Module 197

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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: 3
Num genes: 174 (see 1064 additional genes for this module)
Num experiments: 612 (228 induced, 384 repressed)
Parent module: 252
Children modules: 123


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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.
sensory perception
chemosensory perception
regulation of transcription, DNA_dependent


Jump to: Home | General properties | Gene sets | Enriched clinical annotations | Enriched Go annotations | Visual display
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
Hematologic cancer and cell line (Stimulated PBMC) Stimulated PBMC 6.9e-20 26 74.2 35 30 182
Macrophages (Stimulated PBMC) Stimulated PBMC 6.9e-20 26 74.2 35 30 182
Chronic lymphocytic leukemia (B lymphoma) B lymphoma 3.4e-12 32 50 64 46 245
Leukemia (B lymphoma) B lymphoma 3.4e-12 32 50 64 46 245
Leukemia or leukemia cell line (B lymphoma) B lymphoma 3.4e-12 32 50 64 46 245
Cell line (B lymphoma) B lymphoma 1.6e-09 11 39.2 28 14 245
Non-tumor liver tissue (Liver cancer) Liver cancer 2.0e-09 35 74.4 47 76 207
Normal lung tissue (Lung cancer) Lung cancer 5.3e-09 18 26.4 68 22 276
Normal tissue (Lung cancer) Lung cancer 2.0e-08 18 26.4 68 23 276
Liver cancer cell line (Liver cancer) Liver cancer 2.6e-08 10 25 40 10 207
Small cell lung cancer (Lung cancer) Lung cancer 3.9e-08 8 33.3 24 10 276
Cell line (Liver cancer) Liver cancer 2.5e-07 10 25 40 11 207
Cancer and cell line (Various tumors*) Various tumors* 5.5e-06 40 10.4 384 105 1945
Cancer (Various tumors*) Various tumors* 5.5e-06 40 10.4 384 105 1945
B. petrussis stimulated immune cells (Stimulated PBMC) Stimulated PBMC 6.1e-06 23 85.1 27 67 144
Grade 3 (Breast cancer) Breast cancer 7.3e-06 13 100 13 38 85
Breast tissue or cancer (NCI60) NCI60 8.4e-06 4 44.4 9 4 139
Female hormonal tissue or cancer (NCI60) NCI60 8.4e-06 4 44.4 9 4 139
Cancer and cell line (Liver cancer) Liver cancer 8.5e-06 36 90 40 126 207
Invasive liver tumor (Liver cancer) Liver cancer 9.2e-06 18 45 40 38 207
Hematologic cancer and cell line (Stimulated immune*) Stimulated immune* 1.2e-05 18 7.9 227 53 1945
Hematologic samples and cell lines (Stimulated immune*) Stimulated immune* 1.2e-05 18 7.9 227 53 1945
Macrophages (Stimulated immune*) Stimulated immune* 1.2e-05 18 7.9 227 53 1945
Monocytes (Stimulated immune*) Stimulated immune* 1.2e-05 18 7.9 227 53 1945
p53 positive hepatocellular carcinoma (Liver cancer) Liver cancer 1.4e-05 13 86.6 15 23 60
CNS tissue, cancer or cell line (Neuro tumors*) Neuro tumors* 2.4e-05 33 8.5 384 85 1945
Prostate (Various tumors) Various tumors 3.6e-05 12 17.3 69 12 154
B. petrussis A2 stimulated immune cells (Stimulated PBMC) Stimulated PBMC 0.0001 5 18.5 27 5 144
B. petrussis Tox 6 stimulated immune cells (Stimulated PBMC) Stimulated PBMC 0.0001 5 18.5 27 5 144
Breast cancer (NCI60) NCI60 0.0001 3 33.3 9 3 139
Renal tissue (Various tumors) Various tumors 0.0002 10 14.4 69 10 154
Gram negative bacteria stimulated immune cells (Stimulated PBMC) Stimulated PBMC 0.0002 23 85.1 27 78 144
1X dose immune stimulation (Stimulated PBMC) Stimulated PBMC 0.0002 5 100 5 13 59
Acute myelogeous leukemia (Leukemia) Leukemia 0.0003 14 73.6 19 50 141
Breast tissue, cancer or cell line (NCI60) NCI60 0.0003 7 77.7 9 31 139
CNS cancer or cell line (Neuro tumors*) Neuro tumors* 0.0004 29 7.5 384 81 1945
CNS tumor (Neuro tumors*) Neuro tumors* 0.0004 29 7.5 384 81 1945
Mesenchemal cell line (Breast cancer) Breast cancer 0.0004 4 17.3 23 4 152


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
regulation of transcription\, DNA-dependent 1.6e-144 166 95.4 174 595 4566
chemosensory perception 6.1e-78 133 76.4 174 682 4566
sensory perception 2.3e-76 133 76.4 174 700 4566
nucleus 8.3e-61 136 78.1 174 966 4566
endomembrane system 1.0e-53 133 76.4 174 1029 4566
transcription regulator activity 3.6e-53 114 65.5 174 703 4566
response to abiotic stimulus 6.9e-46 135 77.5 174 1228 4566
transcription\, DNA-dependent 4.5e-38 54 31.0 174 167 4566
transcription 1.4e-35 54 31.0 174 184 4566
transcription factor activity 7.5e-34 68 39.0 174 340 4566
mitosis 1.1e-32 31 17.8 174 50 4566
regulation of transcription 9.8e-31 35 20.1 174 76 4566
DNA binding 1.1e-28 64 36.7 174 357 4566
regulation of transcription from Pol II promoter 8.6e-25 40 22.9 174 146 4566
transcription from Pol II promoter 2.5e-17 31 17.8 174 130 4566
cell cycle 8.0e-17 31 17.8 174 135 4566
RNA polymerase II transcription factor activity 1.9e-13 24 13.7 174 102 4566
regulation of transcription by pheromones 2.6e-13 26 14.9 174 123 4566
regulation of cell cycle 4.0e-11 27 15.5 174 163 4566
cytokinesis 1.4e-10 15 8.6 174 49 4566
transcription factor binding 3.4e-10 22 12.6 174 119 4566
transcription cofactor activity 4.0e-09 21 12.0 174 123 4566
M phase 1.5e-08 10 5.7 174 26 4566
nucleoplasm 2.3e-08 17 9.7 174 89 4566
mitotic cell cycle 2.7e-07 12 6.8 174 51 4566
oncogenesis 3.0e-07 23 13.2 174 184 4566
nuclear division 3.2e-07 8 4.5 174 20 4566
transcription co-activator activity 5.9e-07 14 8.0 174 75 4566
viral host cell process manipulation 1.0e-06 16 9.1 174 102 4566
G1/S transition of mitotic cell cycle 1.1e-06 6 3.4 174 11 4566
M phase of mitotic cell cycle 1.4e-06 7 4.0 174 17 4566
transcription factor complex 4.5e-06 8 4.5 174 27 4566
chromatin 1.3e-05 10 5.7 174 50 4566
transcription co-repressor activity 2.5e-05 9 5.1 174 43 4566
mitotic anaphase 2.9e-05 5 2.8 174 11 4566
transcription factor TFIID complex 0.0001 4 2.2 174 8 4566


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.
Note: Since there are 612 experiments, this image does not display the individual experiment names, but rather condenses each experiment to a single pixel without displaying its name. You can fully view the image for this module within GeneXPress, by loading any of the four files mentioned in the line above
 
 





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