Module 112

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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: 9
Num genes: 260 (see 2053 additional genes for this module)
Num experiments: 1210 (302 induced, 908 repressed)
Parent module: 176
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.
Shipp02 10
Staunton01 15
Ramaswamy01 4
Ramaswamy01 22
Golub99 23
Shipp02 23
Ramaswamy01 44
Shipp02 9
Staunton01 3


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
Liver tissue (Liver cancer*) Liver cancer* 4.7e-45 107 35.4 302 187 1945
Liver tissue, cancer or cell line (Liver cancer*) Liver cancer* 4.9e-42 107 35.4 302 197 1945
Lymphoma (B lymphoma) B lymphoma 2.1e-33 60 89.5 67 77 245
Hepatitis infected liver (Liver cancer*) Liver cancer* 1.0e-32 85 28.1 302 156 1945
Non-tumor liver tissue (Liver cancer) Liver cancer 1.0e-31 76 71.0 107 76 207
Lung tissue, cancer or cell line (Lung cancer*) Lung cancer* 6.2e-29 213 23.4 907 276 1945
Cancer and cell line (Lung cancer*) Lung cancer* 3.0e-27 196 21.6 907 252 1945
Cancer (Lung cancer*) Lung cancer* 3.0e-27 196 21.6 907 252 1945
Lung cancer (Lung cancer*) Lung cancer* 1.4e-25 185 20.3 907 238 1945
Lung cancer or cell line (Lung cancer*) Lung cancer* 1.4e-25 185 20.3 907 238 1945
Non small cell lung cancer and cell line (Lung cancer*) Lung cancer* 4.3e-25 164 18.0 907 205 1945
Non small cell lung cancer (Lung cancer*) Lung cancer* 4.3e-25 164 18.0 907 205 1945
Hematologic samples and cell lines (B lymphoma) B lymphoma 9.6e-25 66 98.5 67 121 245
Cancer and cell line (Liver cancer) Liver cancer 9.9e-25 84 98.8 85 126 207
Acute leukemia (Leukemia*) Leukemia* 2.4e-20 117 12.8 907 141 1945
Cancer and cell line (Leukemia*) Leukemia* 2.4e-20 117 12.8 907 141 1945
Cancer (Leukemia*) Leukemia* 2.4e-20 117 12.8 907 141 1945
Hematologic cancer and cell line (Leukemia*) Leukemia* 2.4e-20 117 12.8 907 141 1945
Hematologic cancer (Leukemia*) Leukemia* 2.4e-20 117 12.8 907 141 1945
Hematologic samples and cell lines (Leukemia*) Leukemia* 2.4e-20 117 12.8 907 141 1945
Leukemia (Leukemia*) Leukemia* 2.4e-20 117 12.8 907 141 1945
Leukemia or leukemia cell line (Leukemia*) Leukemia* 2.4e-20 117 12.8 907 141 1945
Monocytes (Leukemia*) Leukemia* 2.4e-20 117 12.8 907 141 1945
Cancer and cell line (Various tumors*) Various tumors* 1.2e-17 90 9.9 907 105 1945
Cancer (Various tumors*) Various tumors* 1.2e-17 90 9.9 907 105 1945
Cancer (Liver cancer) Liver cancer 3.6e-15 74 87.0 85 115 207
Breast tissue or cancer (Breast cancer*) Breast cancer* 7.3e-12 48 15.8 302 118 1945
Female hormonal tissue or cancer (Breast cancer*) Breast cancer* 7.3e-12 48 15.8 302 118 1945
Lymphoma or lymphoma cell line (B lymphoma) B lymphoma 3.9e-11 65 97.0 67 167 245
Adenocarcinoma (Liver cancer) Liver cancer 2.4e-10 62 72.9 85 97 207
Adenocarcinoma (Breast cancer*) Breast cancer* 2.4e-10 44 14.5 302 112 1945
Breast cancer (Breast cancer*) Breast cancer* 2.4e-10 44 14.5 302 112 1945
Cancer (Breast cancer*) Breast cancer* 2.4e-10 44 14.5 302 112 1945
Female hormonal cancer (Breast cancer*) Breast cancer* 2.4e-10 44 14.5 302 112 1945
Hepatocellular carcinoma (Liver cancer) Liver cancer 1.1e-09 64 75.2 85 104 207
Female hormonal tissue, cancer or cell line (Breast cancer*) Breast cancer* 3.2e-09 49 16.2 302 141 1945
Breast tissue, cancer or cell line (Breast cancer*) Breast cancer* 4.3e-09 49 16.2 302 142 1945
Female hormonal cancer or cell line (Breast cancer*) Breast cancer* 7.8e-09 45 14.9 302 127 1945
Breast cancer or cell line (Breast cancer*) Breast cancer* 1.0e-08 45 14.9 302 128 1945
Cell line (NCI60*) NCI60* 1.4e-07 92 10.1 907 135 1945
Cancer and cell line (Breast cancer*) Breast cancer* 4.7e-07 45 14.9 302 143 1945
Cancer and cell line (NCI60*) NCI60* 6.9e-07 92 10.1 907 138 1945
Acute lymphocytic leukemia (Leukemia) Leukemia 7.2e-07 94 75.2 125 99 149
Invasive liver tumor (Liver cancer) Liver cancer 1.2e-06 29 34.1 85 38 207
Lymphocytes (Leukemia) Leukemia 2.0e-06 86 73.5 117 91 141
Stage T2 (Lung cancer) Lung cancer 3.8e-05 10 62.5 16 35 195
Normal tissue (Liver cancer) Liver cancer 6.2e-05 14 13.0 107 14 207
Diffuse large B cell lymphoma - DLBCL (B lymphoma) B lymphoma 7.6e-05 48 71.6 67 126 245
Liver cancer cell line (Liver cancer) Liver cancer 9.8e-05 10 11.7 85 10 207
Metastasis (Liver cancer) Liver cancer 9.8e-05 10 11.7 85 10 207
Cancer and cell line (NCI60*) NCI60* 0.0001 38 12.5 302 138 1945
Hematologic samples and cell lines (Various tumors) Various tumors 0.0002 37 29.1 127 37 154
Hematologic samples (Various tumors) Various tumors 0.0002 37 29.1 127 37 154
Diffuse large B cell lymphoma tumor or cell line (B lymphoma) B lymphoma 0.0002 49 73.1 67 134 245
Breast cancer cell line (Breast cancer) Breast cancer 0.0003 13 24.0 54 17 152
B cells (Leukemia) Leukemia 0.0004 59 50.4 117 62 141


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
morphogenesis 1.7e-06 38 17.6 215 366 4566
organogenesis 7.8e-06 33 15.3 215 315 4566
development 1.2e-05 48 22.3 215 554 4566
microsome 1.9e-05 12 5.5 215 61 4566
neurogenesis 3.4e-05 21 9.7 215 169 4566
extracellular space 0.0001 23 10.6 215 212 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 1210 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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