1
00:00:00,531 --> 00:00:03,133
This is a quick-start tutorial for
Cytoscape 3.

2
00:00:04,046 --> 00:00:07,856
Cytoscape is an open source, cross-
platform bioinformatics program written

3
00:00:07,856 --> 00:00:12,477
in Java. It is used to visualize molecular 
interaction networks and integrate these

4
00:00:12,479 --> 00:00:15,910
with expression profiles and other high 
throughput data sets. Additional

5
00:00:15,910 --> 00:00:20,070
functionality can be added by installing 
plugins called "apps". We won't be

6
00:00:20,076 --> 00:00:23,076
discussing apps any further in this video 
but we wanted you to know that they

7
00:00:23,076 --> 00:00:28,901
are available. For this tutorial, we'll be
using Cytoscape 3.6.1. If you're using

8
00:00:28,901 --> 00:00:32,231
a different version of Cytoscape, some
options may have been changed or moved.

9
00:00:32,231 --> 00:00:35,411
If any features discussed in this video
are different, please refer to the

10
00:00:35,411 --> 00:00:39,984
documentation at manual.cytoscape.org.
We'll be following along with the

11
00:00:39,984 --> 00:00:44,017
Basic Expression Analysis Tutorial in the
documentation. There is a more

12
00:00:44,017 --> 00:00:46,858
in-depth version of this tutorial there
if you need additional guidance.

13
00:00:47,134 --> 00:00:51,116
The original tutorial is covered by the
Creative Commons Zero v1.0

14
00:00:51,116 --> 00:00:52,516
Universal license.

15
00:00:53,608 --> 00:00:56,804
Let's jump right in!
Our first step will be to import a network

16
00:00:56,804 --> 00:01:00,572
from the sample data provided by
Cytoscape. Click on the "Import Network

17
00:01:00,572 --> 00:01:04,578
from File" button in the Tool Bar.
Navigate to the installation directory

18
00:01:04,578 --> 00:01:08,908
and find the folder called "sampleData".
Inside that folder, let's open

19
00:01:08,908 --> 00:01:14,498
"galFiltered.csv". Cytoscape is pretty
smart about choosing default settings

20
00:01:14,498 --> 00:01:17,648
as long as your data is in a reasonable
format, so we're going to accept the

21
00:01:17,648 --> 00:01:20,936
settings it chose for us. Just know that
there are a lot of options when you're

22
00:01:20,936 --> 00:01:24,956
importing data for choosing the type of
data each column contains. Click "OK".

23
00:01:26,258 --> 00:01:29,369
Cytoscape automatically tries to find a
good network structure for your data

24
00:01:29,369 --> 00:01:33,689
after you first import it. We can play with
the layout later, but first let's get a view

25
00:01:33,689 --> 00:01:37,392
of the entire network. Click the "Zoom
out to display all of current network"

26
00:01:37,392 --> 00:01:42,047
button in the toolbar. The edges may be
gone in your network when you do this,

27
00:01:42,047 --> 00:01:46,023
but you can get those back by clicking
"View > Show Graphics Details". This

28
00:01:46,023 --> 00:01:49,166
option does use a bit more resources
when there is a lot of nodes in your

29
00:01:49,166 --> 00:01:53,064
network, so it may be best to leave it off
when viewing large networks. The details

30
00:01:53,064 --> 00:01:54,894
will reappear when you zoom in.

31
00:01:55,985 --> 00:01:59,832
Now let's import our expression data.
Click on "Import Table from File" in the

32
00:01:59,832 --> 00:02:05,685
toolbar, then choose "galExpData.csv".
Cytoscape should choose the proper default

33
00:02:05,685 --> 00:02:09,465
settings, however you may need to choose
the proper key column to match with your

34
00:02:09,465 --> 00:02:11,645
network depending on how your data is
structured.

35
00:02:12,438 --> 00:02:16,128
If the import succeded, you should see the
new information in the Node Table. Let's

36
00:02:16,128 --> 00:02:20,008
limit the columns shown by clicking on the
"Show Columns" button in the Table Panel.

37
00:02:20,290 --> 00:02:27,130
Deselect the gal1RGsig, gal4RGsig, and
gal80Rsig columns.

38
00:02:27,786 --> 00:02:32,184
The "shared name" contains the Ensembl ID,
but let's change the node labels to HUGO

39
00:02:32,184 --> 00:02:35,814
Gene Nomenclature symbols contained in the
"COMMON" column.

40
00:02:36,405 --> 00:02:40,172
Click on the "Style" tab. If you click on
"default", you'll see there are a lot of

41
00:02:40,172 --> 00:02:44,557
different styles included with Cytoscape.
The button with 3 horizontal bars next to

42
00:02:44,557 --> 00:02:48,547
the style selection dropdown has options
for managing the styles such as creating a

43
00:02:48,547 --> 00:02:52,745
new style, copying the current style, and
renaming or removing the style.

44
00:02:53,726 --> 00:02:58,159
Click on the second column of the "Label"
option. Change the column to "COMMON" and

45
00:02:58,159 --> 00:03:00,129
you'll see the node labels change.

46
00:03:00,997 --> 00:03:05,020
Now we want to see the expression values
shown on the network. Click on the second

47
00:03:05,020 --> 00:03:10,670
column for the "Fill Color" option. For
the column, choose "gal80Rexp". For the

48
00:03:10,670 --> 00:03:13,595
mapping type, let's choose "Continuous
Mapping".

49
00:03:14,540 --> 00:03:18,235
Double click on the gradient to bring up
the "Continuous Mapping Editor". You can

50
00:03:18,235 --> 00:03:21,812
delete individual gradient handles by
single clicking on them then hitting

51
00:03:21,812 --> 00:03:26,062
"Delete". We need at least two handles to
have a gradient though, otherwise you'll

52
00:03:26,062 --> 00:03:27,683
end up with a binary scale.

53
00:03:30,160 --> 00:03:32,930
Click the "Add" button to add another
gradient handle.

54
00:03:34,050 --> 00:03:35,950
Click and drag a handle to move it,

55
00:03:37,947 --> 00:03:40,917
or single click it and edit the value in
the bottom-left.

56
00:03:42,373 --> 00:03:45,597
The scale should contain your
largest and smallest values for your data,

57
00:03:45,597 --> 00:03:48,972
but if it doesn't you can click on the
"Set Min and Max..." button, then click

58
00:03:48,972 --> 00:03:50,842
"Reset" and "OK".

59
00:03:52,009 --> 00:03:56,214
Let's create a blue-white-yellow gradient.
First, make sure there are three handles

60
00:03:56,214 --> 00:03:57,214
at the top.

61
00:03:57,311 --> 00:04:01,653
Drag the first handle or edit it to
approximately -1.2.

62
00:04:01,653 --> 00:04:03,023
Double-click the handle

63
00:04:05,563 --> 00:04:08,823
or single-click it and click the
"Node Fill Color" button,

64
00:04:11,803 --> 00:04:13,745
then pick a color in the blue range.

65
00:04:17,518 --> 00:04:20,971
Set the second handle to
approximately 0.5 and change the

66
00:04:20,971 --> 00:04:22,121
color to white.

67
00:04:25,705 --> 00:04:29,785
For the third handle,
change it to about 2.5 and yellow.

68
00:04:36,925 --> 00:04:40,115
Double-click on the maximum handle and set
it to green,

69
00:04:43,740 --> 00:04:45,980
then set the minimum handle to black.

70
00:04:52,180 --> 00:04:56,667
Note that the default value is set to
light blue. A good trick is to set it to a

71
00:04:56,667 --> 00:05:00,347
color outside the spectrum you're using to
see nodes without a value.

72
00:05:01,726 --> 00:05:06,067
The columns with "sig" at the end contain
significance values. We can use those to

73
00:05:06,067 --> 00:05:10,245
change the node shape so that nodes with a
significance below a set threshold can have

74
00:05:10,245 --> 00:05:13,295
one shape, while those above it
can have another.

75
00:05:14,032 --> 00:05:18,565
Click on the second column in "Shape",
then set the Column to "gal80Rsig" and the

76
00:05:18,565 --> 00:05:24,244
mapping to "Continuous". Double-click on
the "Current Mapping" box, then click the

77
00:05:24,244 --> 00:05:26,084
"Add" button in the bottom right.

78
00:05:26,676 --> 00:05:29,906
Double-click on the left circle and change
it to a rectangle.

79
00:05:31,557 --> 00:05:35,727
Click the handle between the shapes
and change the value to 0.05.

80
00:05:37,580 --> 00:05:42,198
The "shared interaction" column in the
Edge Table uses "pp" for protein-protein

81
00:05:42,198 --> 00:05:47,631
interactions, and "pd" for protein-DNA
interactions. Let's filter out the

82
00:05:47,631 --> 00:05:49,501
protein-protein interactions.

83
00:05:49,868 --> 00:05:54,208
Click on the "Select" tab in the Control
Panel. Click the "+" icon, then choose

84
00:05:54,208 --> 00:05:59,670
"Column Filter". Choose "Edge: interaction"
and leave the next option as "contains".

85
00:06:02,914 --> 00:06:08,274
Type "pp" into the text search box. The
filter should automatically be applied.

86
00:06:09,067 --> 00:06:13,772
The "Apply when filter changes" option is
usually selected by default. For very

87
00:06:13,772 --> 00:06:17,362
large networks, it is recommended to
disable this option, change all of the

88
00:06:17,362 --> 00:06:19,882
filters at once, then click the "Apply"
button.

89
00:06:20,509 --> 00:06:24,134
You should now see many edges in the
network selected. Let's remove the

90
00:06:24,134 --> 00:06:29,055
protein-protein edges we just chose.
Click "Edit", then "Delete Selected Nodes

91
00:06:29,055 --> 00:06:33,372
and Edges". Now there will be many
unconnected nodes. Let's clean it up by

92
00:06:33,372 --> 00:06:34,732
changing the layout.

93
00:06:35,596 --> 00:06:39,498
Click "Layout", then "Settings". You can
try different layouts and options here,

94
00:06:39,498 --> 00:06:43,349
but we're interested in the "Preferred
Layout" tab. Make sure it is set to

95
00:06:43,349 --> 00:06:45,167
"Prefuse Force Directed Layout".

96
00:06:45,797 --> 00:06:49,327
Go back to "Layout", then select
"Apply Preferred Layout".

97
00:06:52,406 --> 00:06:56,422
If we zoom in we can see that there are
three highly expressed nodes connected by

98
00:06:56,422 --> 00:07:00,952
two intermediate nodes. Let's create a new
network from those two nodes.

99
00:07:01,232 --> 00:07:04,721
Click on the first node, then hold control 
and click on the second node.

100
00:07:05,277 --> 00:07:11,419
Then click "Select > Nodes > 
First Neighbors of Selected Nodes >


101
00:07:11,419 --> 00:07:16,109
Undirected". Finally, click on "New
Network from Selection" in the toolbar.

102
00:07:17,616 --> 00:07:21,286
You'll notice in the Network Panel that
this has created a new child network.

103
00:07:22,649 --> 00:07:26,649
If our data contains identifiers used by
external databases, Cytoscape can

104
00:07:26,649 --> 00:07:31,153
automatically link us to them. Right click
on the "GAL4" node, then choose

105
00:07:31,153 --> 00:07:36,749
"External Links > Sequences and Proteins >
Entrez Gene". This will open your default

106
00:07:36,749 --> 00:07:40,049
browser and perform a search using the
"name" identifier.

107
00:07:40,828 --> 00:07:45,078
Cytoscape also provides the option to draw
charts and graphs on each node.

108
00:07:45,714 --> 00:07:49,380
Let's remove the old fill color mappings
by right-clicking on the fill mapping

109
00:07:49,380 --> 00:07:53,450
gradient and choosing "Edit > Remove
Mappings from Selected Visual Properties".

110
00:07:54,056 --> 00:07:56,406
Change the default value back to gray.

111
00:07:58,856 --> 00:08:01,654
Choose "Properties" at the top of the
panel, then choose

112
00:08:01,654 --> 00:08:05,604
"Paint > Custom Paint 1 > Image/Chart 1".

113
00:08:07,484 --> 00:08:10,995
Select the "Default" box, which will bring
up the "Graphics" dialogue.

114
00:08:11,395 --> 00:08:16,015
Choose the "Charts tab" and move all of
the expression columns to the right side.

115
00:08:18,155 --> 00:08:21,476
Change the type of graph to "Heat
Strips" and hit apply.

116
00:08:22,562 --> 00:08:25,842
Thank you for watching this Quickstart
Tutorial for Cytoscape 3.

117
00:08:26,125 --> 00:08:30,264
For more Cytoscape Tutorials, visit
tutorials.cytoscape.org

118
00:08:30,264 --> 00:08:32,744
or visit my YouTube channel.