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19 March 2024
- 13:0313:03, 19 March 2024 diff hist −489 22140/22141 - Introduction to Systems Biology →Lecture plan current
18 March 2024
- 10:2710:27, 18 March 2024 diff hist +14,526 N Autumn2021 Created page with "= Course 22140 (previously 36040) - plan for autumn 2021 = <!-- = General information = --> '''Teachers:''' * [https://www.biosurf.org Lars Rønn Olsen] (course organizer) - '''contact:''' [mailto:lronn@dtu.dk lronn@dtu.dk] * Kristoffer Vitting-Seerup (course organizer) - '''contact:''' [mailto:krivi@dtu.dk krivi@dtu.dk] * [http://www.cbs.dtu.dk/~raz/ Rasmus Wernersson] (lecturer) - '''contact:''' [mailto:rawe@dtu.dk rawe@dtu.dk] * Giorgia Moranzoni (teaching assistant..." current
6 March 2024
- 09:5609:56, 6 March 2024 diff hist −96 m 22140/22141 - Introduction to Systems Biology →Lecture plan
5 March 2024
- 17:1217:12, 5 March 2024 diff hist 0 N File:Cytoscape icon.png No edit summary current
- 17:1117:11, 5 March 2024 diff hist +14,638 N Autumn2022 Created page with "= Course 22140 (previously 36040) - plan for autumn 2022 = <!-- = General information = --> '''Teachers:''' * Kristoffer Vitting-Seerup (course organizer) - '''contact:''' [mailto:krivi@dtu.dk krivi@dtu.dk] * [http://www.cbs.dtu.dk/~raz/ Rasmus Wernersson] (external lecturer) - '''contact:''' [mailto:rawe@dtu.dk rawe@dtu.dk] * Giorgia Moranzoni (teaching assistant) - '''contact:''' [mailto:gimo@dtu.dk gimo@dtu.dk] * Lars Rønn Olsen (course organizer) is on parental lea..." current
- 17:0917:09, 5 March 2024 diff hist 0 N File:Community2.png No edit summary current
- 17:0917:09, 5 March 2024 diff hist +11,835 N DiscoNet2 answers Created page with "= Multiomics data integration exercise - Answers = '''Answers written by:''' Lars Rønn Olsen First, load the data for today's exercise: <pre> load("/home/projects/22140/exercise10.Rdata") </pre> Then, randomly pick a patient number. Let's use R to make sure it is random: <pre> sample(1:10, 1) </pre> For that patient calculate the log2 fold change of gene expression in cancer vs normal log2(cancer expression / normal expression). Consider genes with a log2 fold chan..." current
- 17:0817:08, 5 March 2024 diff hist +7,985 N DiscoNet2 Created page with "= Multiomics data integration exercise = '''Exercise written by:''' Lars Rønn Olsen '''Learning objectives:''' * Overall objective: learn how to extract meaningful networks from human PPI data *# Virtual pulldowns: sampling 1st order networks and filtering "sticky proteins" *# Finding tightly connected clusters in larger networks *# Using the DiscoNet package in R == Introduction == Today’s exercise requires the use of many of the methods you learned throughout this..." current
- 17:0517:05, 5 March 2024 diff hist 0 N File:Community2 w9.png No edit summary current
- 17:0417:04, 5 March 2024 diff hist 0 N File:Community1.png No edit summary current
- 17:0417:04, 5 March 2024 diff hist 0 N File:G3.png No edit summary current
- 17:0317:03, 5 March 2024 diff hist 0 N File:G2.png No edit summary current
- 17:0317:03, 5 March 2024 diff hist 0 N File:G1.png No edit summary current
- 17:0217:02, 5 March 2024 diff hist +7,982 N DiscoNet answers Created page with "= Human diseases / virtual pulldown exercise = '''Exercise written by:''' Lars Rønn Olsen, Giorgia Moranzoni, and Rasmus Wernersson 30px|left '''TASK/REPORT QUESTION #1:''' # Load the packages <pre> library(DiscoNet) library(msigdbr) library(fgsea) The PPI database we will use is InWeb: db <- translate_database("inweb") </pre> # Run DiscoNet with this list of proteins with the following parameters: <pre> network_ex2 <- virtu..."
- 17:0017:00, 5 March 2024 diff hist 0 N File:Heart+networks.png No edit summary current
- 16:5616:56, 5 March 2024 diff hist +9,185 N DiscoNet Created page with "= Human diseases / virtual pulldown exercise = '''Exercise written by:''' Lars Rønn Olsen, Giorgia Moranzoni, and Rasmus Wernersson '''Learning objectives:''' * Overall objective: learn how to extract meaningful networks from human PPI data *# Virtual pulldowns: sampling 1st order networks and filtering "sticky proteins" *# Finding tightly connected clusters in larger networks *# Using the DiscoNet package in R == Introduction == Image:Heart+networks.png|600px|right..."
- 16:5516:55, 5 March 2024 diff hist −9 m Autumn2023 →Lecture 09 (Nov 2) - Systems Biology in Biomedical Research (Heart diseases) 2 current
- 16:5416:54, 5 March 2024 diff hist 0 N File:XKCD significant.png No edit summary current
- 16:5116:51, 5 March 2024 diff hist +5,765 N ExYeastCellCycleTranscriptomics2 R answers Created page with "===Question 1=== <pre> library(igraph) library(ggraph) load("home/projects/22140/exercise4.Rdata") load("home/projects/22140/exercise6.Rdata") expr$log2fc <- log2(expr$GSM287992/expr$GSM287991) node_attributes_updated <- merge(x = node_attributes, y = expr[!duplicated(expr$SysName),c(1,6)], by.x = "ID", by.y = "SysName", all.x = TRUE) g <- graph_from_data_frame(interactions, directed = FALSE, vertices = node_attributes_updated) ggraph(g) + geom_edge_link() + g..." current
- 16:4916:49, 5 March 2024 diff hist 0 N File:YBL002W.cdc15.png No edit summary current
- 16:4916:49, 5 March 2024 diff hist 0 N File:YBL002W.30.png No edit summary current
- 16:4816:48, 5 March 2024 diff hist 0 N File:HTB2-peaktime.png No edit summary current
- 16:4616:46, 5 March 2024 diff hist 0 N File:YKL185W.30.png No edit summary current
- 16:4516:45, 5 March 2024 diff hist +14,838 N ExYeastCellCycleTranscriptomics2 R Created page with "= Yeast cell cycle / transcriptomics exercise #2 = '''Exercise written by:''' Rasmus Wernersson and Lars Rønn Olsen = PART 1: Network analysis of the Alpha Factor Arrest data = left IMPORTANT: We continue working with the data set from week 4. == Network analysis == The final part of the analysis of the alpha-factor arrest data set we started in the previous exercise, is to map it onto the Yeast protein-protein interaction netwo..." current
- 16:4316:43, 5 March 2024 diff hist −27 m Autumn2023 →Lecture 02 (Sep 7) - Intro 2
- 16:3916:39, 5 March 2024 diff hist −1 m IgraphIntro Ex v1 →Collecting node attributes
- 16:3716:37, 5 March 2024 diff hist 0 m IgraphIntro Ex v1 →Visualizing the graph using ggraph
- 16:3516:35, 5 March 2024 diff hist −9 m Autumn2023 →Lecture 01 (August 31) - Intro 1
- 16:3316:33, 5 March 2024 diff hist +43 m Autumn2023 →Lecture 07 (Oct 12) - Yeast Systems Biology 4
- 16:3016:30, 5 March 2024 diff hist +5,033 N ExYeastCellCycle answers Created page with "===Question 1=== Q:How much RNA ("total RNA") was used in the experiment? A: 50 ug of total RNA (found on the Protocols page). Q: Which type/brand of array was used? A: Affymetrix GeneChip Yeast Genome 2.0 Array (found on the main page). Q: How many individual arrays were used in the study? A: 2 arrays (found both on the main page and the samples page) Q: IMPORTANT: note down which arrays were used for CONTROL (asynchronous; "mock treated") and which were use for CAS..." current
- 16:2816:28, 5 March 2024 diff hist 0 N File:Log2 graph.png No edit summary current
- 16:2716:27, 5 March 2024 diff hist 0 N File:Checkmark from openclipart.png No edit summary current
- 16:2716:27, 5 March 2024 diff hist +11,343 N ExYeastCellCycleTranscriptomics R Created page with "= Yeast cell cycle / transcriptomics exercise #1 = '''Exercise written by:''' Rasmus Wernersson and Lars Rønn Olsen '''Learning objectives:''' * Introduction to practical work on array CASE/CONTROL studies. * Introduction to ArrayExpress as a way to download DNA microarray experimental data. * Introduction to basic expression data transformation: ** Calculation of Log2 expression values ** Basic evaluation of the comparability of two arrays. ** Calculation of FOLD CHA..." current
- 16:2616:26, 5 March 2024 diff hist −9 m Autumn2023 →Lecture 06 (Oct 5) - Yeast Systems Biology 3
- 16:2316:23, 5 March 2024 diff hist 0 N File:Graphpad pvalue 02.png No edit summary current
- 16:2216:22, 5 March 2024 diff hist 0 N File:Graphpad pvalue 01.png No edit summary current
- 16:2216:22, 5 March 2024 diff hist 0 N File:DNA pol act tree.png No edit summary current
- 16:2016:20, 5 March 2024 diff hist −1 ExGeneOntology Yeast1.5 →How to run the analysis current
- 16:1916:19, 5 March 2024 diff hist 0 N File:Document-save.png No edit summary current
- 16:1816:18, 5 March 2024 diff hist 0 N File:GOrilla webinterface1+boxes.png No edit summary current
- 16:1716:17, 5 March 2024 diff hist 0 N File:Cluster1 biological process.png No edit summary current
- 16:1616:16, 5 March 2024 diff hist +22,662 N ExGeneOntology Yeast1.5 Created page with "= Gene Ontology - yeast cell cycle examples = thumb|right|250px|'''Cellular component''' example: the GO term '''mitochondrion''' '''Exercise written by:''' [http://www.dtu.dk/service/telefonbog/person?id=18103&cpid=214039&tab=2&qt=dtupublicationquery Rasmus Wernersson] '''Purpose of this exercise:''' * Understand how Gene Ontology terms are defined and organized: ** The relationship between GO terms (IS A, PART OF, etc) ** The three..."
- 16:1516:15, 5 March 2024 diff hist +8,861 N ExGeneOntology Yeast R answers Created page with "= Answers to the gene ontology exercise = Answers by Aron Eklund, created 25 November 2014.Updated by Rasmus Wernersson, October 2020. Here is a link to the exercise. leftPlease remember that the web servers and their underlying data could be updated any time, so it is possible that your results may not exactly match the results listed here. == Report question #1 == Q: ''How many ancestor terms are def..."
- 16:1316:13, 5 March 2024 diff hist 0 N File:Cogs brain.png No edit summary current
- 16:1216:12, 5 March 2024 diff hist 0 N File:Cluster1 subnetwork.png No edit summary current
- 16:1116:11, 5 March 2024 diff hist 0 N File:QuickGO negative regulation example.png No edit summary current
- 16:1116:11, 5 March 2024 diff hist 0 N File:Animal cell structure en.png No edit summary current
- 16:1016:10, 5 March 2024 diff hist 0 N File:QuickGO CellDivision cropped.png No edit summary current
- 16:0916:09, 5 March 2024 diff hist 0 N File:QuickGO Mitochondrion.png No edit summary current
- 15:4815:48, 5 March 2024 diff hist +22,952 N ExGeneOntology Yeast R Created page with "= Gene Ontology - yeast cell cycle examples = thumb|right|250px|'''Cellular component''' example: the GO term '''mitochondrion''' '''Exercise written by:''' [http://www.dtu.dk/service/telefonbog/person?id=18103&cpid=214039&tab=2&qt=dtupublicationquery Rasmus Wernersson] '''Purpose of this exercise:''' * Understand how Gene Ontology terms are defined and organized: ** The relationship between GO terms (IS A, PART OF, etc) ** The three..." current
