Pathway Studio Web now includes the capability to analyze both NGS variant and RNA-Seq data.

1. | 1
Country Long Distance
Australia +61 3 8488 8993
Austria +43 (0) 7 2088 2171
Belgium +32 (0) 42 68 0164
Canada +1 (647) 497-9386
Denmark +45 (0) 89 88 04 43
Finland +358 (0) 931 58 4587
France +33 (0) 182 880 933
Germany +49 (0) 692 5736 7304
Ireland +353 (0) 19 036 186
Country Long Distance
Italy +39 0 294 75 15 36
Netherlands +31 (0) 108 080 115
New Zealand +64 (0) 9 801 0293
Norway +47 21 03 72 89
Spain +34 911 23 4247
Sweden +46 (0) 852 500 292
Switzerland +41 (0) 435 0824 40
United Kingdom +44 (0) 330 221 9921
United States +1 (646) 307-1726
TO USE YOUR COMPUTER'S AUDIO: When the webinar begins, you will be connected to audio using
your computer's microphone and speakers (VoIP). A headset is recommended.
--OR--
TO USE YOUR TELEPHONE: If you prefer to use your phone, you must select "Use Telephone" after
joining the webinar and call in using the numbers below.
Dial your country’s number and then use Access Code: 131-004-283
Next Generation Sequence Data Analysis in Pathway Studio
Our Webinar will begin in a few minutes

2. Next Generation
Sequence Data
Analysis in
Pathway Studio
For Current Pathway
Studio Users
May 6, 2014

3. | 3
Pathway Studio Web Now Includes Analysis
Capabilities for NGS (Variant and RNA-Seq data)
Pathway Studio Web customers with a subscription to the
Mammal+ChemEffect+DiseaseFx database
can now analyze Next Generation Sequencing (NGS) data results
using new tools released in Pathway Studio Web v. 11.0
Variant analysis requires the data included in the
ChemEffect and DiseaseFx database.

4. | 4
Types of Output and Analysis Options for NGS Data
Two data output types can be analyzed in Pathway Studio
RNA-Seq Whole Genome Sequence
or Exome Sequence

5. RNA-Seq Analysis
in Pathway Studio
Web

6. | 6
Analysis of RNA-Seq Data in Pathway Studio Web
File Format Requirements
X
?
1. Gene Identifiers that can be used in
Pathway Studio
a) Identifiers in the database
b) Identifiers that are mapped (using
a mapping file) to identifiers in the
database
2. Normalized measured values for each
gene
a) Can be RPKM, FPKM or fold
change
b) Need to pedestal data to avoid “0”
values. Zero values will remove
genes from inclusion in enrichment
analysis.
Cannot have multiple values in one field
Identifiers not in the database require a mapping file

7. | 7
Analysis of RNA-Seq Data in Pathway Studio Web
File Format Requirements
Gene ID Normalized Measured Values

8. | 8
Analysis of RNA-Seq Data in Pathway Studio Web
The import steps are similar to the Gene Expression analysis options
for microarray data.

9. | 9
Analysis of RNA-Seq Data in Pathway Studio Web

10. Variant Analysis

11. | 11
Variant Analysis in Pathway Studio
Data from the dbSNP database is includes in Pathway Studio
http://www.ncbi.nlm.nih.gov/snp

12. | 12
Variant Analysis in Pathway Studio
Data from the dbNSFP and 1000 Genomes databases are includes
in Pathway Studio
1000 Genomes [http://www.1000genomes.org/about] A Catalog of
Human Genetic Variation information provided by The 1000 Genomes
Project Consortium
dbNSFP [https://sites.google.com/site/jpopgen/dbNSFP and
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4109890/#R19 ] A
database developed for functional prediction and annotation of all
potential non-synonymous single-nucleotide variants (nsSNVs) in the
human genome.

13. | 13
Variant Analysis in Pathway Studio
Search dbSNP database
Find variants in an individual genome
Analyze variants in a population
Upload genomic files

14. | 14
Variant Analysis in Pathway Studio
Search the dbSNP database – targeted filters
• Is the mutation within the coding region of a gene, the intron, the
regulatory region for expression of the gene, or is it in a region between
genes?
• Does the SNP affect the protein’s sequence, and if so, will the amino acid
change have a profound deleterious effect on the structure and function
of the protein, or will the change be well tolerated by the protein (not
impact its function and activity)?
• Is the mutation in a specific protein’s amino acid position or within a
region of the protein sequence that is known to be generally conserved
(very few changes) within the human population?
• Is the protein mutation within a region that is known to be conserved
(very few changes) across species other than just human?
• What chromosome and region of a chromosome is the SNP is located
on?

15. | 15
Variant Analysis in Pathway Studio
Search the dbSNP database – targeted filters
• What diseases or cell processes are associated with the gene containing
the SNP of interest? (This information is derived from Elsevier’s Pathway
Studio database.)
• Is there any known clinical impact reported for a specific SNP (such as:
pathogenic, drug response, etc.)?
• Does the SNP alter the splicing of the gene, or terminate the protein
sequence prematurely?
• How common or frequently is a particular SNP found within the standard
1000 Genome Project reference data?
[http://www.1000genomes.org/about]

16. | 16
Variant Analysis in Pathway Studio
Search dbSNP database

17. | 17
Variant Analysis in Pathway Studio
Search the dbSNP database – targeted filters

18. | 18
Variant Analysis in Pathway Studio
Search the dbSNP database – filter definitions

19. | 19
Variant Analysis in Pathway Studio
Search the dbSNP database – filter definitions

20. | 20
Variant Analysis in Pathway Studio
Search the dbSNP database – filter definitions

21. | 21
Variant Analysis in Pathway Studio
Search the dbSNP database – filter definitions

22. | 22
Variant Analysis in Pathway Studio
Search the dbSNP database – filter definitions

23. | 23
Variant Analysis in Pathway Studio
Search the dbSNP database – filter definitions

24. | 24
Variant Analysis in Pathway Studio
Search the dbSNP database – example
Example biological query:
Find SNP(s) that are potentially deleterious to the function of a protein(s) that
are known to be associated with Hodgkin Lymphoma.

25. | 25
Variant Analysis in Pathway Studio
Search the dbSNP database – example
Example biological query:
Find SNP(s) that are potentially deleterious to the function of a protein(s) that
are known to be associated with Hodgkin Lymphoma.

26. | 26
Variant Analysis in Pathway Studio
Search the dbSNP database – example filter definitions
Example biological query:
Find SNP(s) that are potentially deleterious to the function of a protein(s) that
are known to be associated with Hodgkin Lymphoma.

27. | 27
Variant Analysis in Pathway Studio
Search the dbSNP database – example
Example biological query:
Find SNP(s) that are potentially deleterious to the function of a protein(s) that
are known to be associated with Hodgkin Lymphoma.

28. | 28
Variant Analysis in Pathway Studio
Search the dbSNP database – example
Example biological query:
Find SNP(s) that are potentially deleterious to the function of a protein(s) that
are known to be associated with Hodgkin Lymphoma.

29. | 29
Variant Analysis in Pathway Studio
Search the dbSNP database – example
Example biological query:
Find SNP(s) that are potentially deleterious to the function of a protein(s) that
are known to be associated with Hodgkin Lymphoma.

30. | 30
Variant Analysis in Pathway Studio
Example biological query:
Find SNP(s) that are potentially deleterious to the function of a protein(s) that
are known to be associated with Hodgkin Lymphoma.
Search the dbSNP database – example

31. Importing Genomic
Data into Pathway
Studio Web

32. | 32
Variant Analysis in Pathway Studio
Importing individual genomic data into Pathway Studio
Upload genomic files

33. | 33
Variant Analysis in Pathway Studio
Importing individual genomic data into Pathway Studio – file formats
The format required for both genomic or exome
data is .vcf files
[http://www.1000genomes.org/node/101].
The time to upload a file is dependent on the size
of the file and the number of files.
.vcf files need to have been generated using the
same version of the reference genome as is loaded
into the database.

34. | 34
Variant Analysis in Pathway Studio
Importing individual genomic data into Pathway Studio

35. | 35
Variant Analysis in Pathway Studio
Importing individual genomic data into Pathway Studio

36. | 36
Variant Analysis in Pathway Studio
Importing individual genomic data into Pathway Studio
Find variants in an individual genome

37. | 37
Variant Analysis in Pathway Studio
Importing individual genomic data into Pathway Studio

38. Analysis of an
Individual Genome

39. | 39
Variant Analysis in Pathway Studio
Search single exome file for interesting variants
Example biological query:
Question: Are there any novel (not yet reported) potentially damaging variants in this
dataset in genes known through Elsevier’s text-mining to be associated with the
cellular processes apoptosis.

40. | 40
Variant Analysis in Pathway Studio
Example biological query:
Question: Are there any novel (not yet reported) potentially damaging variants in this
dataset in genes known through Elsevier’s text-mining to be associated with the
cellular processes apoptosis.
Search single exome file for interesting variants

41. | 41
Variant Analysis in Pathway Studio
Example biological query:
Question: Are there any novel (not yet reported) potentially damaging variants in this
dataset in genes known through Elsevier’s text-mining to be associated with the
cellular processes apoptosis.
Search single exome file for interesting variants

42. | 42
Variant Analysis in Pathway Studio
Example biological query:
Question: Are there any novel (not yet reported) potentially damaging variants in this
dataset in genes known through Elsevier’s text-mining to be associated with the
cellular processes apoptosis.
Search single exome file for interesting variants

43. | 43
Variant Analysis in Pathway Studio
Example biological query:
Question: Are there any novel (not yet reported) potentially damaging variants in this
dataset in genes known through Elsevier’s text-mining to be associated with the
cellular processes apoptosis.
Search single exome file for interesting variants

44. | 44
Variant Analysis in Pathway Studio
Example biological query:
Question: Are there any novel (not yet reported) potentially damaging variants in this
dataset in genes known through Elsevier’s text-mining to be associated with the
cellular processes apoptosis.
Search single exome file for interesting variants

45. Analysis of an
Multiple Genomes

46. | 46
Variant Analysis in Pathway Studio
Variant analysis of multiple genomes – import
Upload genomic files

47. | 47
Variant Analysis in Pathway Studio
Variant analysis of multiple genomes – import

48. | 48
Variant Analysis in Pathway Studio
Analyze variants in a population

49. | 49
Variant Analysis in Pathway Studio
Variant analysis of multiple genomes - comparisons

50. | 50
Variant Analysis in Pathway Studio
Variant analysis of multiple genomes - comparisons

51. | 51
Variant Analysis in Pathway Studio
Variant analysis of multiple genomes - comparisons

52. | 52
Variant Analysis in Pathway Studio
Variant analysis of multiple genomes
Example biological query:
Question: Find homozygous variants that are present in at least three of the case
samples but not in any of the control samples that are also in the coding region and
are known to be associated with breast cancer.

53. | 53
Variant Analysis in Pathway Studio
Variant analysis of multiple genomes
Example biological query:
Question: Find homozygous variants that are present in at least three of the case
samples but not in any of the control samples that are also in the coding region and
are known to be associated with breast cancer.

54. | 54
Variant Analysis in Pathway Studio
Variant analysis of multiple genomes
Example biological query:
Question: Find homozygous variants that are present in at least three of the case
samples but not in any of the control samples that are also in the coding region and
are known to be associated with breast cancer.

55. | 55
Variant Analysis in Pathway Studio
Variant analysis of multiple genomes
Example biological query:
Question: Find homozygous variants that are present in at least three of the case
samples but not in any of the control samples that are also in the coding region and
are known to be associated with breast cancer.

56. | 56
Variant Analysis in Pathway Studio
Variant analysis of multiple genomes
Example biological query:
Question: Find homozygous variants that are present in at least three of the case
samples but not in any of the control samples that are also in the coding region and
are known to be associated with breast cancer.

57. | 57
Variant Analysis in Pathway Studio
Variant analysis of multiple genomes
Example biological query:
Question: Find homozygous variants that are present in at least three of the case
samples but not in any of the control samples that are also in the coding region and
are known to be associated with breast cancer.
Note: in the Case and Control column, the
number of times the specific variant is identified
are represented by four numbers in this order:
• homozygous
• heterozygous
• hemizygous
• ambiguous

58. | 58
Variant Analysis in Pathway Studio
Variant analysis of multiple genomes
Example biological query:
Question: Find homozygous variants that are present in at least three of the case
samples but not in any of the control samples that are also in the coding region and
are known to be associated with breast cancer.

59. | 59
Variant Analysis in Pathway Studio
Variant analysis of multiple genomes
Example biological query:
Question: Find homozygous variants that are present in at least three of the case
samples but not in any of the control samples that are also in the coding region and
are known to be associated with breast cancer.

60. | 60
NGS data analysis Pathway Studio
Where to find help

61. | 61
Variant Analysis in Pathway Studio
http://help.elsevier.com/app/answers/detail/a_id/5549/p/9047/
Where to find help

62. | 62
Variant Analysis in Pathway Studio
Where to find help

63. | 63
Variant Analysis in Pathway Studio
Where to find help
http://help.elsevier.com/app/pathway_select/p/9048

64. Questions?