the TAI curve is returned by the FlatLineTest. As described in the documentation of PlotPattern() (?PlotPattern or ?FlatLineTest), the FlatLineTest is the default statistical test to quantify the statistical significance of the observed phylotranscriptomic pattern. In detail, the test quantifies any statistically significant deviation of the phylotranscriptomic pattern from a flat line. Here, we define any significant deviation of a phylotranscriptomic pattern from a flat line as evolutionary signature Furthermore, we define corresponding stages of deviation as evolutionary conserved or variable (less conserved) depending on the magnitude of TAI and corresponding p-values.

### Reductive Hourglass Test

In case the observed phylotranscriptomic pattern not only significantly deviates from a flat line but also visually resembles an hourglass shape, one can obtain a p-value quantifying the statistical significance of a visual hourglass pattern based on the ReductiveHourglassTest (?ReductiveHourglassTest).

Since the ReductiveHourglassTest has been defined for a priori biological knowledge (Drost et al., 2015), the modules argument within the ReductiveHourglassTest() function needs to be specified.

Three modules need to be specified: an early-module, phylotypic module (mid), and a late-module.

For this example we divide A. thaliana embryo development stored within the PhyloExpressionSetExample into the following three modules:

• early = stages 1 - 2 (Zygote and Quadrant)
• mid = stages 3 - 5 (Globular, Heart, and Torpedo)
• late = stages 6 - 7 (Bent and Mature)
# Plot the Transcriptome Age Index of a given PhyloExpressionSet
# Test Statistic : Reductive Hourglass Test
PlotPattern( ExpressionSet = PhyloExpressionSetExample,
TestStatistic = "ReductiveHourglassTest",
modules       = list(early = 1:2, mid = 3:5, late = 6:7),
type          = "l",
lwd           = 6,
xlab          = "Ontogeny",
ylab          = "TAI" )

The corresponding p-value p_rht now denotes the p-value returned by the ReductiveHourglassTest which is different from the p-value returned by the FlatLineTest (p_flt).

To make sure that correct modules have been selected to perform the ReductiveHourglassTest, users can use the shaded.area argument to visualize chosen modules:

# Visualize the phylotypic period used for the Reductive Hourglass Test
PlotPattern( ExpressionSet = PhyloExpressionSetExample,
TestStatistic = "ReductiveHourglassTest",
modules       = list(early = 1:2, mid = 3:5, late = 6:7),
type          = "l",
lwd           = 6,
xlab          = "Ontogeny",
ylab          = "TAI" )

Note that for defining a priori knowledge for the ReductiveHourglassTest using the modules argument, modules need to start at stage 1, …, N and do not correspond to the column position in the PhyloExpressionSet/DivergenceExpressionSet which in contrast would start at position 3, … N + 2.

### Reductive Early Conservation Test

The third test statistic that is implemented in the myTAI package is the EarlyConservationTest.

The EarlyConservationTest tests whether an observed phylotranscriptomic pattern follows a low-high-high pattern (monotonically increasing function) supporting the Early Conservation Model of embryogenesis.

Analogous to the ReductiveHourglassTest, the EarlyConservationTest needs a priori biological knowledge Drost et al., 2015. So again three modules have to be specified for the EarlyConservationTest() function.

Three modules need to be specified: an early-module, phylotypic module (mid), and a late-module.

For this example we divide A. thaliana embryo development stored within the PhyloExpressionSetExample into the following three modules:

• early = stages 1 - 2 (Zygote and Quadrant)
• mid = stages 3 - 5 (Globular, Heart, and Torpedo)
• late = stages 6 - 7 (Bent and Mature)
# Plot the Transcriptome Age Index of a given PhyloExpressionSet
# Test Statistic : Reductive Early Conservation Test
PlotPattern( ExpressionSet = PhyloExpressionSetExample,
TestStatistic = "EarlyConservationTest",
modules       = list(early = 1:2, mid = 3:5, late = 6:7),
type          = "l",
lwd           = 6,
xlab          = "Ontogeny",
ylab          = "TAI" )

The corresponding p-value p_ect now denotes the p-value returned by the EarlyConservationTest which is different from the p-value returned by the FlatLineTest (p_flt) and ReductiveHourglassTest (p_rht).

Since the present TAI pattern of the PhyloExpressionSetExample doesn’t support the Early Conservation Hypothesis, the p-value p_ect = 1.

Again note that for defining a priori knowledge for the EarlyConservationTest using the modules argument, modules need to start at stage 1, …, N and do not correspond to the column position in the PhyloExpressionSet/DivergenceExpressionSet which in contrast would start at position 3, … N + 2.

To obtain the numerical TAI values, the TAI() function can be used:

# Compute the Transcriptome Age Index values of a given PhyloExpressionSet
TAI(PhyloExpressionSetExample) 
  Zygote Quadrant Globular    Heart  Torpedo     Bent   Mature
3.229942 3.225614 3.107135 3.116693 3.073993 3.176511 3.390334


## Transcriptome Divergence Index Analyses

Analogous to the TAI computations and visualization, the TDI computations can be performed in a similar fashion:

# Plot the Transcriptome Divergence Index of a given DivergenceExpressionSet
# Test Statistic : Flat Line Test (default)
PlotPattern( ExpressionSet = DivergenceExpressionSetExample,
type          = "l",
lwd           = 6,
xlab          = "Ontogeny",
ylab          = "TDI" )

Again, for the ReductiveHourglassTest we divide A. thaliana embryo development into three modules:

• early = stages 1 - 2 (Zygote and Quadrant)
• mid = stages 3 - 5 (Globular, Heart, and Torpedo)
• late = stages 6 - 7 (Bent and Mature)
# Plot the Transcriptome Divergence Index of a given DivergenceExpressionSet
# Test Statistic : Reductive Hourglass Test
PlotPattern( ExpressionSet = DivergenceExpressionSetExample,
TestStatistic = "ReductiveHourglassTest",
modules       = list(early = 1:2, mid = 3:5, late = 6:7),
type          = "l",
lwd           = 6,
xlab          = "Ontogeny",
ylab          = "TDI" )

And for the EarlyConservationTest we again divide A. thaliana embryo development into three modules:

• early = stages 1 - 2 (Zygote and Quadrant)
• mid = stages 3 - 5 (Globular, Heart, and Torpedo)
• late = stages 6 - 7 (Bent and Mature)
# Plot the Transcriptome Divergence Index of a given DivergenceExpressionSet
# Test Statistic : Reductive Early Conservation Test
PlotPattern( ExpressionSet = DivergenceExpressionSetExample,
TestStatistic = "EarlyConservationTest",
modules       = list(early = 1:2, mid = 3:5, late = 6:7),
type          = "l",
lwd           = 6,
xlab          = "Ontogeny",
ylab          = "TDI" )

To obtain the numerical TDI values for a given DivergenceExpressionSet simply run:

# Compute the Transcriptome Divergence Index values of a given DivergenceExpressionSet
TDI(DivergenceExpressionSetExample) 
  Zygote Quadrant Globular    Heart  Torpedo     Bent   Mature
4.532029 4.563200 4.485705 4.500868 4.466477 4.530704 4.690292


### Phylostratum or Divergence Stratum specific contribution to the global transcriptome index profile

Another way to visualize the cumulative contribution of each Phylostratum or Divergence Stratum to the global Transcriptome Age Index or Transcriptome Divergence Index profile was introduced by Domazet-Loso and Tautz, 2010 (Fig. 1b). The advantage of visualizing the cumulative contribution of each Phylostratum or Divergence Stratum to the global pattern is to study how the final (global) TAI or TDI profile emerges from the cumulative distribution of each Phylostratum or Divergence Stratum. This Phylostratum or Divergence Stratum specific contribution on the global TAI or TDI pattern can be visualized using PlotContribution():

#### Example: Phylostrata

# visualize phylostrata contribution to the global TAI pattern
PlotContribution( ExpressionSet = PhyloExpressionSetExample,
legendName    = "PS",
lwd           = 6,
cex           = 0.5)

The exact values of the Phylostratum specific cumulative TAI profiles can be obtained using the pTAI() function:

pTAI(PhyloExpressionSetExample)
      Zygote  Quadrant  Globular     Heart   Torpedo      Bent    Mature
1  0.3929533 0.3935308 0.4142106 0.4115399 0.4216806 0.4178302 0.3883815
2  0.9521021 0.9547833 0.9748522 0.9674842 0.9632213 0.9285336 0.8661883
3  1.0502814 1.0477016 1.0576104 1.0556300 1.0549156 1.0187303 0.9722031
4  1.3861830 1.3810595 1.3837548 1.3928030 1.3876006 1.3632945 1.3656170
5  1.5527473 1.5489829 1.5360986 1.5500708 1.5468767 1.5531699 1.5769758
6  1.8114772 1.8171167 1.7806803 1.7968463 1.8020203 1.8223456 1.9207232
7  1.8766090 1.8739449 1.8317327 1.8530276 1.8573216 1.8776292 1.9952325
8  1.9417254 1.9357499 1.8877436 1.9089144 1.9117438 1.9478303 2.0778287
9  2.0339192 2.0294517 1.9823091 1.9982678 1.9915249 2.0413791 2.1878074
10 2.4215868 2.4361137 2.3489524 2.3347670 2.3028346 2.3797112 2.5142773
11 2.4900201 2.5079107 2.4104647 2.3980760 2.3651571 2.4422093 2.5961316
12 3.2299418 3.2256139 3.1071348 3.1166934 3.0739935 3.1765113 3.3903336

#### Example: Divergence Strata

Analogously, the Divergence Stratum specific influence on the global TDI pattern can be visualized using:

# visualize divergence stratum contribution to global TDI
PlotContribution( ExpressionSet = DivergenceExpressionSetExample,
legendName    = "DS",
lwd           = 6,
cex           = 0.5)

The exact values of the Divergence Stratum specific cumulative TDI values can be obtained using the pTDI() function:

pTDI(DivergenceExpressionSetExample)
      Zygote  Quadrant  Globular     Heart   Torpedo      Bent    Mature
1  0.2174378 0.2207644 0.2309211 0.2214881 0.2195601 0.2047938 0.1704023
2  0.4800055 0.4762352 0.4821244 0.4752145 0.4799418 0.4695871 0.4288670
3  0.7742988 0.7597816 0.7797646 0.7826244 0.8033702 0.8034316 0.7769026
4  1.1463780 1.1285545 1.1408903 1.1528497 1.1694967 1.1784113 1.1933157
5  1.5652686 1.5489672 1.5545589 1.5698173 1.5934158 1.6003011 1.6330444
6  2.0899161 2.0609661 2.0666314 2.1015199 2.1163138 2.1306059 2.1932280
7  2.6262330 2.6035894 2.6012719 2.6453427 2.6477490 2.6664143 2.8085434
8  3.2211299 3.1990804 3.1767694 3.2319604 3.2292835 3.2693046 3.4412353
9  3.8396769 3.8299654 3.7793476 3.8353941 3.8272391 3.8971210 4.0753877
10 4.5320286 4.5632002 4.4857052 4.5008685 4.4664774 4.5307040 4.6902921

In both cases (Phylostrata and Divergence Strata) the pTAI() and pTDI() functions return a numeric matrix storing the cumulative TAI or TDI values for each Phylostratum and Divergence Stratum. Note, that the TAI values of Phylostratum 12 (in the pTAI() matrix) are equivalent to TAI(PhyloExpressionSetExample).

# show that the cumulative TAI value of PS 12 is
# equavalent to the global TAI() values
pTAI(PhyloExpressionSetExample)[12 , ]

# >  Zygote Quadrant Globular    Heart  Torpedo     Bent   Mature
# > 3.229942 3.225614 3.107135 3.116693 3.073993 3.176511 3.390334

TAI(PhyloExpressionSetExample)

# >  Zygote Quadrant Globular    Heart  Torpedo     Bent   Mature
# > 3.229942 3.225614 3.107135 3.116693 3.073993 3.176511 3.390334

This can be explained by the definition of the TAI. Here the sum of all partial TAI values over all Phylostrata is equals the global TAI values:

# show that the colSum() of partial TAI values
# over all Phylostrata equals the global TAI() values
apply(pStrata(PhyloExpressionSetExample) , 2 , sum)

# >  Zygote Quadrant Globular    Heart  Torpedo     Bent   Mature
# > 3.229942 3.225614 3.107135 3.116693 3.073993 3.176511 3.390334

Now, the PlotContribution() only differs from apply(pStrata(PhyloExpressionSetExample) , 2 , sum) by exchanging the sum() by cumsum().

# show that apply(pStrata(PhyloExpressionSetExample) , 2 , cumsum)
# is equivalent to pTAI()
apply(pStrata(PhyloExpressionSetExample) , 2 , cumsum)
      Zygote  Quadrant  Globular     Heart   Torpedo      Bent    Mature
1  0.3929533 0.3935308 0.4142106 0.4115399 0.4216806 0.4178302 0.3883815
2  0.9521021 0.9547833 0.9748522 0.9674842 0.9632213 0.9285336 0.8661883
3  1.0502814 1.0477016 1.0576104 1.0556300 1.0549156 1.0187303 0.9722031
4  1.3861830 1.3810595 1.3837548 1.3928030 1.3876006 1.3632945 1.3656170
5  1.5527473 1.5489829 1.5360986 1.5500708 1.5468767 1.5531699 1.5769758
6  1.8114772 1.8171167 1.7806803 1.7968463 1.8020203 1.8223456 1.9207232
7  1.8766090 1.8739449 1.8317327 1.8530276 1.8573216 1.8776292 1.9952325
8  1.9417254 1.9357499 1.8877436 1.9089144 1.9117438 1.9478303 2.0778287
9  2.0339192 2.0294517 1.9823091 1.9982678 1.9915249 2.0413791 2.1878074
10 2.4215868 2.4361137 2.3489524 2.3347670 2.3028346 2.3797112 2.5142773
11 2.4900201 2.5079107 2.4104647 2.3980760 2.3651571 2.4422093 2.5961316
12 3.2299418 3.2256139 3.1071348 3.1166934 3.0739935 3.1765113 3.3903336
pTAI(PhyloExpressionSetExample)
      Zygote  Quadrant  Globular     Heart   Torpedo      Bent    Mature
1  0.3929533 0.3935308 0.4142106 0.4115399 0.4216806 0.4178302 0.3883815
2  0.9521021 0.9547833 0.9748522 0.9674842 0.9632213 0.9285336 0.8661883
3  1.0502814 1.0477016 1.0576104 1.0556300 1.0549156 1.0187303 0.9722031
4  1.3861830 1.3810595 1.3837548 1.3928030 1.3876006 1.3632945 1.3656170
5  1.5527473 1.5489829 1.5360986 1.5500708 1.5468767 1.5531699 1.5769758
6  1.8114772 1.8171167 1.7806803 1.7968463 1.8020203 1.8223456 1.9207232
7  1.8766090 1.8739449 1.8317327 1.8530276 1.8573216 1.8776292 1.9952325
8  1.9417254 1.9357499 1.8877436 1.9089144 1.9117438 1.9478303 2.0778287
9  2.0339192 2.0294517 1.9823091 1.9982678 1.9915249 2.0413791 2.1878074
10 2.4215868 2.4361137 2.3489524 2.3347670 2.3028346 2.3797112 2.5142773
11 2.4900201 2.5079107 2.4104647 2.3980760 2.3651571 2.4422093 2.5961316
12 3.2299418 3.2256139 3.1071348 3.1166934 3.0739935 3.1765113 3.3903336

This pTAI() matrix is what is being visualized inside PlotContribution().

Note that the pStrata() function returns the partial TAI or TDI values for each Phylostratum or Divergence Stratum, whereas pMatrix() returns the partial TAI or TDI value for each gene.

# compute partial TAI values for each Phylostratum
pStrata(PhyloExpressionSetExample)
       Zygote   Quadrant   Globular      Heart    Torpedo       Bent     Mature
1  0.39295331 0.39353082 0.41421061 0.41153988 0.42168061 0.41783018 0.38838151
2  0.55914875 0.56125250 0.56064163 0.55594427 0.54154068 0.51070341 0.47780681
3  0.09817938 0.09291830 0.08275821 0.08814585 0.09169432 0.09019669 0.10601483
4  0.33590159 0.33335787 0.32614435 0.33717297 0.33268496 0.34456426 0.39341385
5  0.16656429 0.16792339 0.15234382 0.15726786 0.15927610 0.18987539 0.21135880
6  0.25872990 0.26813378 0.24458170 0.24677547 0.25514358 0.26917571 0.34374736
7  0.06513175 0.05682826 0.05105236 0.05618130 0.05530130 0.05528356 0.07450933
8  0.06511643 0.06180498 0.05601089 0.05588683 0.05442226 0.07020109 0.08259620
9  0.09219381 0.09370185 0.09456557 0.08935340 0.07978112 0.09354879 0.10997873
10 0.38766762 0.40666192 0.36664326 0.33649918 0.31130963 0.33833215 0.32646984
11 0.06843326 0.07179705 0.06151227 0.06330899 0.06232254 0.06249801 0.08185437
12 0.73992167 0.71770319 0.69667019 0.71861745 0.70883635 0.73430205 0.79420194
# compute partial TAI values for each gene
dplyr::glimpse(pMatrix(PhyloExpressionSetExample))
Observations: 25260
Variables:
$Zygote (dbl) 3.597950e-05, 2.484581e-05, 2.007498e-05, 1.683276e-05, 1.891073e-...$ Quadrant (dbl) 3.203218e-05, 3.045853e-05, 2.066542e-05, 1.569402e-05, 2.812062e-...
$Globular (dbl) 2.013329e-05, 2.909027e-05, 1.640631e-05, 2.063608e-05, 6.003300e-...$ Heart    (dbl) 2.311604e-05, 2.800871e-05, 1.663988e-05, 2.379714e-05, 7.119708e-...
$Torpedo (dbl) 1.813626e-05, 2.713080e-05, 1.566972e-05, 2.525094e-05, 1.019572e-...$ Bent     (dbl) 1.685284e-05, 1.950712e-05, 1.535178e-05, 2.254055e-05, 1.172208e-...
\$ Mature   (dbl) 2.684331e-05, 1.695727e-05, 1.415911e-05, 1.362810e-05, 1.229886e-...

You can receive all gene specific partial TAI values by typing pMatrix(PhyloExpressionSetExample).

Analogously, pStrata() and pMatrix() can be used for Divergence Strata by substituting PhyloExpressionSetExample by DivergenceExpressionSetExample.

### Mean Expression and Relative Expression of Single Phylostrata or Divergence Strata

TAI or TDI patterns are very useful to gain a first insight into the mean transcriptome age or mean sequence divergence of genes being most active during the corresponding developmental stage or experiment.

To further investigate the origins of the global TAI or TDI pattern it is useful to visualize the mean gene expression of each Phylostratum or Divergence-Stratum class.

### Mean Expression Levels of a PhyloExpressionSet and DivergenceExpressionSet

Visualizing the mean gene expression of genes corresponding to the same Phylostratum or Divergence Stratum class allows users to detect biological process specific groups of Phylostrata or Divergence Strata that are most expressed during the underlying biological process. This might lead to correlating specific groups of Phylostrata or Divergence Strata sharing similar evolutionary origins with common functions or functional contributions to a specific developmental process.

# Visualizing the mean gene expression of each Phylostratum class
PlotMeans( ExpressionSet = PhyloExpressionSetExample,
Groups        = list(1:12),
legendName    = "PS",
xlab          = "Ontogeny",
lty           = 1,
cex           = 0.7,
lwd           = 5 ) 

Here we see that the mean gene expression of Phylostratum group: PS1-3 (genes evolved before the establishment of embryogenesis in plants) are more expressed during A. thaliana embryogenesis than PS4-12 (genes evolved during or after the establishment of embryogenesis in plants).

In different biological processes different Phylostratum groups or combination of groups might resemble the majority of expressed genes.

The PlotMeans() function takes an PhyloExpressionSet or DivergenceExpressionSet and visualizes for each Phylostratum the mean expression levels of all genes that correspond to this Phylostratum. The Groups argument takes a list storing the Phylostrata (classified into the same group) that shall be visualized on the same plot.

For this example we separate groups of Phylostrata into evolutionary old Phylostrata (PS1-3) in one plot versus evolutionary younger Phylostrata (PS4-12) into another plot:

# Visualizing the mean gene expression of each Phylostratum class
# in two separate plots (groups)
PlotMeans( ExpressionSet = PhyloExpressionSetExample,
Groups        = list(group_1 = 1:3, group_2 = 4:12),
legendName    = "PS",
xlab          = "Ontogeny",
lty           = 1,
cex           = 0.7,
lwd           = 5 ) 

To obtain the numerical values (mean expression levels for all Phylostrata) run:

# Using the age.apply() function to compute the mean expression levels
# of all Phylostrata
age.apply( ExpressionSet = PhyloExpressionSetExample,
FUN           = colMeans ) 

Zygote Quadrant Globular    Heart  Torpedo     Bent   Mature
1  2607.882 2579.372 2604.856 2525.704 2554.825 2622.757 2696.331
2  2597.258 2574.745 2467.679 2388.045 2296.410 2243.716 2321.709
3  2528.272 2363.159 2019.436 2099.079 2155.642 2196.875 2855.866
4  1925.320 1887.078 1771.399 1787.175 1740.823 1867.981 2358.893
5  2378.883 2368.593 2061.729 2077.087 2076.693 2564.904 3157.761
6  1658.253 1697.242 1485.401 1462.613 1492.861 1631.741 2304.683
7  1993.321 1717.659 1480.525 1590.009 1545.078 1600.264 2385.409
8  1781.653 1670.106 1452.180 1414.052 1359.376 1816.718 2364.070
9  1758.119 1764.748 1708.815 1575.727 1388.920 1687.314 2193.930
10 2414.456 2501.390 2163.810 1938.060 1770.039 1993.032 2127.015
11 1999.163 2071.456 1702.779 1710.290 1662.099 1726.865 2501.443
12 2126.189 2036.804 1896.964 1909.578 1859.485 1995.732 2387.343


Here the age.apply() function (?age.apply) takes a function as argument that itself receives a data.frame as argument (e.g. colMeans()).

For a DivergenceExpressionSet run:

# Visualizing the mean gene expression of each Divergence Stratum class
PlotMeans( ExpressionSet = DivergenceExpressionSetExample,
Groups        = list(1:10),
legendName    = "DS",
xlab          = "Ontogeny",
lty           = 1,
cex           = 0.7,
lwd           = 5 ) 

To obtain the numerical values (mean expression levels for all Divergence Strata) run:

# Using the age.apply() function to compute the mean expression levels
# of all Divergence Strata
age.apply( ExpressionSet = DivergenceExpressionSetExample,
FUN           = colMeans ) 

Zygote Quadrant Globular    Heart  Torpedo     Bent   Mature
1  5222.189 5230.547 5254.464 4911.494 4807.936 4654.683 4277.490
2  3146.510 3020.156 2852.072 2807.367 2845.025 3002.967 3237.315
3  2356.008 2239.344 2257.539 2272.270 2360.816 2529.276 2912.164
4  2230.350 2180.706 2050.895 2049.035 2001.043 2127.165 2608.903
5  2014.600 1994.640 1884.899 1851.554 1858.913 1920.185 2210.391
6  2096.593 2018.440 1938.765 1961.828 1905.246 2005.523 2339.767
7  1836.290 1832.815 1734.319 1719.186 1659.044 1736.141 2201.981
8  1784.470 1762.151 1635.529 1624.682 1590.489 1711.439 1983.607
9  1649.254 1659.455 1522.214 1485.560 1453.689 1584.176 1767.276
10 1660.750 1735.086 1605.275 1473.854 1398.067 1438.258 1541.633


### Relative Expression Levels of a PhyloExpressionSet and DivergenceExpressionSet

Introduced by Domazet-Loso and Tautz, (2010), relative expression levels are defined as a linear transformation of the mean expression levels (of each Phylostratum or Divergence-Stratum) into the interval $$[0,1]$$ (Quint et al., 2012 and Drost et al., 2015). This procedure allows users to compare mean expression patterns between Phylostrata or Divergence Strata independent from their actual magnitude. Hence, relative expression profiles aim to correlate the mean expression profiles of groups of Phylostrata or Divergence Strata due to the assumption that genes or groups of genes sharing a similar expression profile might be regulated by similar gene regulatory mechanisms or contribute to similar biological processes.

The PlotRE() function can be used (analogous to the PlotMeans() function) to visualize the relative expression levels of a given PhyloExpressionSet and DivergenceExpressionSet:

# Visualizing the mean gene expression of each Phylostratum class
PlotRE( ExpressionSet = PhyloExpressionSetExample,
Groups        = list(1:10),
legendName    = "PS",
xlab          = "Ontogeny",
lty           = 1,
cex           = 0.7,
lwd           = 5 ) 
# Visualizing the mean gene expression of each Divergence Stratum class
PlotRE( ExpressionSet = DivergenceExpressionSetExample,
Groups        = list(1:10),
legendName    = "DS",
xlab          = "Ontogeny",
lty           = 1,
cex           = 0.7,
lwd           = 5 ) 

or again by assigning Phylostratum or Divergence Stratum groups that shall be visualized in different plots:

# Visualizing the mean gene expression of each Phylostratum class
PlotRE( ExpressionSet = PhyloExpressionSetExample,
Groups        = list(group_1 = 1:3, group_2 = 4:12),
legendName    = "PS",
xlab          = "Ontogeny",
lty           = 1,
cex           = 0.7,
lwd           = 5 ) 

The relative expression levels can be obtained using the REMatrix() function:

# Getting the relative expression levels for all Phylostrata
REMatrix(PhyloExpressionSetExample) 

Zygote  Quadrant   Globular      Heart    Torpedo       Bent    Mature
1  0.4816246 0.3145330 0.46389184 0.00000000 0.17067495 0.56880234 1.0000000
2  1.0000000 0.9363209 0.63348381 0.40823711 0.14904726 0.00000000 0.2206063
3  0.6083424 0.4109402 0.00000000 0.09521758 0.16284114 0.21213845 1.0000000
4  0.2985050 0.2366309 0.04946941 0.07499453 0.00000000 0.20573325 1.0000000
5  0.2893657 0.2799777 0.00000000 0.01401191 0.01365328 0.45908792 1.0000000
6  0.2323316 0.2786335 0.02706119 0.00000000 0.03592044 0.20084761 1.0000000
7  0.5666979 0.2620602 0.00000000 0.12099252 0.07133814 0.13232551 1.0000000
8  0.4203039 0.3092784 0.09237036 0.05442042 0.00000000 0.45520558 1.0000000
9  0.4586261 0.4668613 0.39738003 0.23205534 0.00000000 0.37067096 1.0000000
10 0.8811321 1.0000000 0.53841500 0.22974016 0.00000000 0.30490542 0.4881046
11 0.4015809 0.4877111 0.04846721 0.05741594 0.00000000 0.07716367 1.0000000
12 0.5052572 0.3359211 0.07100055 0.09489782 0.00000000 0.25811214 1.0000000

# Getting the relative expression levels for all Divergence-Strata
REMatrix(DivergenceExpressionSetExample) 
      Zygote  Quadrant   Globular      Heart    Torpedo      Bent    Mature
1  0.9669643 0.9755188 1.00000000 0.64894653 0.54294759 0.3860827 0.0000000
2  0.7888009 0.4949178 0.10397567 0.00000000 0.08758660 0.4549387 1.0000000
3  0.1733953 0.0000000 0.02704324 0.04893726 0.18054185 0.4309208 1.0000000
4  0.3772372 0.2955661 0.08201140 0.07895260 0.00000000 0.2074848 1.0000000
5  0.4543752 0.3987496 0.09292474 0.00000000 0.02050713 0.1912595 1.0000000
6  0.4403615 0.2605017 0.07713944 0.13021586 0.00000000 0.2307754 1.0000000
7  0.3264585 0.3200581 0.13864386 0.11077270 0.00000000 0.1420009 1.0000000
8  0.4934416 0.4366671 0.11457069 0.08697865 0.00000000 0.3076689 1.0000000
9  0.6236387 0.6561674 0.21851855 0.10163374 0.00000000 0.4161087 1.0000000
10 0.7794318 1.0000000 0.61482564 0.22487531 0.00000000 0.1192539 0.4259882


The same result could also be obtained by using the age.apply() function in combination with the RE() function:

# Getting the relative expression levels for all Phylostrata
age.apply( ExpressionSet = PhyloExpressionSetExample,
FUN           = RE ) 
      Zygote  Quadrant   Globular      Heart    Torpedo       Bent    Mature
1  0.4816246 0.3145330 0.46389184 0.00000000 0.17067495 0.56880234 1.0000000
2  1.0000000 0.9363209 0.63348381 0.40823711 0.14904726 0.00000000 0.2206063
3  0.6083424 0.4109402 0.00000000 0.09521758 0.16284114 0.21213845 1.0000000
4  0.2985050 0.2366309 0.04946941 0.07499453 0.00000000 0.20573325 1.0000000
5  0.2893657 0.2799777 0.00000000 0.01401191 0.01365328 0.45908792 1.0000000
6  0.2323316 0.2786335 0.02706119 0.00000000 0.03592044 0.20084761 1.0000000
7  0.5666979 0.2620602 0.00000000 0.12099252 0.07133814 0.13232551 1.0000000
8  0.4203039 0.3092784 0.09237036 0.05442042 0.00000000 0.45520558 1.0000000
9  0.4586261 0.4668613 0.39738003 0.23205534 0.00000000 0.37067096 1.0000000
10 0.8811321 1.0000000 0.53841500 0.22974016 0.00000000 0.30490542 0.4881046
11 0.4015809 0.4877111 0.04846721 0.05741594 0.00000000 0.07716367 1.0000000
12 0.5052572 0.3359211 0.07100055 0.09489782 0.00000000 0.25811214 1.0000000


Quint et al. (2012) introduced an additional way of visualizing the difference of relative expression levels between groups of Phylostrata/Divergence-Strata.

This bar plot comparing the mean relative expression levels of one Phylostratum/Divergence-Stratum group with all other groups can be plotted analogous to the PlotMeans() and PlotRE() functions:

# Visualizing the mean relative expression of two Phylostratum groups
PlotBarRE( ExpressionSet = PhyloExpressionSetExample,
Groups        = list(group_1 = 1:3, group_2 = 4:12),
xlab          = "Ontogeny",
ylab          = "Mean Relative Expression",
cex           = 2) 

Here the argument Groups = list(1:3, 4:12) corresponds to dividing Phylostrata 1-12 into Phylostratum groups defined as origin before embryogenesis (group one: PS1-3) and origin during or after embryogenesis (group two: PS4-12). A Kruskal-Wallis Rank Sum Test is then performed to test the statistical significance of the different bars that are compared. The ’*’ corresponds to a statistically significant difference.

Additionally the ratio between both values represented by the bars to be compared can be visualized as function within the bar plot using the ratio = TRUE argument:

# Visualizing the mean relative expression of two Phylostratum groups
PlotBarRE( ExpressionSet = PhyloExpressionSetExample,
Groups        = list(group_1 = 1:3, group_2 = 4:12),
ratio         = TRUE,
xlab          = "Ontogeny",
ylab          = "Mean Relative Expression",
cex           = 2 ) 

It is also possible to compare more than two groups:

# Visualizing the mean relative expression of three Phylostratum groups
PlotBarRE( ExpressionSet = PhyloExpressionSetExample,
Groups        = list(group_1 = 1:3, group_2 = 4:6, group_3 = 7:12),
wLength       = 0.05,
xlab          = "Ontogeny",
ylab          = "Mean Relative Expression",
cex           = 2 ) 

For the corresponding statistically significant stages, a Posthoc test can be performed to detect the combinations of differing bars that cause the global statistical significance.

# Supplementary Information

Most visualization functions in the myTAI package have an ellipsis argument (?dotsMethods) which allows you to modify the cex.lab, cex.axis, and cex arguments within the plot.

# cex = 0.5, cex.lab = 0.5, cex.axis = 0.5
PlotPattern( ExpressionSet = PhyloExpressionSetExample,
type          = "l",
lwd           = 6,
xlab          = "Ontogeny",
ylab          = "TAI",
cex           = 0.5,
cex.lab       = 0.5,
cex.axis      = 0.5 )

The cex argument modifies the the p-value font size, the cex.lab argument modifies the font size of the x-axis and y-axis labels, and the cex.axis argument modifies the font size of the axis labels.

More examples:

# cex = 2, cex.lab = 1, cex.axis = 0.5
PlotPattern( ExpressionSet = PhyloExpressionSetExample,
type          = "l",
lwd           = 6,
xlab          = "Ontogeny",
ylab          = "TAI",
cex           = 2,
cex.lab       = 1,
cex.axis      = 0.5 )
# cex = 0.5, cex.lab = 0.7, cex.axis = 1.5
PlotPattern( ExpressionSet = PhyloExpressionSetExample,
type          = "l",
lwd           = 6,
xlab          = "Ontogeny",
ylab          = "TAI",
cex           = 0.5,
cex.lab       = 0.7,
cex.axis      = 1.5 )

These arguments can analogously be used for all other plot functions, e.g. PlotMeans(), PlotRE(), etc.

### Saving Plots on Local Machine

To save plots generated with myTAI on a local machine users can use the following functions implemented in the R language: png, pdf, svg.

# save the TAI profile to a local machine with png()
png("ExampleTAIProfile.png", width = 800, height = 600)

PlotPattern( ExpressionSet = PhyloExpressionSetExample,
type          = "l",
lwd           = 6,
xlab          = "Ontogeny",
ylab          = "TAI",
cex           = 1,
cex.lab       = 1,
cex.axis      = 1.2 )

dev.off()

## References

Domazet-Loso T. and Tautz D. A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns. Nature (2010) 468: 815-8.

Quint M. et al. A transcriptomic hourglass in plant embryogenesis. Nature (2012) 490: 98-101.

Drost HG, Gabel A, Grosse I, Quint M. Evidence for Active Maintenance of Phylotranscriptomic Hourglass Patterns in Animal and Plant Embryogenesis. Mol. Biol. Evol. (2015) 32 (5): 1221-1231.