Module 6 -- Trachea 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: 416 (see 3237 additional genes for this module)
Num experiments: 1333 (365 induced, 968 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.
Trachea_2
Trachea_1


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* 4.6e-34 105 28.7 365 187 1945
Liver tissue, cancer or cell line (Liver cancer*) Liver cancer* 2.5e-31 105 28.7 365 197 1945
Prostate (Prostate cancer*) Prostate cancer* 1.6e-30 100 10.3 967 101 1945
Hepatitis infected liver (Liver cancer*) Liver cancer* 7.1e-26 85 23.2 365 156 1945
Cancer and cell line (Lung cancer*) Lung cancer* 3.5e-25 200 20.6 967 252 1945
Cancer (Lung cancer*) Lung cancer* 3.5e-25 200 20.6 967 252 1945
Lung cancer (Lung cancer*) Lung cancer* 1.8e-22 187 19.3 967 238 1945
Lung cancer or cell line (Lung cancer*) Lung cancer* 1.8e-22 187 19.3 967 238 1945
Lung tissue, cancer or cell line (Lung cancer*) Lung cancer* 4.4e-22 210 21.7 967 276 1945
Non-tumor liver tissue (Liver cancer) Liver cancer 1.6e-17 68 62.9 108 76 207
Hematologic samples and cell lines (B lymphoma) B lymphoma 1.7e-16 67 87.0 77 121 245
Non small cell lung cancer and cell line (Lung cancer*) Lung cancer* 3.1e-16 156 16.1 967 205 1945
Non small cell lung cancer (Lung cancer*) Lung cancer* 3.1e-16 156 16.1 967 205 1945
Acute lymphocytic leukemia (Leukemia) Leukemia 1.7e-15 94 84.6 111 99 149
Cancer and cell line (Liver cancer) Liver cancer 1.0e-14 68 94.4 72 126 207
Lymphocytes (Leukemia) Leukemia 1.2e-14 86 83.4 103 91 141
Lymphoma (B lymphoma) B lymphoma 4.7e-12 48 62.3 77 77 245
B cells (Leukemia) Leukemia 2.1e-09 60 58.2 103 62 141
Activated B like DLBCL (B lymphoma) B lymphoma 3.5e-09 16 51.6 31 30 245
CNS tissue, cancer or cell line (Neuro tumors*) Neuro tumors* 3.9e-09 68 7.0 967 85 1945
Acute leukemia (Leukemia*) Leukemia* 4.2e-09 103 10.6 967 141 1945
Cancer and cell line (Leukemia*) Leukemia* 4.2e-09 103 10.6 967 141 1945
Cancer (Leukemia*) Leukemia* 4.2e-09 103 10.6 967 141 1945
Hematologic cancer and cell line (Leukemia*) Leukemia* 4.2e-09 103 10.6 967 141 1945
Hematologic cancer (Leukemia*) Leukemia* 4.2e-09 103 10.6 967 141 1945
Hematologic samples and cell lines (Leukemia*) Leukemia* 4.2e-09 103 10.6 967 141 1945
Leukemia (Leukemia*) Leukemia* 4.2e-09 103 10.6 967 141 1945
Leukemia or leukemia cell line (Leukemia*) Leukemia* 4.2e-09 103 10.6 967 141 1945
Monocytes (Leukemia*) Leukemia* 4.2e-09 103 10.6 967 141 1945
Hematologic samples and cell lines (Various tumors) Various tumors 9.5e-09 37 36.6 101 37 154
Hematologic samples (Various tumors) Various tumors 9.5e-09 37 36.6 101 37 154
CNS cancer or cell line (Neuro tumors*) Neuro tumors* 2.9e-08 64 6.6 967 81 1945
CNS tumor (Neuro tumors*) Neuro tumors* 2.9e-08 64 6.6 967 81 1945
Cancer and cell line (Various tumors*) Various tumors* 3.6e-08 79 8.1 967 105 1945
Cancer (Various tumors*) Various tumors* 3.6e-08 79 8.1 967 105 1945
Cancer and cell line (Neuro tumors*) Neuro tumors* 3.9e-08 67 6.9 967 86 1945
Cancer (Neuro tumors*) Neuro tumors* 3.9e-08 67 6.9 967 86 1945
Hematologic cancer and cell line (Stimulated PBMC) Stimulated PBMC 6.1e-08 15 60 25 30 182
Macrophages (Stimulated PBMC) Stimulated PBMC 6.1e-08 15 60 25 30 182
Cancer (Liver cancer) Liver cancer 6.6e-08 58 80.5 72 115 207
Hematologic cancer and cell line (Various tumors) Various tumors 3.0e-07 31 30.6 101 31 154
Hematologic cancer (Various tumors) Various tumors 3.0e-07 31 30.6 101 31 154
Primary blood mononuclear cells (Various tumors) Various tumors 3.0e-07 31 30.6 101 31 154
Epithelial cell line (NCI60) NCI60 6.6e-07 32 33.6 95 32 139
Breast tissue or cancer (Breast cancer*) Breast cancer* 7.9e-07 44 12.0 365 118 1945
Female hormonal tissue or cancer (Breast cancer*) Breast cancer* 7.9e-07 44 12.0 365 118 1945
Cell line (Breast cancer) Breast cancer 9.1e-07 20 46.5 43 30 152
Cell line (NCI60*) NCI60* 9.6e-07 94 9.7 967 135 1945
Breast cancer cell line (Breast cancer) Breast cancer 1.2e-06 14 32.5 43 17 152
Lymphocytes (Various tumors) Various tumors 1.6e-06 28 27.7 101 28 154
Monocytes (Various tumors) Various tumors 1.6e-06 28 27.7 101 28 154
B. petrussis A2 stimulated immune cells (Stimulated PBMC) Stimulated PBMC 2.6e-06 5 38.4 13 5 144
Cancer and cell line (NCI60*) NCI60* 4.5e-06 94 9.7 967 138 1945
Adenocarcinoma (Breast cancer*) Breast cancer* 9.3e-06 40 10.9 365 112 1945
Breast cancer (Breast cancer*) Breast cancer* 9.3e-06 40 10.9 365 112 1945
Cancer (Breast cancer*) Breast cancer* 9.3e-06 40 10.9 365 112 1945
Female hormonal cancer (Breast cancer*) Breast cancer* 9.3e-06 40 10.9 365 112 1945
Diffuse large B cell lymphoma - DLBCL (B lymphoma) B lymphoma 1.0e-05 27 87.0 31 126 245
Hepatocellular carcinoma (Liver cancer) Liver cancer 1.1e-05 51 70.8 72 104 207
Liver cancer cell line (Liver cancer) Liver cancer 1.6e-05 10 13.8 72 10 207
Female hormonal cancer cell line (Breast cancer) Breast cancer 1.7e-05 12 27.9 43 15 152
B cells (Various tumors) Various tumors 2.2e-05 23 22.7 101 23 154
Cell line (B lymphoma) B lymphoma 2.4e-05 12 15.5 77 14 245
Adenocarcinoma (Liver cancer) Liver cancer 2.6e-05 48 66.6 72 97 207
Cancer and cell line (Gliomas*) Gliomas* 3.4e-05 37 3.8 967 47 1945
Cancer (Gliomas*) Gliomas* 3.4e-05 37 3.8 967 47 1945
CNS cancer or cell line (Gliomas*) Gliomas* 3.4e-05 37 3.8 967 47 1945
CNS tissue, cancer or cell line (Gliomas*) Gliomas* 3.4e-05 37 3.8 967 47 1945
CNS tumor (Gliomas*) Gliomas* 3.4e-05 37 3.8 967 47 1945
Diffuse large B cell lymphoma tumor or cell line (B lymphoma) B lymphoma 5.3e-05 27 87.0 31 134 245
CNS tissue, cancer or cell line (Various tumors) Various tumors 6.3e-05 21 20.7 101 21 154
Lymphoma (Various tumors) Various tumors 0.0001 20 19.8 101 20 154
Cell line (Liver cancer) Liver cancer 0.0001 10 13.8 72 11 207
Female hormonal tissue, cancer or cell line (Breast cancer*) Breast cancer* 0.0001 44 12.0 365 141 1945
Breast tissue, cancer or cell line (Breast cancer*) Breast cancer* 0.0001 44 12.0 365 142 1945
Female hormonal cancer or cell line (Breast cancer*) Breast cancer* 0.0002 40 10.9 365 127 1945
Cancer and cell line (Various tumors) Various tumors 0.0002 79 78.2 101 105 154
Cancer (Various tumors) Various tumors 0.0002 79 78.2 101 105 154
Breast cancer or cell line (Breast cancer*) Breast cancer* 0.0003 40 10.9 365 128 1945
Lymphoma or lymphoma cell line (B lymphoma) B lymphoma 0.0003 64 83.1 77 167 245
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
extracellular space 5.5e-07 34 11.4 298 212 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 1333 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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