Module 252 -- TFs and nuclear

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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: 7
Num genes: 237 (see 1067 additional genes for this module)
Num experiments: 660 (280 induced, 380 repressed)
Parent module: None
Children modules: 198 197


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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.
sensory perception
chemosensory perception
regulation of transcription, DNA_dependent
nucleus
endomembrane system
transcription regulator activity
DNA binding


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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
Non-tumor liver tissue (Liver cancer) Liver cancer 2.0e-28 63 85.1 74 76 207
Hematologic cancer and cell line (Stimulated PBMC) Stimulated PBMC 2.6e-27 28 90.3 31 30 182
Macrophages (Stimulated PBMC) Stimulated PBMC 2.6e-27 28 90.3 31 30 182
Chronic lymphocytic leukemia (B lymphoma) B lymphoma 1.5e-17 39 52 75 46 245
Leukemia (B lymphoma) B lymphoma 1.5e-17 39 52 75 46 245
Leukemia or leukemia cell line (B lymphoma) B lymphoma 1.5e-17 39 52 75 46 245
Cell line (B lymphoma) B lymphoma 1.2e-14 14 45.1 31 14 245
Cancer and cell line (Liver cancer) Liver cancer 4.0e-13 53 98.1 54 126 207
Normal lung tissue (Lung cancer) Lung cancer 1.2e-11 19 32.2 59 22 276
Liver tissue (Liver cancer*) Liver cancer* 1.6e-11 74 19.4 380 187 1945
Normal tissue (Lung cancer) Lung cancer 6.2e-11 19 32.2 59 23 276
Liver tissue, cancer or cell line (Liver cancer*) Liver cancer* 3.2e-10 74 19.4 380 197 1945
Invasive liver tumor (Liver cancer) Liver cancer 8.7e-10 26 48.1 54 38 207
Hepatitis infected liver (Liver cancer*) Liver cancer* 1.6e-07 57 15 380 156 1945
Cell line (Liver cancer) Liver cancer 1.6e-07 11 20.3 54 11 207
Hematologic cancer and cell line (Stimulated immune*) Stimulated immune* 1.8e-07 23 8.2 279 53 1945
Hematologic samples and cell lines (Stimulated immune*) Stimulated immune* 1.8e-07 23 8.2 279 53 1945
Macrophages (Stimulated immune*) Stimulated immune* 1.8e-07 23 8.2 279 53 1945
Monocytes (Stimulated immune*) Stimulated immune* 1.8e-07 23 8.2 279 53 1945
Grade 3 (Breast cancer) Breast cancer 2.8e-07 16 100 16 38 85
Acute myelogeous leukemia (Leukemia) Leukemia 4.1e-07 18 85.7 21 50 141
Liver cancer cell line (Liver cancer) Liver cancer 7.4e-07 10 18.5 54 10 207
Small cell lung cancer (Lung cancer) Lung cancer 9.0e-07 8 23.5 34 10 276
Breast tissue or cancer (NCI60) NCI60 1.0e-06 4 66.6 6 4 139
Female hormonal tissue or cancer (NCI60) NCI60 1.0e-06 4 66.6 6 4 139
B cells (B lymphoma*) B lymphoma* 2.0e-06 73 19.2 380 231 1945
Lymphocytes (B lymphoma*) B lymphoma* 4.8e-06 75 19.7 380 244 1945
Normal tissue (Liver cancer) Liver cancer 7.4e-06 13 17.5 74 14 207
Liver tissue, cancer or cell line (Liver cancer*) Liver cancer* 1.0e-05 50 17.9 279 197 1945
B. petrussis stimulated immune cells (Stimulated PBMC) Stimulated PBMC 1.7e-05 20 86.9 23 67 144
Breast cancer (NCI60) NCI60 4.5e-05 3 50 6 3 139
Adenocarcinoma (Liver cancer) Liver cancer 4.8e-05 38 70.3 54 97 207
Cancer (B lymphoma*) B lymphoma* 5.8e-05 61 16.0 380 200 1945
Hematologic cancer (B lymphoma*) B lymphoma* 5.8e-05 61 16.0 380 200 1945
B. petrussis A2 stimulated immune cells (Stimulated PBMC) Stimulated PBMC 6.9e-05 5 21.7 23 5 144
B. petrussis Tox 6 stimulated immune cells (Stimulated PBMC) Stimulated PBMC 6.9e-05 5 21.7 23 5 144
p53 positive hepatocellular carcinoma (Liver cancer) Liver cancer 8.2e-05 17 68 25 23 60
Cancer (Liver cancer) Liver cancer 8.8e-05 42 77.7 54 115 207
Hematologic samples and cell lines (Various tumors) Various tumors 0.0001 9 75 12 37 154
Hematologic samples (Various tumors) Various tumors 0.0001 9 75 12 37 154
1X dose immune stimulation (Stimulated PBMC) Stimulated PBMC 0.0001 9 60 15 13 59
Acute lymphocytic leukemia (Leukemia) Leukemia 0.0002 19 100 19 99 149
Gram negative bacteria stimulated immune cells (Stimulated PBMC) Stimulated PBMC 0.0003 20 86.9 23 78 144
Lymphoma or lymphoma cell line (B lymphoma) B lymphoma 0.0004 29 93.5 31 167 245


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
nucleus 9.0e-152 229 96.6 237 966 4566
endomembrane system 1.0e-117 214 90.2 237 1029 4566
DNA metabolism 4.1e-31 55 23.2 237 169 4566
DNA binding 1.0e-28 75 31.6 237 357 4566
transcription regulator activity 1.3e-24 100 42.1 237 703 4566
regulation of transcription\, DNA-dependent 2.3e-24 91 38.3 237 595 4566
DNA repair 4.6e-20 33 13.9 237 93 4566
cell cycle 5.6e-19 38 16.0 237 135 4566
DNA replication 5.4e-18 24 10.1 237 52 4566
nucleoplasm 1.4e-16 29 12.2 237 89 4566
replication fork 2.8e-14 13 5.4 237 17 4566
DNA replication and chromosome cycle 6.2e-14 16 6.7 237 29 4566
mitosis 1.0e-13 20 8.4 237 50 4566
nucleotidyltransferase activity 3.0e-13 59 24.8 237 425 4566
RNA splicing 1.7e-12 21 8.8 237 63 4566
RNA metabolism 2.1e-12 25 10.5 237 92 4566
regulation of cell cycle 4.3e-12 33 13.9 237 163 4566
cytokinesis 1.0e-11 18 7.5 237 49 4566
mRNA splicing 1.0e-11 18 7.5 237 49 4566
RNA processing 1.3e-11 25 10.5 237 99 4566
chemosensory perception 1.7e-11 75 31.6 237 682 4566
DNA dependent DNA replication 2.7e-11 14 5.9 237 29 4566
transcription 2.9e-11 34 14.3 237 184 4566
transcription\, DNA-dependent 4.4e-11 32 13.5 237 167 4566
mRNA binding 5.5e-11 17 7.1 237 47 4566
sensory perception 6.6e-11 75 31.6 237 700 4566
response to DNA damage stimulus 7.9e-11 45 18.9 237 310 4566
DNA recombination 1.5e-10 13 5.4 237 27 4566
chromatin 1.7e-10 17 7.1 237 50 4566
pre-mRNA splicing factor activity 9.6e-10 14 5.9 237 36 4566
ATP binding 1.3e-09 50 21.0 237 399 4566
S phase of mitotic cell cycle 1.4e-09 12 5.0 237 26 4566
DNA packaging 1.7e-09 16 6.7 237 50 4566
transcription factor activity 1.8e-09 45 18.9 237 340 4566
nucleic acid binding 2.2e-09 53 22.3 237 444 4566
regulation of transcription 5.1e-09 19 8.0 237 76 4566
mitotic cell cycle 2.0e-08 15 6.3 237 51 4566
primary active transporter activity 3.0e-08 7 2.9 237 9 4566
M phase of mitotic cell cycle 3.9e-08 9 3.7 237 17 4566
DNA dependent ATPase activity 5.7e-08 11 4.6 237 28 4566
RNA binding 1.0e-07 34 14.3 237 249 4566
transcription from Pol II promoter 1.3e-07 23 9.7 237 130 4566
chromosome organization and biogenesis (sensu Eukarya) 2.1e-07 14 5.9 237 52 4566
M phase 2.9e-07 10 4.2 237 26 4566
establishment and/or maintenance of chromatin architecture 3.1e-07 13 5.4 237 46 4566
chromosome 3.5e-07 15 6.3 237 62 4566
DNA-directed DNA polymerase activity 4.7e-07 6 2.5 237 8 4566
P-P-bond-hydrolysis-driven transporter activity 5.8e-07 7 2.9 237 12 4566
RNA polymerase II transcription factor activity 7.9e-07 19 8.0 237 102 4566
chromatin assembly/disassembly 8.0e-07 11 4.6 237 35 4566
nuclear chromosome 1.4e-06 14 5.9 237 60 4566
damaged DNA binding 1.5e-06 9 3.7 237 24 4566
oncogenesis 2.0e-06 26 10.9 237 184 4566
chromatin binding 2.1e-06 8 3.3 237 19 4566
nuclear division 3.4e-06 8 3.3 237 20 4566
single-stranded DNA binding 3.4e-06 8 3.3 237 20 4566
mRNA processing 3.5e-06 11 4.6 237 40 4566
transcription factor complex 4.8e-06 9 3.7 237 27 4566
pore complex 1.2e-05 9 3.7 237 30 4566
nucleosome assembly 1.6e-05 8 3.3 237 24 4566
regulation of mitosis 2.3e-05 6 2.5 237 13 4566
regulation of transcription from Pol II promoter 5.1e-05 20 8.4 237 146 4566
nuclear pore 5.7e-05 7 2.9 237 21 4566
DNA replication initiation 7.3e-05 5 2.1 237 10 4566
transcription initiation 9.4e-05 6 2.5 237 16 4566
mitotic recombination 9.7e-05 4 1.6 237 6 4566
nu DNA polymerase activity 9.7e-05 4 1.6 237 6 4566
nuclease activity 9.8e-05 25 10.5 237 215 4566
nucleocytoplasmic transport 0.0001 7 2.9 237 23 4566
mitotic anaphase 0.0001 5 2.1 237 11 4566


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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 660 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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