Module 5 -- Lung genes

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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: 435 (see 3084 additional genes for this module)
Num experiments: 1433 (449 induced, 984 repressed)
Parent module: None
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.
Lung_2
Lung_1


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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
Liver tissue (Liver cancer*) Liver cancer* 5.5e-23 102 22.7 449 187 1945
Liver tissue, cancer or cell line (Liver cancer*) Liver cancer* 1.1e-20 102 22.7 449 197 1945
Cancer and cell line (Liver cancer) Liver cancer 6.6e-20 76 97.4 78 126 207
Hepatitis infected liver (Liver cancer*) Liver cancer* 2.5e-18 84 18.7 449 156 1945
Non-tumor liver tissue (Liver cancer) Liver cancer 2.9e-18 67 65.0 103 76 207
Normal lung tissue (Lung cancer) Lung cancer 9.2e-15 21 35 60 22 276
Acute lymphocytic leukemia (Leukemia) Leukemia 1.6e-14 97 81.5 119 99 149
Normal tissue (Lung cancer) Lung cancer 9.0e-14 21 35 60 23 276
Lymphocytes (Leukemia) Leukemia 9.1e-14 89 80.1 111 91 141
Cancer and cell line (Lung cancer*) Lung cancer* 1.4e-13 181 18.4 982 252 1945
Cancer (Lung cancer*) Lung cancer* 1.4e-13 181 18.4 982 252 1945
Acute leukemia (Leukemia*) Leukemia* 7.5e-13 111 11.3 982 141 1945
Cancer and cell line (Leukemia*) Leukemia* 7.5e-13 111 11.3 982 141 1945
Cancer (Leukemia*) Leukemia* 7.5e-13 111 11.3 982 141 1945
Hematologic cancer and cell line (Leukemia*) Leukemia* 7.5e-13 111 11.3 982 141 1945
Hematologic cancer (Leukemia*) Leukemia* 7.5e-13 111 11.3 982 141 1945
Hematologic samples and cell lines (Leukemia*) Leukemia* 7.5e-13 111 11.3 982 141 1945
Leukemia (Leukemia*) Leukemia* 7.5e-13 111 11.3 982 141 1945
Leukemia or leukemia cell line (Leukemia*) Leukemia* 7.5e-13 111 11.3 982 141 1945
Monocytes (Leukemia*) Leukemia* 7.5e-13 111 11.3 982 141 1945
Diffuse large B cell lymphoma - DLBCL (B lymphoma) B lymphoma 8.0e-12 44 93.6 47 126 245
Lung cancer (Lung cancer*) Lung cancer* 1.5e-11 168 17.1 982 238 1945
Lung cancer or cell line (Lung cancer*) Lung cancer* 1.5e-11 168 17.1 982 238 1945
Cancer (Liver cancer) Liver cancer 1.4e-10 65 83.3 78 115 207
Diffuse large B cell lymphoma tumor or cell line (B lymphoma) B lymphoma 1.7e-10 44 93.6 47 134 245
Prostate (Prostate cancer*) Prostate cancer* 2.3e-10 81 8.2 982 101 1945
Chronic lymphocytic leukemia (B lymphoma) B lymphoma 7.7e-09 38 34.5 110 46 245
Leukemia (B lymphoma) B lymphoma 7.7e-09 38 34.5 110 46 245
Leukemia or leukemia cell line (B lymphoma) B lymphoma 7.7e-09 38 34.5 110 46 245
Activated B like DLBCL (B lymphoma) B lymphoma 9.3e-09 19 40.4 47 30 245
Hematologic cancer and cell line (Stimulated PBMC) Stimulated PBMC 1.0e-08 19 51.3 37 30 182
Macrophages (Stimulated PBMC) Stimulated PBMC 1.0e-08 19 51.3 37 30 182
Lung tissue, cancer or cell line (Lung cancer*) Lung cancer* 3.5e-08 181 18.4 982 276 1945
B cells (Leukemia) Leukemia 5.2e-08 61 54.9 111 62 141
Non small cell lung cancer and cell line (Lung cancer*) Lung cancer* 2.0e-07 138 14.0 982 205 1945
Non small cell lung cancer (Lung cancer*) Lung cancer* 2.0e-07 138 14.0 982 205 1945
Medulloblastoma (Neuro tumors) Neuro tumors 7.8e-07 53 82.8 64 60 90
Vincristine chemotherapy (Neuro tumors) Neuro tumors 7.8e-07 53 82.8 64 60 90
Cell line (Breast cancer) Breast cancer 9.1e-07 20 46.5 43 30 152
Cell line (NCI60*) NCI60* 9.5e-07 95 9.6 982 135 1945
Epithelial cell line (NCI60) NCI60 9.9e-07 32 33.3 96 32 139
Hepatocellular carcinoma (Liver cancer) Liver cancer 1.1e-06 56 71.7 78 104 207
Breast cancer cell line (Breast cancer) Breast cancer 1.2e-06 14 32.5 43 17 152
Adenocarcinoma (Liver cancer) Liver cancer 1.9e-06 53 67.9 78 97 207
Cancer and cell line (Various tumors*) Various tumors* 2.2e-06 76 7.7 982 105 1945
Cancer (Various tumors*) Various tumors* 2.2e-06 76 7.7 982 105 1945
Cancer and cell line (NCI60*) NCI60* 4.6e-06 95 9.6 982 138 1945
CNS tissue, cancer or cell line (Neuro tumors*) Neuro tumors* 4.7e-06 63 6.4 982 85 1945
Lymphoma or lymphoma cell line (B lymphoma) B lymphoma 5.8e-06 44 93.6 47 167 245
Hematologic samples (Stimulated PBMC*) Stimulated PBMC* 9.4e-06 58 12.9 449 152 1945
Lymphocytes (Stimulated PBMC*) Stimulated PBMC* 9.4e-06 58 12.9 449 152 1945
Primary blood mononuclear cells (Stimulated PBMC*) Stimulated PBMC* 9.4e-06 58 12.9 449 152 1945
Cell line (Liver cancer) Liver cancer 1.3e-05 11 14.1 78 11 207
Female hormonal cancer cell line (Breast cancer) Breast cancer 1.7e-05 12 27.9 43 15 152
CNS cancer or cell line (Neuro tumors*) Neuro tumors* 2.4e-05 59 6.0 982 81 1945
CNS tumor (Neuro tumors*) Neuro tumors* 2.4e-05 59 6.0 982 81 1945
Hematologic cancer and cell line (Stimulated immune*) Stimulated immune* 2.4e-05 26 5.7 449 53 1945
Hematologic samples and cell lines (Stimulated immune*) Stimulated immune* 2.4e-05 26 5.7 449 53 1945
Macrophages (Stimulated immune*) Stimulated immune* 2.4e-05 26 5.7 449 53 1945
Monocytes (Stimulated immune*) Stimulated immune* 2.4e-05 26 5.7 449 53 1945
Liver cancer cell line (Liver cancer) Liver cancer 3.9e-05 10 12.8 78 10 207
B. petrussis A2 stimulated immune cells (Stimulated PBMC) Stimulated PBMC 8.8e-05 5 20.8 24 5 144
Stimulated immune cells (Stimulated PBMC*) Stimulated PBMC* 0.0001 52 11.5 449 143 1945
Hematologic samples and cell lines (Stimulated PBMC*) Stimulated PBMC* 0.0001 63 14.0 449 182 1945
Monocytes (Stimulated PBMC*) Stimulated PBMC* 0.0001 63 14.0 449 182 1945
Lung carcinoid (Lung cancer) Lung cancer 0.0001 20 11.0 181 20 276
Cancer and cell line (Neuro tumors*) Neuro tumors* 0.0001 60 6.1 982 86 1945
Cancer (Neuro tumors*) Neuro tumors* 0.0001 60 6.1 982 86 1945
Cell line (B lymphoma) B lymphoma 0.0001 13 11.8 110 14 245
CNS tissue, cancer or cell line (Various tumors) Various tumors 0.0001 21 19.8 106 21 154
Hematologic samples and cell lines (Various tumors) Various tumors 0.0002 34 32.0 106 37 154
Hematologic samples (Various tumors) Various tumors 0.0002 34 32.0 106 37 154
Hematologic cancer and cell line (Various tumors) Various tumors 0.0003 29 27.3 106 31 154
Hematologic cancer (Various tumors) Various tumors 0.0003 29 27.3 106 31 154
Primary blood mononuclear cells (Various tumors) Various tumors 0.0003 29 27.3 106 31 154
After doxorubicin chemotherapy (Breast cancer) Breast cancer 0.0004 16 84.2 19 21 38


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 biotic stimulus 1.5e-09 80 25.0 319 600 4566
immune response 1.7e-08 65 20.3 319 469 4566
cell adhesion 3.5e-07 37 11.5 319 222 4566
cell communication 5.7e-07 109 34.1 319 1030 4566
inflammatory response 9.1e-07 23 7.2 319 108 4566
response to pest/pathogen/parasite 1.8e-06 29 9.0 319 163 4566
cell adhesion molecule activity 2.4e-06 23 7.2 319 114 4566
extracellular space 2.7e-06 34 10.6 319 212 4566
response to stress 2.9e-06 87 27.2 319 792 4566
thermoregulation 7.9e-06 21 6.5 319 105 4566
extracellular matrix structural constituent 9.2e-06 26 8.1 319 149 4566
phospholipase inhibitor activity 3.0e-05 5 1.5 319 7 4566
protein kinase activity 6.1e-05 19 5.9 319 102 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 1433 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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