Download QA_CoPub

Practical Session
Day2: CoPub
Q&A CoPub Assignment 1
• Q1.1: Look into the assocation of "HMOX1" with
"Anti-inflammatory response", by reading some
abstracts (pressing + and having some
patience). Is HMOX1 pro- or anti-inflammatory?
Discuss a down-side of automatic text-mining.
– HMOX1 is anti-inflammatory
– co-citation of two concepts may occur also for the
opposite case, leading to a false assumption.
– Note: althought the actual relation between concepts
is often lost, a significant co-citation is shown to be an
accurate prediction of relatedness (in broad sense)
Q&A CoPub Assignment 1
• Q1.2: What are the most associated
"biological processes", "diseases" and
"Drugs" with liver carcinoma and do they
make sense? (one concept per category)
– Yes, cell invasion and lack of arrest
– Yes, carcinoma => cancer
– Yes, aflatoxin b1 is defined in IARC as
carcinogenic in humans
Q&A CoPub Assignment 1
• Q1.3 What is your general impression of
the relevance? Do you see many concepts
that are clearly unrelated and falsely
associated?
– most of the found concepts make sense (for
as far as I can tell)
– despite answer Q1.1 it seems to produce
useful associations
Q&A CoPub – Assignment 2
• Q2.1: How many genes are in this selection?
– A1: 104 (e.g. open file in excel)
• Q2.2: How many search strings are linked with
CoPub?
– A2: 250.000 (“Altogether more than 250,000 search strings are linked with
CoPub.”)
• Q2.3: How many genes of our list are actually
used in CoPub?
– 104/104 Entrez IDs used (in top description)
– 102/104 Entrez IDs used (when saved)
• Q2.4: How many keywords are co-cited (as
defined by our criteria) with our set of genes?
– 244 analyzed, but (139-16 =) 123 fulfil criteria
Q&A CoPub – Assignment 2
•
Q2.5: Which enriched keywords can be explained by the known effects of
HCB? (Name at least two keywords for at least two known effects.)
– HCB is carcinogenic
• hepatoma
• mutagenesis
• liver tumour, liver tumor
– HCB causes “porphyria cutanea tarda”, disturbs the metabolism of hemoglobin
• heme transport, heme oxidation, heme metabolism, heme catabolism, heme biosynthesis
• blood coagulation
– HCB causes “porphyria cutanea tarda”, gives lesions
• Acute-phase response
• inflammatory response
– general response to drugs:
• drug metabolism
• response to oxidative stress, …
Q&A CoPub – Assignment 2
• Q2.6: Which subclusters can be
distinguished, which effects do they
describe and which key genes are
involved? (Try at least to identify the
clusters related to the two effects of HCB
you described in Q5)
– no single answer is right, this is exploration!
– see next sheet for some interpretation
Q6: CoPub Network
inflammation (S100xx)
liver failure
tumor (GADD45a, EM1)
fatty acids
(FABP4)
oxidative stress, drug response
(HMOX1 is key with heme)
heme (ALAS2, HMOX1)
(cholesterol) metabolism
(CYPs)