Module 118 -- Cell line expressed 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: 31
Num genes: 411 (see 1251 additional genes for this module)
Num experiments: 1519 (458 induced, 1061 repressed)
Parent module: None
Children modules: 52 53


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.
A2058_2
A2058_1
Myelogenous_k_562_2
Myelogenous_k_562_1
HUVEC_1
HUVEC_3
HUVEC_2
Hep3b_2
Hep3b_1
HL60_2
HL60_1
THY__2
THY__1
THY+
Lymphoblastic_molt_4_2
Lymphoblastic_molt_4_3
Lymphoblastic_molt_4_1
GA10_1
K422_2
Ramos_2
Ramos_1
GA10_2
WSU_2
WSU_1
DOHH2_2
DOHH2_1
K422_1
Burkitts_Daudi_2
Burkitts_Daudi_1
Burkitts_Raji_2
Burkitts_Raji_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
Hematologic cancer and cell line (Stimulated PBMC) Stimulated PBMC 7.3e-20 30 55.5 54 30 182
Macrophages (Stimulated PBMC) Stimulated PBMC 7.3e-20 30 55.5 54 30 182
Liver tissue, cancer or cell line (Liver cancer*) Liver cancer* 2.4e-16 96 20.9 458 197 1945
Lung tissue, cancer or cell line (Lung cancer*) Lung cancer* 1.1e-14 208 19.6 1060 276 1945
Liver tissue (Liver cancer*) Liver cancer* 2.8e-13 87 18.9 458 187 1945
Chronic lymphocytic leukemia (B lymphoma) B lymphoma 5.6e-13 44 35.2 125 46 245
Leukemia (B lymphoma) B lymphoma 5.6e-13 44 35.2 125 46 245
Leukemia or leukemia cell line (B lymphoma) B lymphoma 5.6e-13 44 35.2 125 46 245
CNS tissue, cancer or cell line (Neuro tumors*) Neuro tumors* 1.4e-12 76 7.1 1060 85 1945
Diffuse large B cell lymphoma tumor or cell line (B lymphoma) B lymphoma 9.1e-12 62 87.3 71 134 245
CNS cancer or cell line (Neuro tumors*) Neuro tumors* 1.1e-11 72 6.7 1060 81 1945
CNS tumor (Neuro tumors*) Neuro tumors* 1.1e-11 72 6.7 1060 81 1945
Cancer and cell line (Lung cancer*) Lung cancer* 3.2e-11 185 17.4 1060 252 1945
Cancer (Lung cancer*) Lung cancer* 3.2e-11 185 17.4 1060 252 1945
Non small cell lung cancer and cell line (Lung cancer*) Lung cancer* 3.7e-11 155 14.6 1060 205 1945
Non small cell lung cancer (Lung cancer*) Lung cancer* 3.7e-11 155 14.6 1060 205 1945
Lung cancer (Lung cancer*) Lung cancer* 3.8e-11 176 16.6 1060 238 1945
Lung cancer or cell line (Lung cancer*) Lung cancer* 3.8e-11 176 16.6 1060 238 1945
Hepatitis infected liver (Liver cancer*) Liver cancer* 2.4e-10 71 15.5 458 156 1945
Diffuse large B cell lymphoma - DLBCL (B lymphoma) B lymphoma 5.8e-10 58 81.6 71 126 245
Activated B like DLBCL (B lymphoma) B lymphoma 7.1e-10 24 33.8 71 30 245
Cancer and cell line (Neuro tumors*) Neuro tumors* 5.0e-09 72 6.7 1060 86 1945
Cancer (Neuro tumors*) Neuro tumors* 5.0e-09 72 6.7 1060 86 1945
Epithelial cell line (NCI60) NCI60 8.0e-08 32 35.5 90 32 139
Lymphoma or lymphoma cell line (B lymphoma) B lymphoma 8.8e-08 65 91.5 71 167 245
Prostate (Prostate cancer*) Prostate cancer* 1.0e-07 80 7.5 1060 101 1945
Hematologic cancer and cell line (Stimulated immune*) Stimulated immune* 6.7e-07 29 6.3 458 53 1945
Hematologic samples and cell lines (Stimulated immune*) Stimulated immune* 6.7e-07 29 6.3 458 53 1945
Macrophages (Stimulated immune*) Stimulated immune* 6.7e-07 29 6.3 458 53 1945
Monocytes (Stimulated immune*) Stimulated immune* 6.7e-07 29 6.3 458 53 1945
Follicular lymphoma (B lymphoma) B lymphoma 7.3e-07 26 20.8 125 28 245
Mutated p53 tumor (Breast cancer) Breast cancer 8.0e-06 22 78.5 28 35 78
Hematologic samples and cell lines (B lymphoma) B lymphoma 8.0e-06 79 63.2 125 121 245
Classical malignant glioblastoma (Gliomas) Gliomas 0.0001 10 100 10 14 27
Non-classic malignant glioblastoma (Gliomas) Gliomas 0.0001 13 76.4 17 13 27
B. petrussis stimulated immune cells (Stimulated PBMC) Stimulated PBMC 0.0001 31 70.4 44 67 144
Wild type p53 tumor (Breast cancer) Breast cancer 0.0001 16 94.1 17 43 78
Gram negative bacteria stimulated immune cells (Stimulated PBMC) Stimulated PBMC 0.0001 34 77.2 44 78 144
Large cell lung cancer (Lung cancer) Lung cancer 0.0003 4 10.5 38 4 276
GC B like DLBCL (B lymphoma) B lymphoma 0.0003 26 36.6 71 53 245


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
mitosis 3.2e-08 16 5.5 290 50 4566
DNA replication 2.5e-06 14 4.8 290 52 4566
cell cycle 2.8e-06 24 8.2 290 135 4566
regulation of transcription 3.4e-06 17 5.8 290 76 4566
DNA metabolism 5.6e-06 27 9.3 290 169 4566
DNA replication and chromosome cycle 4.8e-05 9 3.1 290 29 4566
regulation of cell cycle 7.5e-05 24 8.2 290 163 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 1519 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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