Module 98

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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: 393 (see 1813 additional genes for this module)
Num experiments: 615 (257 induced, 358 repressed)
Parent module: 198
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.
nucleus
endomembrane system


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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
Hematologic cancer and cell line (Stimulated PBMC) Stimulated PBMC 1.2e-25 27 90 30 30 182
Macrophages (Stimulated PBMC) Stimulated PBMC 1.2e-25 27 90 30 30 182
Non-tumor liver tissue (Liver cancer) Liver cancer 2.4e-18 48 84.2 57 76 207
Normal lung tissue (Lung cancer) Lung cancer 3.5e-13 20 33.8 59 22 276
Normal tissue (Lung cancer) Lung cancer 2.3e-12 20 33.8 59 23 276
Chronic lymphocytic leukemia (B lymphoma) B lymphoma 3.4e-12 32 50 64 46 245
Leukemia (B lymphoma) B lymphoma 3.4e-12 32 50 64 46 245
Leukemia or leukemia cell line (B lymphoma) B lymphoma 3.4e-12 32 50 64 46 245
Cell line (B lymphoma) B lymphoma 6.1e-10 11 42.3 26 14 245
Cancer and cell line (Liver cancer) Liver cancer 7.2e-10 42 97.6 43 126 207
Hematologic cancer and cell line (Stimulated immune*) Stimulated immune* 6.4e-09 24 9.3 257 53 1945
Hematologic samples and cell lines (Stimulated immune*) Stimulated immune* 6.4e-09 24 9.3 257 53 1945
Macrophages (Stimulated immune*) Stimulated immune* 6.4e-09 24 9.3 257 53 1945
Monocytes (Stimulated immune*) Stimulated immune* 6.4e-09 24 9.3 257 53 1945
Small cell lung cancer (Lung cancer) Lung cancer 8.2e-08 8 30.7 26 10 276
Invasive liver tumor (Liver cancer) Liver cancer 1.2e-07 21 48.8 43 38 207
Acute myelogeous leukemia (Leukemia) Leukemia 4.1e-07 18 85.7 21 50 141
Liver cancer cell line (Liver cancer) Liver cancer 2.9e-06 9 20.9 43 10 207
Breast tissue or cancer (NCI60) NCI60 4.7e-06 4 50 8 4 139
Female hormonal tissue or cancer (NCI60) NCI60 4.7e-06 4 50 8 4 139
Grade 3 (Breast cancer) Breast cancer 7.3e-06 13 100 13 38 85
Cell line (Liver cancer) Liver cancer 1.3e-05 9 20.9 43 11 207
CNS tissue, cancer or cell line (Neuro tumors*) Neuro tumors* 1.5e-05 32 8.9 358 85 1945
Liver tissue (Liver cancer*) Liver cancer* 1.6e-05 57 15.9 358 187 1945
B. petrussis A2 stimulated immune cells (Stimulated PBMC) Stimulated PBMC 5.4e-05 5 22.7 22 5 144
B. petrussis Tox 6 stimulated immune cells (Stimulated PBMC) Stimulated PBMC 5.4e-05 5 22.7 22 5 144
Liver tissue, cancer or cell line (Liver cancer*) Liver cancer* 9.1e-05 57 15.9 358 197 1945
Breast cancer (NCI60) NCI60 0.0001 3 37.5 8 3 139
p53 positive hepatocellular carcinoma (Liver cancer) Liver cancer 0.0001 14 73.6 19 23 60
Acute lymphocytic leukemia (Leukemia) Leukemia 0.0002 19 100 19 99 149
B cells (B lymphoma*) B lymphoma* 0.0002 63 17.5 358 231 1945
B. petrussis stimulated immune cells (Stimulated PBMC) Stimulated PBMC 0.0002 18 81.8 22 67 144
Hepatitis infected liver (Liver cancer*) Liver cancer* 0.0002 46 12.8 358 156 1945
CNS cancer or cell line (Neuro tumors*) Neuro tumors* 0.0002 28 7.8 358 81 1945
CNS tumor (Neuro tumors*) Neuro tumors* 0.0002 28 7.8 358 81 1945
Lymphoma or lymphoma cell line (B lymphoma) B lymphoma 0.0003 25 96.1 26 167 245
Cancer and cell line (Neuro tumors*) Neuro tumors* 0.0003 29 8.1 358 86 1945
Cancer (Neuro tumors*) Neuro tumors* 0.0003 29 8.1 358 86 1945


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 2.0e-281 387 98.4 393 966 4566
endomembrane system 1.7e-216 362 92.1 393 1029 4566
transcription regulator activity 1.3e-53 182 46.3 393 703 4566
DNA binding 5.0e-51 126 32.0 393 357 4566
regulation of transcription\, DNA-dependent 2.2e-47 159 40.4 393 595 4566
DNA metabolism 2.0e-37 75 19.0 393 169 4566
chemosensory perception 1.5e-27 141 35.8 393 682 4566
sensory perception 7.6e-27 142 36.1 393 700 4566
DNA repair 1.8e-24 45 11.4 393 93 4566
nucleoplasm 2.5e-22 42 10.6 393 89 4566
transcription factor activity 1.8e-21 85 21.6 393 340 4566
DNA replication 1.7e-19 30 7.6 393 52 4566
RNA processing 3.4e-19 41 10.4 393 99 4566
cell cycle 5.3e-19 48 12.2 393 135 4566
RNA metabolism 8.5e-18 38 9.6 393 92 4566
replication fork 1.0e-16 16 4.0 393 17 4566
RNA splicing 2.3e-16 30 7.6 393 63 4566
transcription 2.7e-16 53 13.4 393 184 4566
transcription\, DNA-dependent 1.8e-15 49 12.4 393 167 4566
DNA packaging 1.9e-14 25 6.3 393 50 4566
mRNA splicing 1.1e-13 24 6.1 393 49 4566
RNA polymerase II transcription factor activity 1.4e-13 35 8.9 393 102 4566
chromatin 2.0e-13 24 6.1 393 50 4566
mitosis 2.0e-13 24 6.1 393 50 4566
regulation of cell cycle 3.3e-13 45 11.4 393 163 4566
DNA replication and chromosome cycle 6.6e-13 18 4.5 393 29 4566
chromosome 1.0e-12 26 6.6 393 62 4566
DNA recombination 2.1e-12 17 4.3 393 27 4566
nucleic acid binding 2.2e-12 82 20.8 393 444 4566
establishment and/or maintenance of chromatin architecture 2.3e-12 22 5.5 393 46 4566
nuclear chromosome 3.4e-12 25 6.3 393 60 4566
DNA dependent DNA replication 1.1e-11 17 4.3 393 29 4566
cytokinesis 1.1e-11 22 5.5 393 49 4566
RNA binding 1.4e-11 55 13.9 393 249 4566
nucleotidyltransferase activity 3.3e-11 77 19.5 393 425 4566
transcription factor complex 3.6e-11 16 4.0 393 27 4566
chromosome organization and biogenesis (sensu Eukarya) 5.0e-11 22 5.5 393 52 4566
mRNA processing 9.1e-11 19 4.8 393 40 4566
response to DNA damage stimulus 5.0e-10 60 15.2 393 310 4566
chromatin assembly/disassembly 5.9e-10 17 4.3 393 35 4566
nuclease activity 7.4e-10 47 11.9 393 215 4566
pre-mRNA splicing factor activity 1.0e-09 17 4.3 393 36 4566
nuclear pore 1.2e-09 13 3.3 393 21 4566
mRNA binding 2.7e-09 19 4.8 393 47 4566
regulation of transcription from Pol II promoter 2.8e-09 36 9.1 393 146 4566
S phase of mitotic cell cycle 3.6e-09 14 3.5 393 26 4566
transcription from Pol II promoter 6.1e-09 33 8.3 393 130 4566
regulation of transcription 7.7e-09 24 6.1 393 76 4566
DNA dependent ATPase activity 1.2e-08 14 3.5 393 28 4566
response to abiotic stimulus 1.8e-08 154 39.1 393 1228 4566
regulation of transcription by pheromones 2.1e-08 31 7.8 393 123 4566
pore complex 3.9e-08 14 3.5 393 30 4566
M phase 4.3e-08 13 3.3 393 26 4566
mitotic cell cycle 8.9e-08 18 4.5 393 51 4566
transcription initiation 9.9e-08 10 2.5 393 16 4566
transcription initiation from Pol II promoter 1.2e-07 9 2.2 393 13 4566
ATP binding 1.2e-07 65 16.5 393 399 4566
transcription factor binding 1.4e-07 29 7.3 393 119 4566
nucleosome assembly 1.4e-07 12 3.0 393 24 4566
general RNA polymerase II transcription factor activity 2.2e-07 10 2.5 393 17 4566
M phase of mitotic cell cycle 2.2e-07 10 2.5 393 17 4566
DNA-directed DNA polymerase activity 2.4e-07 7 1.7 393 8 4566
protein-nucleus import 4.9e-07 11 2.7 393 22 4566
nucleocytoplasmic transport 8.7e-07 11 2.7 393 23 4566
histone acetyltransferase complex 1.0e-06 7 1.7 393 9 4566
primary active transporter activity 1.0e-06 7 1.7 393 9 4566
transcription cofactor activity 1.0e-06 28 7.1 393 123 4566
26S proteasome 1.1e-06 12 3.0 393 28 4566
regulation of CDK activity 1.4e-06 11 2.7 393 24 4566
nuclear division 1.6e-06 10 2.5 393 20 4566
proteasome complex (sensu Eukarya) 2.9e-06 10 2.5 393 21 4566
oncogenesis 4.2e-06 35 8.9 393 184 4566
nucleosome disassembly 5.0e-06 10 2.5 393 22 4566
transcription factor TFIID complex 9.4e-06 6 1.5 393 8 4566
chromatin binding 1.0e-05 9 2.2 393 19 4566
damaged DNA binding 1.2e-05 10 2.5 393 24 4566
P-P-bond-hydrolysis-driven transporter activity 1.7e-05 7 1.7 393 12 4566
condensed chromosome 1.9e-05 8 2.0 393 16 4566
DNA replication factor C complex 2.5e-05 5 1.2 393 6 4566
nu DNA polymerase activity 2.5e-05 5 1.2 393 6 4566
cell cycle checkpoint 3.6e-05 7 1.7 393 13 4566
regulation of mitosis 3.6e-05 7 1.7 393 13 4566
nucleotide binding 3.8e-05 15 3.8 393 55 4566
transcription co-repressor activity 3.8e-05 13 3.3 393 43 4566
DNA replication initiation 6.0e-05 6 1.5 393 10 4566
phosphorus metabolism 8.9e-05 26 6.6 393 138 4566
ATPase activity\, coupled 0.0001 12 3.0 393 41 4566
kinetochore 0.0001 6 1.5 393 11 4566
mitotic anaphase 0.0001 6 1.5 393 11 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 615 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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