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Martijn Masoed Nick Rico

Martijn Masoed Nick Rico. Index. Dataset Pipeline (1) Tophat results Pipeline (2) Pipeline (3) CV genes Future perspectives. Dataset. Arabidopsis thaliana (advanced) Six conditions: Cold stress Drought stress Heat stress Highlight stress Salt stress Control . Pipeline (1).

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Martijn Masoed Nick Rico

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  1. Martijn Masoed Nick Rico

  2. Index • Dataset • Pipeline (1) • Tophat results • Pipeline (2) • Pipeline (3) • CV genes • Future perspectives

  3. Dataset • Arabidopsis thaliana (advanced) • Six conditions: • Cold stress • Drought stress • Heat stress • Highlight stress • Salt stress • Control

  4. Pipeline (1) Input data (FastQ) Tophat Bamfile Cufflinks Transcripts.gtf

  5. Tophat results

  6. Pipeline (2) Control vs condition Annotation Cluster 1 Enrichment Score: 15.666358755842273 Category Term Count % Pvalue Genes List Total Pop Hits Pop Total Fold Enrichment BonferroniBenjamini FDR GOTERM_BP_ALL GO:0009408~response to heat 20 17.699115044247787 2.543194667342153E-24 Q42410, Q8GWL1, Q38931, Q9S9N1, Q9LDZ0, P29830, P13853, Q9XIE3, Q9SR96, O82133, Q9ZW31, Q9SYG1, Q9SSQ8, Q38806, O82345, Q9FHQ3, Q9SKY8, Q9FGM9, Q9LV09, Q9LNW0 70 127 15221 34.2429696287964 9.435252215839387E-22 9.435252215839387E-22 3.508393055720954E-21 GOTERM_BP_ALL GO:0009266~response to temperature stimulus 23 20.353982300884958 1.2588535583693627E-19 Q42410, Q8GWL1, Q38931, Q9S9N1, Q9M0L0, Q9LDZ0, P29830, P18612, P13853, Q9XIE3, Q9SR96, O82133, Q9ZW31, Q9SYG1, Q9SSQ8, Q38806, O82345, P93735, Q9FHQ3, Q9SKY8, Q9FGM9, Q9LV09, Q9LNW0 70 354 15221 14.1276 43260694107 4.6703467015503354E-17 2.3351733507751677E-17 1.7366162091588314E-16 XLOC_005119 XLOC_005119 Hsp70b 1:5502205-5504535 WT_controlheat_stress OK 1.88554 4668.1 11.2736 -4.26394 2.00852e-05 0.00596 568 yesQ9S9N1 Heat shock 70 kDa protein 5 (Heat shock protein 70-5) (AtHsp70-5) (Heat shock protein 70b) FUNCTION: In cooperation with other chaperones, Hsp70s stabilize preexistent proteins against aggregation and mediate the folding of newly translated polypeptides in the cytosol as well as within organelles. These chaperones participate in all these processes through their ability to recognize nonnative conformations of other proteins. They bind extended peptide segments with a net hydrophobic character exposed by polypeptides during translation and membrane translocation, or following stress-induced damage (By similarity). Cytopla sm. ATP binding; cell wall; chloroplast; plasma membrane; response to heat; response to virus GO:0005524; GO:0005618; GO:0009507; GO:0005886; GO:0009408; GO: 0009615 Cuffmerge transcript.gtf Merged.gtf Cuffdiff Bamfile DE-genes Get_functions (DE) David

  7. Pipeline (3) Data location Tophat results DE Statistic Overlap Retrieve AT-codes R Analysis ......

  8. R: Clustering CV genes

  9. Future perspectives • Finish pipeline (3) • R -> WGCNA • Basic.pl • Test tomato (7 different time points) • Paired end implementation • Biological interpretation

  10. Suggestions for further analysis?

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