Module 53 -- Cell line expressed genes

Jump to: Home | General properties | Gene sets | Enriched clinical annotations | Enriched Go annotations | Visual display
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: 22
Num genes: 406 (see 1271 additional genes for this module)
Num experiments: 1298 (422 induced, 876 repressed)
Parent module: 118
Children modules: 16 15


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.
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 1.6e-19 30 54.5 55 30 182
Macrophages (Stimulated PBMC) Stimulated PBMC 1.6e-19 30 54.5 55 30 182
Chronic lymphocytic leukemia (B lymphoma) B lymphoma 1.0e-17 44 43.1 102 46 245
Leukemia (B lymphoma) B lymphoma 1.0e-17 44 43.1 102 46 245
Leukemia or leukemia cell line (B lymphoma) B lymphoma 1.0e-17 44 43.1 102 46 245
Liver tissue, cancer or cell line (Liver cancer*) Liver cancer* 1.4e-14 88 20.9 421 197 1945
Lung tissue, cancer or cell line (Lung cancer*) Lung cancer* 2.8e-11 175 19.9 876 276 1945
Liver tissue (Liver cancer*) Liver cancer* 5.1e-11 78 18.5 421 187 1945
Activated B like DLBCL (B lymphoma) B lymphoma 4.1e-10 23 36.5 63 30 245
Diffuse large B cell lymphoma tumor or cell line (B lymphoma) B lymphoma 2.6e-09 54 85.7 63 134 245
Hepatitis infected liver (Liver cancer*) Liver cancer* 8.7e-09 64 15.2 421 156 1945
Follicular lymphoma (B lymphoma) B lymphoma 4.1e-08 25 24.5 102 28 245
Lymphoma or lymphoma cell line (B lymphoma) B lymphoma 4.9e-08 59 93.6 63 167 245
Lung cancer (Lung cancer*) Lung cancer* 5.1e-08 146 16.6 876 238 1945
Lung cancer or cell line (Lung cancer*) Lung cancer* 5.1e-08 146 16.6 876 238 1945
Non small cell lung cancer and cell line (Lung cancer*) Lung cancer* 9.1e-08 128 14.6 876 205 1945
Non small cell lung cancer (Lung cancer*) Lung cancer* 9.1e-08 128 14.6 876 205 1945
Cancer and cell line (Lung cancer*) Lung cancer* 1.3e-07 152 17.3 876 252 1945
Cancer (Lung cancer*) Lung cancer* 1.3e-07 152 17.3 876 252 1945
Diffuse large B cell lymphoma - DLBCL (B lymphoma) B lymphoma 7.5e-07 49 77.7 63 126 245
Hematologic cancer and cell line (Stimulated immune*) Stimulated immune* 1.7e-06 27 6.4 421 53 1945
Hematologic samples and cell lines (Stimulated immune*) Stimulated immune* 1.7e-06 27 6.4 421 53 1945
Macrophages (Stimulated immune*) Stimulated immune* 1.7e-06 27 6.4 421 53 1945
Monocytes (Stimulated immune*) Stimulated immune* 1.7e-06 27 6.4 421 53 1945
Prostate (Prostate cancer*) Prostate cancer* 2.9e-06 68 7.7 876 101 1945
Gram negative bacteria stimulated immune cells (Stimulated PBMC) Stimulated PBMC 3.3e-06 37 82.2 45 78 144
Mutated p53 tumor (Breast cancer) Breast cancer 5.4e-06 20 83.3 24 35 78
B. petrussis stimulated immune cells (Stimulated PBMC) Stimulated PBMC 1.2e-05 33 73.3 45 67 144
Hematologic samples and cell lines (Various tumors) Various tumors 2.9e-05 7 100 7 37 154
Hematologic samples (Various tumors) Various tumors 2.9e-05 7 100 7 37 154
Hematologic samples (B lymphoma) B lymphoma 7.0e-05 18 17.6 102 22 245
Breast cancer cell line (Breast cancer) Breast cancer 0.0001 12 28.5 42 17 152
Grade 1 (Breast cancer) Breast cancer 0.0001 7 41.1 17 9 85
Cell line (Liver cancer) Liver cancer 0.0001 11 11.7 94 11 207
Female hormonal cancer cell line (Breast cancer) Breast cancer 0.0001 11 26.1 42 15 152
Grade 3 (Breast cancer) Breast cancer 0.0002 20 74.0 27 38 85
Normal tissue (Lung cancer) Lung cancer 0.0002 22 12.5 175 23 276
Cancer and cell line (Various tumors*) Various tumors* 0.0002 65 7.4 876 105 1945
Cancer (Various tumors*) Various tumors* 0.0002 65 7.4 876 105 1945
p53 positive hepatocellular carcinoma (Liver cancer) Liver cancer 0.0002 18 62.0 29 23 60
Liver cancer cell line (Liver cancer) Liver cancer 0.0002 10 10.6 94 10 207
Cell line (B lymphoma) B lymphoma 0.0002 10 15.8 63 14 245
Epithelial cell line (NCI60) NCI60 0.0004 25 35.2 71 32 139
Normal lung tissue (Lung cancer) Lung cancer 0.0004 21 12 175 22 276


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
DNA metabolism 2.5e-12 37 13.2 279 169 4566
mitosis 2.5e-11 19 6.8 279 50 4566
DNA replication 5.7e-11 19 6.8 279 52 4566
DNA replication and chromosome cycle 3.5e-09 13 4.6 279 29 4566
S phase of mitotic cell cycle 9.5e-09 12 4.3 279 26 4566
DNA dependent DNA replication 4.3e-08 12 4.3 279 29 4566
regulation of transcription 4.0e-07 18 6.4 279 76 4566
cell cycle 1.4e-06 24 8.6 279 135 4566
replication fork 2.6e-06 8 2.8 279 17 4566
transcription\, DNA-dependent 2.0e-05 25 8.9 279 167 4566
cytokinesis 2.5e-05 12 4.3 279 49 4566
regulation of cell cycle 4.0e-05 24 8.6 279 163 4566
host-pathogen interaction 5.3e-05 27 9.6 279 198 4566
nucleus 0.0001 85 30.4 279 966 4566
transcription 0.0001 25 8.9 279 184 4566
DNA repair 0.0001 16 5.7 279 93 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 1298 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
 
 





 >4x