Module 302

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General Properties
Below we list the number of gene sets from which the module was composed was originally composed, and the number of genes and experiments that it contains. Clicking on the number of genes will display a detailed list of all the genes in the module. Clicking on the number of experiments will display a detailed list of all the experiments in the module.
Num gene sets: 2
Num genes: 97 (see 1043 additional genes for this module)
Num experiments: 265 (125 induced, 140 repressed)
Parent module: 344
Children modules: None


Jump to: Home | General properties | Gene sets | Enriched clinical annotations | Enriched Go annotations | Visual display
Gene sets
Below we list the gene sets from which the module was originally composed. Clicking on a gene set will display all the genes associated with that gene set. Also listed are all the other modules in which the gene set participates.
response to DNA damage stimulus
Perou00 45


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Enriched clinical annotations
For each of the clinical annotations, we tested whether it was enriched in the set of arrays in which the module is significantly induced (or repressed). Below we list all such annotations that were enriched in this module with an FDR corrected p-value of 0.05 ('P-value' column), along with the number ('Hits' column) of induced (or repressed) module's arrays in which they appear. We also show the fraction of the module's induced (or repressed) arrays with the given annotation ('Hits (%)' column). For completeness, we also list the total number of relevant induced arrays in the module ('Module hits in category' column), total number of arrays in the compendium in which the corresponding annotation is present ('Arrays in annotation' column), and the total number of relevant arrays in the compendium ('Arrays' column). Note that the 'relevant' arrays may be different for each annotation, since it includes only arrays in which the annotation was relevant (i.e., present or not present) and excludes arrays where the value of the annotation was not known. Rows that correspond to annotations that were enriched in the induced arrays of the module have a red background, while rows corresponding to annotations enriched in the repressed arrays have a green background. For each annotation, we also list the other modules in which it was enriched.
Clinical annotation Category P-value Hits Hits(%) Module hits in category Arrays in annotation Arrays
Normal lung tissue (Lung cancer) Lung cancer 7.1e-19 19 63.3 30 22 276
Normal tissue (Lung cancer) Lung cancer 3.9e-18 19 63.3 30 23 276
Hematologic cancer and cell line (Stimulated PBMC) Stimulated PBMC 5.3e-13 16 88.8 18 30 182
Macrophages (Stimulated PBMC) Stimulated PBMC 5.3e-13 16 88.8 18 30 182
Leukemia (General compendium) General compendium 1.1e-07 35 25 140 198 1946
Small cell lung cancer (Lung cancer) Lung cancer 5.6e-07 6 46.1 13 10 276
Leukemia or leukemia cell line (General compendium) General compendium 6.6e-07 35 25 140 212 1946
Macrophages (General compendium) General compendium 2.2e-06 18 14.4 125 83 1946
Breast tissue or cancer (NCI60) NCI60 2.3e-06 4 57.1 7 4 139
Female hormonal tissue or cancer (NCI60) NCI60 2.3e-06 4 57.1 7 4 139
Non-tumor liver tissue (Liver cancer) Liver cancer 2.7e-06 16 88.8 18 76 207
Acute myelogeous leukemia (Leukemia) Leukemia 6.2e-06 19 76 25 50 141
EWS/FLI expressing fibroblasts (General compendium) EWS/FLI expressing fibroblasts (General compendium) 2.0e-05 6 4.2 140 10 1946
Hematologic cancer and cell line (General compendium) General compendium 4.1e-05 51 40.8 125 486 1946
Cell line (B lymphoma) B lymphoma 6.3e-05 6 37.5 16 14 245
Breast cancer (NCI60) NCI60 7.9e-05 3 42.8 7 3 139
Invasive liver tumor (Liver cancer) Liver cancer 0.0002 9 60 15 38 207
Chronic lymphocytic leukemia (B lymphoma) B lymphoma 0.0002 10 55.5 18 46 245
Leukemia (B lymphoma) B lymphoma 0.0002 10 55.5 18 46 245
Leukemia or leukemia cell line (B lymphoma) B lymphoma 0.0002 10 55.5 18 46 245


Jump to: Home | General properties | Gene sets | Enriched clinical annotations | Enriched Go annotations | Visual display
Enriched GO annotations
For each GO annotation, we tested whether it was enriched in the set of genes of the module. Below we list all such annotations that were enriched in this module with an FDR corrected p-value of 0.05 ('P-value' column), along with the number ('Hits' column) of the module's genes in which they appear. We also show the fraction of the module's genes with the given GO annotation that are included in this module ('Hits (%)' column). For completeness, we also list the total number of genes in the module ('Module genes' column), total number of genes in the compendium in which the corresponding annotation is present ('Genes in annotation' column), and the total number of genes in the compendium ('Genes' column).
GO annotation P-value Hits Hits(%) Module genes Genes in annotation Genes
response to DNA damage stimulus 9.4e-84 74 93.6 79 313 4609
response to stress 1.8e-51 74 93.6 79 796 4609
ATP binding 3.4e-33 49 62.0 79 401 4609
nucleotidyltransferase activity 1.3e-30 48 60.7 79 427 4609
protein amino acid phosphorylation 1.6e-29 38 48.1 79 231 4609
DNA repair 3.5e-24 25 31.6 79 96 4609
DNA metabolism 1.1e-23 30 37.9 79 171 4609
protein serine/threonine kinase activity 8.5e-21 24 30.3 79 114 4609
catalytic activity 2.3e-14 62 78.4 79 1691 4609
endomembrane system 5.5e-12 46 58.2 79 1040 4609
kinase regulator activity 7.8e-12 14 17.7 79 72 4609
cell cycle 5.3e-11 17 21.5 79 135 4609
nucleus 6.3e-11 43 54.4 79 976 4609
protein tyrosine kinase activity 1.0e-10 16 20.2 79 121 4609
regulation of cell cycle 1.5e-10 18 22.7 79 165 4609
protein kinase regulator activity 1.6e-10 12 15.1 79 59 4609
DNA recombination 8.5e-10 9 11.3 79 30 4609
DNA damage response\, signal transduction 9.0e-09 7 8.8 79 18 4609
signal transducer activity 3.0e-08 40 50.6 79 1035 4609
cell cycle checkpoint 3.2e-08 6 7.5 79 13 4609
cytokinesis 1.3e-07 9 11.3 79 51 4609
DNA dependent DNA replication 3.8e-07 7 8.8 79 29 4609
mitosis 1.5e-06 8 10.1 79 50 4609
cAMP-dependent protein kinase activity 1.8e-06 7 8.8 79 36 4609
damaged DNA binding 2.2e-06 6 7.5 79 24 4609
cGMP biosynthesis 2.6e-06 4 5.0 79 7 4609
chromosome organization and biogenesis (sensu Eukarya) 2.8e-06 8 10.1 79 54 4609
transcription\, DNA-dependent 3.8e-06 13 16.4 79 167 4609
transcription 1.1e-05 13 16.4 79 185 4609
base-excision repair 1.5e-05 4 5.0 79 10 4609
guanylate cyclase activity 1.5e-05 4 5.0 79 10 4609
protein kinase CK2 activity 2.7e-05 6 7.5 79 36 4609
cyclic nucleotide biosynthesis 3.5e-05 4 5.0 79 12 4609
cyclin-dependent protein kinase activity 3.5e-05 4 5.0 79 12 4609
cyclic nucleotide metabolism 5.0e-05 4 5.0 79 13 4609
phosphotransferase activity\, alcohol group as acceptor 8.6e-05 8 10.1 79 85 4609
DNA dependent ATPase activity 9.3e-05 5 6.3 79 28 4609
enzyme regulator activity 9.5e-05 15 18.9 79 291 4609


Jump to: Home | General properties | Gene sets | Enriched clinical annotations | Enriched Go annotations | Visual display
Visual display
Below is a visual display of the module. Shown are those arrays in which the module's genes significantly change, and the direction of change (induction/repression) in each array is indicated (middle, labeled 'Module changes'; red/green row). The arrays that correspond to the significant clinical attributes are also shown (top; brown rows). The gene sets that compose the module are also shown (left) along with an indication of the membership of the module genes in these gene sets.
You can also view the images within GeneXPress by loading the module gxp file file.
 
 





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