Module 124 -- Transcription

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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: 96 (see 1672 additional genes for this module)
Num experiments: 384 (190 induced, 194 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.
transcription, DNA_dependent
transcription


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-23 28 77.7 36 30 182
Macrophages (Stimulated PBMC) Stimulated PBMC 1.6e-23 28 77.7 36 30 182
Chronic lymphocytic leukemia (B lymphoma) B lymphoma 9.9e-17 34 59.6 57 46 245
Leukemia (B lymphoma) B lymphoma 9.9e-17 34 59.6 57 46 245
Leukemia or leukemia cell line (B lymphoma) B lymphoma 9.9e-17 34 59.6 57 46 245
Lymphocytes (B lymphoma*) B lymphoma* 1.9e-11 57 29.5 193 244 1945
B cells (B lymphoma*) B lymphoma* 2.1e-11 55 28.4 193 231 1945
Cell line (B lymphoma) B lymphoma 3.2e-11 12 42.8 28 14 245
Cancer (B lymphoma*) B lymphoma* 1.6e-09 47 24.3 193 200 1945
Hematologic cancer (B lymphoma*) B lymphoma* 1.6e-09 47 24.3 193 200 1945
Non-tumor liver tissue (Liver cancer) Liver cancer 2.7e-09 24 88.8 27 76 207
Cancer and cell line (B lymphoma*) B lymphoma* 1.7e-08 47 24.3 193 214 1945
Hematologic cancer and cell line (B lymphoma*) B lymphoma* 1.7e-08 47 24.3 193 214 1945
Liver cancer cell line (Liver cancer) Liver cancer 5.6e-08 9 31.0 29 10 207
Cancer and cell line (Liver cancer) Liver cancer 1.3e-07 29 100 29 126 207
Cell line (Liver cancer) Liver cancer 2.8e-07 9 31.0 29 11 207
Breast tissue or cancer (NCI60) NCI60 3.3e-07 4 80 5 4 139
Female hormonal tissue or cancer (NCI60) NCI60 3.3e-07 4 80 5 4 139
Acute myelogeous leukemia (Leukemia) Leukemia 4.3e-07 15 93.7 16 50 141
Small cell lung cancer (Lung cancer) Lung cancer 9.7e-07 6 42.8 14 10 276
B. petrussis stimulated immune cells (Stimulated PBMC) Stimulated PBMC 1.4e-06 23 88.4 26 67 144
Invasive liver tumor (Liver cancer) Liver cancer 8.6e-06 15 51.7 29 38 207
Hematologic samples and cell lines (Stimulated PBMC*) Stimulated PBMC* 1.0e-05 36 19.0 189 182 1945
Monocytes (Stimulated PBMC*) Stimulated PBMC* 1.0e-05 36 19.0 189 182 1945
Breast cancer (NCI60) NCI60 2.2e-05 3 60 5 3 139
Grade 3 (Breast cancer) Breast cancer 5.6e-05 11 100 11 38 85
Gram negative bacteria stimulated immune cells (Stimulated PBMC) Stimulated PBMC 5.9e-05 23 88.4 26 78 144
B. petrussis A2 stimulated immune cells (Stimulated PBMC) Stimulated PBMC 0.0001 5 19.2 26 5 144
B. petrussis Tox 6 stimulated immune cells (Stimulated PBMC) Stimulated PBMC 0.0001 5 19.2 26 5 144
Normal lung tissue (Lung cancer) Lung cancer 0.0002 6 42.8 14 22 276
Normal tissue (Lung cancer) Lung cancer 0.0003 6 42.8 14 23 276
Renal cancer or cell line (Neuro tumors) Neuro tumors 0.0003 4 40 10 5 90
Renal tissue (Neuro tumors) Neuro tumors 0.0003 4 40 10 5 90
Hematologic cancer and cell line (Stimulated immune*) Stimulated immune* 0.0004 14 7.2 193 53 1945
Hematologic samples and cell lines (Stimulated immune*) Stimulated immune* 0.0004 14 7.2 193 53 1945
Macrophages (Stimulated immune*) Stimulated immune* 0.0004 14 7.2 193 53 1945
Monocytes (Stimulated immune*) Stimulated immune* 0.0004 14 7.2 193 53 1945
Breast tissue, cancer or cell line (NCI60) NCI60 0.0004 5 100 5 31 139


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
transcription 1.5e-147 96 100 96 184 4566
transcription\, DNA-dependent 9.9e-140 92 95.8 96 167 4566
regulation of transcription 3.0e-56 43 44.7 96 76 4566
mitosis 3.3e-50 35 36.4 96 50 4566
regulation of transcription\, DNA-dependent 1.1e-43 71 73.9 96 595 4566
transcription from Pol I promoter 1.2e-26 21 21.8 96 38 4566
cell cycle 6.8e-24 30 31.2 96 135 4566
cytokinesis 2.4e-20 19 19.7 96 49 4566
transcription from Pol II promoter 2.0e-19 26 27.0 96 130 4566
regulation of cell cycle 4.9e-19 28 29.1 96 163 4566
nucleus 8.5e-19 60 62.5 96 966 4566
endomembrane system 1.3e-16 59 61.4 96 1029 4566
regulation of transcription from Pol II promoter 9.6e-13 21 21.8 96 146 4566
transcription initiation 5.5e-12 9 9.3 96 16 4566
RNA processing 9.8e-12 17 17.7 96 99 4566
nucleoplasm 2.0e-11 16 16.6 96 89 4566
nuclear division 7.6e-11 9 9.3 96 20 4566
M phase of mitotic cell cycle 5.9e-10 8 8.3 96 17 4566
M phase 1.2e-09 9 9.3 96 26 4566
transcription initiation from Pol II promoter 2.2e-09 7 7.2 96 13 4566
viral host cell process manipulation 1.6e-08 14 14.5 96 102 4566
G1/S transition of mitotic cell cycle 3.1e-08 6 6.2 96 11 4566
kinetochore 3.1e-08 6 6.2 96 11 4566
mitotic anaphase 3.1e-08 6 6.2 96 11 4566
mitotic cell cycle 6.5e-08 10 10.4 96 51 4566
heterogeneous nuclear ribonucleoprotein 1.1e-07 6 6.2 96 13 4566
mitotic checkpoint 1.9e-07 5 5.2 96 8 4566
general RNA polymerase II transcription factor activity 7.5e-07 6 6.2 96 17 4566
transcription termination 8.5e-07 5 5.2 96 10 4566
transcription factor complex 9.1e-07 7 7.2 96 27 4566
response to DNA damage stimulus 1.0e-06 21 21.8 96 310 4566
nucleotidyltransferase activity 1.2e-06 25 26.0 96 425 4566
cyclin-dependent protein kinase activity 2.6e-06 5 5.2 96 12 4566
RNA binding 2.9e-06 18 18.7 96 249 4566
regulation of mitosis 4.1e-06 5 5.2 96 13 4566
regulation of CDK activity 7.3e-06 6 6.2 96 24 4566
nuclease activity 7.7e-06 16 16.6 96 215 4566
host-pathogen interaction 1.2e-05 15 15.6 96 198 4566
nucleolus 2.5e-05 7 7.2 96 43 4566
DNA-directed RNA polymerase I activity 3.4e-05 4 4.1 96 10 4566
DNA-directed RNA polymerase II activity 3.4e-05 4 4.1 96 10 4566
DNA binding 3.6e-05 20 20.8 96 357 4566
RNA polymerase II transcription factor activity 4.5e-05 10 10.4 96 102 4566
obsolete 4.5e-05 38 39.5 96 990 4566
DNA-directed RNA polymerase II\, core complex 5.4e-05 4 4.1 96 11 4566
DNA-directed RNA polymerase III activity 5.4e-05 4 4.1 96 11 4566
ATP binding 5.7e-05 21 21.8 96 399 4566
DNA-directed RNA polymerase activity 7.9e-05 4 4.1 96 12 4566
single-stranded RNA binding 7.9e-05 4 4.1 96 12 4566
oncogenesis 0.0001 13 13.5 96 184 4566
kinase regulator activity 0.0001 8 8.3 96 72 4566
cell cycle checkpoint 0.0001 4 4.1 96 13 4566
DNA-directed RNA polymerase II\, holoenzyme 0.0001 4 4.1 96 13 4566
conjugation with cellular fusion 0.0001 5 5.2 96 24 4566
nucleolar preribosome 0.0001 5 5.2 96 24 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.
 
 





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