Download Mining for Meaning:

Laboratory of Parasitic Diseases, NIAID
MINING FOR MEANING:
Data mining &
Knowledge extraction
Data interpretation
Experiment
Results
Knowledge
Conclusions
Data interpretation
Experiment
Results
Knowledge
Conclusions
High publication rates
Data interpretation
Experiment
Results
High-throughput screening
Knowledge
Conclusions
High publication rates
Data interpretation
Experiment
GENE EXPRESSION PROFILING
Results
Identify relevant genes
Identify expression patterns
Pathogens
Bm 5
Mtb
Bm 50
Ld
DC
Tg
Lm
Knowledge
Induced by
Fold Change (log2)
6
5
4
3
intracellular pathog
2
1
0
-1
-2
7
6
5
4
Leishmania & TB
3
2
1
0
-1
-2
7
Fold Change (log2)
6
5
4
3
2
Toxoplasma & TB
1
0
-1
-2
6
5
Fold Change (log2)
Genes
Conclusions
Fold Change (log2)
9
8
4
3
2
1
0
-1
-2
Toxoplasma
Data interpretation
Experiment
GENE EXPRESSION PROFILING
Results
Identify relevant genes
Identify expression patterns
Knowledge
FUNCTIONAL PROFILING
Identify functional implications
Conclusions
MINING FOR MEANING:
FUNCTIONAL PROFILING
IL-4 + GM-CSF
DC
Infection with
5 pathogens
RNA pools
-overnight-
M-CSF
Elutriated Human
Monocytes
U95
Mac
7 donors
Intracellular
Protozoan
Toxoplasma gondii
vs
vs
Bacteria
Extracellular
Brugia malayi
Leishmania
Mycobacterium tuberculosis
Leishmania major
vs
Leishmania donovani
Gene expression profiling

DC
Mac
Dataset
Dataset
Extraction

Filter
12.000 genes
1200
75
Bm 5
Mtb
Bm 50
Tg
Induced by
6
Fold Change (log2)
Pathogens
Ld
Lm
DC
5
4
3
2
intracellular pathogens
1
0
-1
-2
8
7
6
5
4
3
2
Leishmania & TB
1
0
-1
-2
Fold Change (log2)
7
6
5
4
3
2
Toxoplasma & TB
1
0
-1
-2
6
5
Fold Change (log2)
Genes
Fold Change (log2)
9
4
3
2
1
0
-1
-2
Toxoplasma
MINING FOR MEANING:
FUNCTIONAL PROFILING
WITH GENE ONTOLOGIES - GO
http://www.geneontology.org/
http://apps1.niaid.nih.gov/david/
MINING FOR MEANING:
FUNCTIONAL PROFILING
WITH GENE ONTOLOGIES - GO
WITH LITERATURE ONTOLOGIES - MESH
http://www.nlm.nih.gov/mesh/MBrowser.html
http://array.ucsd.edu/hapi/
http://132.239.155.52/HAPI/TEST_377.HTML
MINING FOR MEANING:
FUNCTIONAL PROFILING
WITH GENE ONTOLOGIES - GO
WITH LITERATURE ONTOLOGIES - MESH
WITH LITERATURE ABSTRACTS
Data interpretation
Experiment
Results
Knowledge
Conclusions
12 million references
Data interpretation
Pathogens
Bm 5
Mtb
Bm 50
Ld
DC
Tg
Lm
Experiment
Induced by
Fold Change (log2)
6
5
4
3
intracellular patho
2
1
0
-1
-2
7
6
5
4
Leishmania & T
3
2
1
0
-1
-2
7
6
Fold Change (log2)
Genes
Results
Fold Change (log2)
9
8
5
4
3
2
Toxoplasma & T
1
0
-1
-2
6
Fold Change (log2)
5
4
3
2
1
0
-1
-2
Knowledge
Conclusions
12 million references
Toxoplasma
MINING FOR MEANING:
FUNCTIONAL PROFILING
WITH LITERATURE ABSTRACTS
 Co-citation Network
http://www.pubgene.com/
MINING FOR MEANING:
FUNCTIONAL PROFILING
WITH LITERATURE ABSTRACTS
 Co-citation Network
 Natural Language Processing
MINING FOR MEANING:
FUNCTIONAL PROFILING
WITH LITERATURE ABSTRACTS
 Co-citation Network
 Natural Language Processing
 Literature Profiling
1.Gene - Literature indexation
Gene A
Gene B
Retrieve relevant literature
C…
for each gene Gene
Gene X
Abstracts
2. Analysis of abstract contents
Gene A
Gene B
Gene C… Gene X
Term1
0%
54%
2%
Term 2
12%
0%
6%
Term 3…
60%
1%
35%
Term occurrences in abstracts
Term y
2.5%
5%
7.5%
10%
12.5%
15%
17.5%
20%
22.5%
25%
Determine term occurrence
in abstracts
Term occurrence
in abstracts
Chemokines
Death / Apoptosis
Analyze functional
relationships
Interferon response
Dendrite elongation
MHC class I pathway
3.Term filtering
Select
relevant
Discrimination
terms
Co-occurrence
- Identify functional relationships
1.Gene - Literature indexation
Abstracts
2. Analysis of abstract contents
Gene A
Gene B
Gene C… Gene X
Term1
0%
54%
2%
Term 2
12%
0%
6%
Term 3…
60%
1%
35%
Term occurrences in abstracts
Term y
3.Term filtering
25%
20%
22.5%
Select
relevant
17.5%
12.5%
15%
7.5%
10%
- Interpret data
5%
Determine term occurrence
in abstracts
2.5%
- Translate genelists into
keywords
Gene A
Gene B
Retrieve relevant literature
C…
for each gene Gene
Gene X
Discrimination
terms
CoCo-occurrence
Term occurrence
in abstracts
Chemokines
Death / Apoptosis
Analyze functional
relationships
Interferon response
Dendrite elongation
MHC class I pathway
Pathogens
Bm 5
Mtb
Bm 50
Ld
Tg
Lm
Experimental system
DC
Fold Change (log2)
5
4
3
intracellular pathogens
2
1
0
-1
-2
Fold Change (log2)
9
8
7
6
5
4
Leishmania & TB
3
2
Gene List
1
0
-1
-2
7
Fold Change (log2)
6
5
4
3
2
Toxoplasma & TB
1
0
-1
-2
6
5
Fold Change (log2)
Genes
KNOWLEDGE
Induced by
6
4
3
2
1
0
-1
-2
Toxoplasma
12 million
references
MINING FOR MEANING:
FUNCTIONAL PROFILING
LITERATURE MINING
Data interpretation
Experiment
Results
Knowledge
Conclusions
High publication rates
MINING FOR MEANING:
DATA MINING
LITERATURE MINING
DOCUMENT CLUSTERING
MINING FOR MEANING:
DATA MINING
LITERATURE MINING
DOCUMENT CLUSTERING
NLP
MINING FOR MEANING:
DATA MINING
LITERATURE MINING
DOCUMENT CLUSTERING
NLP
LITERATURE PROFILING
Data interpretation
Experiment
GENE EXPRESSION PROFILING
Results
Identify relevant genes
Identify expression patterns
Pathogens
Bm 5
Mtb
Bm 50
Ld
DC
Tg
Lm
Knowledge
Induced by
Fold Change (log2)
6
5
4
3
intracellular pathog
2
1
0
-1
-2
7
6
5
4
Leishmania & TB
3
2
1
0
-1
-2
7
Fold Change (log2)
6
5
4
3
2
Toxoplasma & TB
1
0
-1
-2
6
5
Fold Change (log2)
Genes
Conclusions
Fold Change (log2)
9
8
4
3
2
1
0
-1
-2
Toxoplasma