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Practical Session Day2: CoPub

Dive into the association of "HMOX1" with "Anti-inflammatory response" and assess co-citation implications. Analyze the relevance of associated biological processes, diseases, and drugs in liver carcinoma. Explore gene selection and enriched keywords related to effects of HCB.

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Practical Session Day2: CoPub

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  1. Practical SessionDay2: CoPub

  2. 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)

  3. 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

  4. 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

  5. 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

  6. 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, …

  7. 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

  8. Q6: CoPub Network inflammation (S100xx) liver failure tumor (GADD45a, EM1) oxidative stress, drug response (HMOX1 is key with heme) fatty acids (FABP4) heme (ALAS2, HMOX1) (cholesterol) metabolism (CYPs)

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