Module 297

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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: 6
Num genes: 80 (see 2441 additional genes for this module)
Num experiments: 738 (201 induced, 537 repressed)
Parent module: 357
Children modules: 153 154


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.
ectoderm development
histogenesis
epidermal differentiation
Garber01 4
Ross01 39
Perou00 41


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
Lung tissue, cancer or cell line (Lung cancer*) Lung cancer* 6.2e-92 224 41.7 536 276 1945
Cancer and cell line (Lung cancer*) Lung cancer* 1.8e-79 202 37.6 536 252 1945
Cancer (Lung cancer*) Lung cancer* 1.8e-79 202 37.6 536 252 1945
Lung cancer (Lung cancer*) Lung cancer* 3.0e-72 189 35.2 536 238 1945
Lung cancer or cell line (Lung cancer*) Lung cancer* 3.0e-72 189 35.2 536 238 1945
Non small cell lung cancer and cell line (Lung cancer*) Lung cancer* 7.4e-58 160 29.8 536 205 1945
Non small cell lung cancer (Lung cancer*) Lung cancer* 7.4e-58 160 29.8 536 205 1945
Squamous cell lung cancer (Lung cancer) Lung cancer 1.7e-22 29 65.9 44 35 276
Lymphoma (B lymphoma) B lymphoma 3.3e-12 21 100 21 77 245
Liver tissue, cancer or cell line (Liver cancer*) Liver cancer* 2.5e-11 51 25.3 201 197 1945
Liver tissue (Liver cancer*) Liver cancer* 1.6e-10 48 23.8 201 187 1945
Female hormonal tissue, cancer or cell line (Breast cancer*) Breast cancer* 4.5e-09 38 18.9 201 141 1945
Breast tissue, cancer or cell line (Breast cancer*) Breast cancer* 5.6e-09 38 18.9 201 142 1945
Hematologic samples and cell lines (Various tumors) Various tumors 6.6e-09 31 46.9 66 37 154
Hematologic samples (Various tumors) Various tumors 6.6e-09 31 46.9 66 37 154
Hepatitis infected liver (Liver cancer*) Liver cancer* 2.8e-08 39 19.4 201 156 1945
Female hormonal cancer or cell line (Breast cancer*) Breast cancer* 4.1e-08 34 16.9 201 127 1945
Breast cancer or cell line (Breast cancer*) Breast cancer* 5.1e-08 34 16.9 201 128 1945
Breast tissue or cancer (Breast cancer*) Breast cancer* 7.8e-08 32 15.9 201 118 1945
Female hormonal tissue or cancer (Breast cancer*) Breast cancer* 7.8e-08 32 15.9 201 118 1945
Hematologic samples and cell lines (B lymphoma) B lymphoma 1.4e-07 21 100 21 121 245
Hematologic cancer and cell line (Various tumors) Various tumors 2.2e-07 26 39.3 66 31 154
Hematologic cancer (Various tumors) Various tumors 2.2e-07 26 39.3 66 31 154
Primary blood mononuclear cells (Various tumors) Various tumors 2.2e-07 26 39.3 66 31 154
Cell line (NCI60*) NCI60* 2.6e-07 64 11.9 536 135 1945
Adenocarcinoma (Lung cancer) Lung cancer 4.0e-07 151 67.4 224 166 276
Cancer and cell line (NCI60*) NCI60* 7.2e-07 64 11.9 536 138 1945
Cancer and cell line (Breast cancer*) Breast cancer* 9.5e-07 34 16.9 201 143 1945
Cancer and cell line (Liver cancer) Liver cancer 1.2e-06 50 86.2 58 126 207
Cancer (Liver cancer) Liver cancer 2.3e-06 47 81.0 58 115 207
Adenocarcinoma (Breast cancer*) Breast cancer* 3.4e-06 28 13.9 201 112 1945
Breast cancer (Breast cancer*) Breast cancer* 3.4e-06 28 13.9 201 112 1945
Cancer (Breast cancer*) Breast cancer* 3.4e-06 28 13.9 201 112 1945
Female hormonal cancer (Breast cancer*) Breast cancer* 3.4e-06 28 13.9 201 112 1945
Lymphocytes (Various tumors) Various tumors 3.5e-06 23 34.8 66 28 154
Monocytes (Various tumors) Various tumors 3.5e-06 23 34.8 66 28 154
Acute lymphocytic leukemia (Leukemia) Leukemia 6.6e-06 26 100 26 99 149
Hepatocellular carcinoma (Liver cancer) Liver cancer 1.3e-05 43 74.1 58 104 207
CNS tissue, cancer or cell line (Various tumors) Various tumors 2.0e-05 18 27.2 66 21 154
Non small cell lung cancer and cell line (Lung cancer*) Lung cancer* 2.0e-05 40 19.9 201 205 1945
Non small cell lung cancer (Lung cancer*) Lung cancer* 2.0e-05 40 19.9 201 205 1945
Cancer and cell line (Various tumors*) Various tumors* 3.2e-05 48 8.9 536 105 1945
Cancer (Various tumors*) Various tumors* 3.2e-05 48 8.9 536 105 1945
B cells (Leukemia) Leukemia 3.6e-05 16 88.8 18 62 141
Lung cancer (Lung cancer*) Lung cancer* 7.1e-05 43 21.3 201 238 1945
Lung cancer or cell line (Lung cancer*) Lung cancer* 7.1e-05 43 21.3 201 238 1945
Cancer and cell line (NCI60*) NCI60* 8.4e-05 29 14.4 201 138 1945
Lymphocytes (Leukemia) Leukemia 0.0001 18 100 18 91 141
Lymphoma or lymphoma cell line (B lymphoma) B lymphoma 0.0002 21 100 21 167 245
Adenocarcinoma (Liver cancer) Liver cancer 0.0002 39 67.2 58 97 207
Non-tumor liver tissue (Liver cancer) Liver cancer 0.0002 32 57.1 56 76 207
B cells (Various tumors) Various tumors 0.0002 18 27.2 66 23 154
Human mammary epithelial cells (HMECs) or normal breast tissue (Various tumors) Various tumors 0.0002 3 42.8 7 4 154
Normal breast tissue (Various tumors) Various tumors 0.0002 3 42.8 7 4 154
Cancer and cell line (Lung cancer*) Lung cancer* 0.0002 43 21.3 201 252 1945
Cancer (Lung cancer*) Lung cancer* 0.0002 43 21.3 201 252 1945
Cell line (NCI60*) NCI60* 0.0003 27 13.4 201 135 1945


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
ectoderm development 1.0e-18 15 26.7 56 46 4566
histogenesis 9.1e-18 15 26.7 56 52 4566
epidermal differentiation 3.0e-16 13 23.2 56 40 4566
nuclear lamina 6.6e-12 10 17.8 56 36 4566
intermediate filament 1.2e-11 10 17.8 56 38 4566
nuclear membrane 7.6e-11 10 17.8 56 45 4566
structural constituent of cytoskeleton 3.9e-08 9 16.0 56 62 4566
organogenesis 9.7e-08 17 30.3 56 315 4566
kinesin complex 1.7e-07 12 21.4 56 151 4566
microtubule associated complex 5.3e-07 12 21.4 56 167 4566
morphogenesis 8.6e-07 17 30.3 56 366 4566
microtubule cytoskeleton 9.3e-07 12 21.4 56 176 4566
serine protease inhibitor activity 8.3e-06 6 10.7 56 41 4566
endopeptidase inhibitor activity 1.1e-05 7 12.5 56 65 4566
cytoskeleton 1.1e-05 13 23.2 56 263 4566
development 1.6e-05 19 33.9 56 554 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 738 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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