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(i) Module enrichment ........................................................................................................................ 15
(ii) Network expansion ........................................................................................................................ 16
(iii) Gene prioritization ....................................................................................................................... 17
b.
Gene Set Enrichment ................................................................................................................ 17
c.
Subtrack annotation ................................................................................................................. 17
d.
Statistical analysis ..................................................................................................................... 18
(i) Gene-level vs Module-level tests.................................................................................................... 18
(ii) Continuous annotation data and CCT/CBT statistical testing ................................................. 19
(iii) Categorical annotation data and CCT statistical testing .......................................................... 20
(iv) Categorical annotation data and CBT statistical testing .......................................................... 21
(v) Binary annotation data and CCT statistical testing ................................................................... 21
(vi) Binary annotation data and CBT statistical testing .................................................................. 21
(vii) Survival annotation data and CCTs/CBTs ............................................................................... 23
e.
Data transformation ................................................................................................................. 24
f.
Value-based filtering ................................................................................................................. 25
g.
Presence-based filtering............................................................................................................ 25
h.
Node-link Graph ....................................................................................................................... 26
i.
Zoom to a gene .......................................................................................................................... 27
j.
Track comparison ..................................................................................................................... 28
k.
Track co-visualization............................................................................................................... 29
l.
Switch between different views ................................................................................................ 29
III. Portal descriptions ....................................................................................................................................... 31
1.
Generating Views ................................................................................................................................ 31
2.
The Colorectal Cancer (CRC) portal track description .................................................................. 31
a. Genomic and proteomic alterations in the TCGA CRC tumor cohort .................................... 32
b. Clinical relevance based on CRC tumor tissue .......................................................................... 34
c. Tracks based on CRC cell lines.................................................................................................... 36
d. Functional tracks .......................................................................................................................... 36
3.
Clinical Proteomic Tumor Analysis Consortium (CPTAC) Portal ................................................ 37
a.
b.
Protomic, phosphoproteomic, and glycoproteomic alterations from CPTAC cohorts ....... 37
i.
Colorectal proteomic profile tracks ........................................................................................... 38
ii.
Ovarian and Breast Proteomic profile tracks .......................................................................... 39
CPTAC portal tsi track data sources ...................................................................................... 42
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