To get the full list of phenotypic variables, please check the menu below.
Tool description
Like PANDA, OTTER reconstructs a gene regulatory network from the TF PPI, TF DNA binding motif, and gene expression samples.
OTTER formulates network inference as a well-defined objective function that optimizes the graph matching of the three network priors. Check the phenotypic information for the clinical variables of the samples that were used to reconstruct the network.
The variable Samples indicates the number of samples used for network reconstruction. For single-sample networks, clicking the number of samples links to the phenotypic variable table and the individual
networks. The number in the Sample variable and the phenotypic variable table may be different because the table can include samples from other studies. For example, in colon cancer, 444 TCGA samples were
used to build LIONESS networks in a first study and 445 samples were used for a more recent study. The superset of both TCGA samples is comprised of 487 samples, which is the size of the pheotypic variables
table. This discrepancy is due to different pre-processinng techniques, inclusion/exclusion criteria, and sample quality-control.
Variable description
This is a description of the primary clinical variables of the gene expression samples that were used to generate the gene regulatory network.
| Sample | Gender | Race | Ethnicity | Weight | Height | Anatomic location | Stage | Diagnosis | Vital status | Time | Age | Network |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| TCGA-3C-AAAU-01A-11R-A41B-07 | female | white | not hispanic or latino | NA | NA | Breast | stage x | c50.9 | alive | NA | 55 | |
| TCGA-3C-AALI-01A-11R-A41B-07 | female | black or african american | not hispanic or latino | NA | NA | Breast | stage iib | c50.9 | alive | NA | 50 | |
| TCGA-3C-AALJ-01A-31R-A41B-07 | female | black or african american | not hispanic or latino | NA | NA | Breast | stage iib | c50.9 | alive | NA | 62 | |
| TCGA-3C-AALK-01A-11R-A41B-07 | female | black or african american | not hispanic or latino | NA | NA | Breast | stage ia | c50.9 | alive | NA | 52 | |
| TCGA-4H-AAAK-01A-12R-A41B-07 | female | white | not hispanic or latino | NA | NA | Breast | stage iiia | c50.9 | alive | NA | 50 | |
| TCGA-5L-AAT0-01A-12R-A41B-07 | female | white | hispanic or latino | NA | NA | Breast | stage iia | c50.9 | alive | NA | 42 | |
| TCGA-5L-AAT1-01A-12R-A41B-07 | female | white | hispanic or latino | NA | NA | Breast | stage iv | c50.9 | alive | NA | 63 | |
| TCGA-5T-A9QA-01A-11R-A41B-07 | female | black or african american | not hispanic or latino | NA | NA | Breast | stage iia | c50.9 | alive | NA | 52 | |
| TCGA-A1-A0SB-01A-11R-A144-07 | female | white | not hispanic or latino | NA | NA | Breast | stage i | c50.9 | alive | NA | 70 | |
| TCGA-A1-A0SD-01A-11R-A115-07 | female | white | not hispanic or latino | NA | NA | Breast | stage iia | c50.9 | alive | NA | 59 |
Variable description
BONOBO estimates single-sample co-expression networks for each individual patient. Networks for each individual sample can be downloaded as a miRNA-by-gene adjacency matrix named after the GEO sample reference.
| Sample | Gender | Subtype | Mutation | HER2 status | Estrogen receptor status | Anatomic location | Time | Vital status | Network |
|---|---|---|---|---|---|---|---|---|---|
| GSM496794 | Female | - | tp53 mutation status: Mut | - | Negative | Breast Primary Tumor | 105.625 | Dead of other disease than BC | |
| GSM496795 | Female | breast cancer subtype: Lum A | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 127.4013158 | Alive | |
| GSM496796 | Female | breast cancer subtype: Lum A | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 126.6118421 | Alive | |
| GSM496797 | Female | breast cancer subtype: Lum A | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 126.5131579 | Alive | |
| GSM496798 | Female | breast cancer subtype: Lum A | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 80.98684211 | Dead of other disease than BC | |
| GSM496799 | Female | breast cancer subtype: Basal | tp53 mutation status: Mut | Negative | Negative | Breast Primary Tumor | - | - | |
| GSM496800 | Female | breast cancer subtype: Lum A | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 52.56578947 | Dead of BC | |
| GSM496801 | Female | breast cancer subtype: Normal-like | tp53 mutation status: WT | Negative | Negative | Breast Primary Tumor | 81.67763158 | Dead of other disease than BC | |
| GSM496802 | Female | breast cancer subtype: Lum B | tp53 mutation status: Mut | Negative | Positive | Breast Primary Tumor | 126.25 | Alive | |
| GSM496803 | Female | breast cancer subtype: Normal-like | tp53 mutation status: WT | Positive | Positive | Breast Primary Tumor | 32.59868421 | Dead of BC | |
| GSM496804 | Female | breast cancer subtype: Lum A | tp53 mutation status: WT | Negative | Negative | Breast Primary Tumor | 101.0526316 | Dead of BC | |
| GSM496805 | Female | breast cancer subtype: Basal | tp53 mutation status: Mut | Negative | Negative | Breast Primary Tumor | 32.79605263 | Dead of BC | |
| GSM496806 | Female | breast cancer subtype: Normal-like | tp53 mutation status: WT | Negative | Negative | Breast Primary Tumor | 125.4934211 | Alive | |
| GSM496807 | Female | breast cancer subtype: Basal | tp53 mutation status: Mut | Negative | Negative | Breast Primary Tumor | 49.96710526 | Dead of BC | |
| GSM496808 | Female | breast cancer subtype: ERBB2 | tp53 mutation status: Mut | Positive | Negative | Breast Primary Tumor | 8.256578947 | Dead of other disease than BC | |
| GSM496809 | Female | breast cancer subtype: ERBB2 | tp53 mutation status: Mut | Positive | Negative | Breast Primary Tumor | 124.4078947 | Alive | |
| GSM496810 | Female | breast cancer subtype: ERBB2 | tp53 mutation status: Mut | - | Negative | Breast Primary Tumor | 34.14473684 | Dead of BC | |
| GSM496811 | Female | breast cancer subtype: ERBB2 | tp53 mutation status: WT | Positive | Negative | Breast Primary Tumor | 20.39473684 | Dead of BC | |
| GSM496812 | Female | breast cancer subtype: Lum A | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 92.33552632 | Dead of other disease than BC | |
| GSM496813 | Female | breast cancer subtype: ERBB2 | tp53 mutation status: Mut | - | Positive | Breast Primary Tumor | 123.0592105 | Alive | |
| GSM496814 | Female | breast cancer subtype: Basal | tp53 mutation status: Mut | Negative | Negative | Breast Primary Tumor | 123.0263158 | Alive | |
| GSM496815 | Female | breast cancer subtype: Lum A | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 122.9934211 | Alive | |
| GSM496816 | Female | breast cancer subtype: Lum A | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 33.45394737 | Dead of BC | |
| GSM496817 | Female | breast cancer subtype: Basal | tp53 mutation status: Mut | Negative | Negative | Breast Primary Tumor | 15.52631579 | Dead of BC | |
| GSM496818 | Female | breast cancer subtype: ERBB2 | tp53 mutation status: Mut | Negative | Negative | Breast Primary Tumor | 55.16447368 | Dead of other disease than BC | |
| GSM496819 | Female | breast cancer subtype: ERBB2 | tp53 mutation status: Mut | Negative | Negative | Breast Primary Tumor | 122.3355263 | Alive | |
| GSM496820 | Female | breast cancer subtype: ERBB2 | tp53 mutation status: Mut | - | Negative | Breast Primary Tumor | 23.45394737 | Dead of BC | |
| GSM496821 | Female | breast cancer subtype: Normal-like | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 19.375 | Dead of BC | |
| GSM496822 | Female | breast cancer subtype: Lum B | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 106.1184211 | dead but cause not registered | |
| GSM496823 | Female | breast cancer subtype: Lum A | tp53 mutation status: WT | - | Positive | Breast Primary Tumor | 72.17105263 | Dead of other disease than BC | |
| GSM496825 | Female | breast cancer subtype: Lum B | tp53 mutation status: Mut | Negative | Positive | Breast Primary Tumor | 15.29605263 | Dead of BC | |
| GSM496826 | Female | breast cancer subtype: Lum B | tp53 mutation status: WT | Positive | Positive | Breast Primary Tumor | 121.8421053 | Alive | |
| GSM496827 | Female | breast cancer subtype: Lum B | tp53 mutation status: Mut | Negative | Positive | Breast Primary Tumor | 121.4144737 | Alive | |
| GSM496828 | Female | breast cancer subtype: Lum A | tp53 mutation status: Mut | Negative | Positive | Breast Primary Tumor | 79.80263158 | Dead of other disease than BC | |
| GSM496830 | Female | breast cancer subtype: Lum A | tp53 mutation status: WT | Negative | Negative | Breast Primary Tumor | 108.4210526 | dead but cause not registered | |
| GSM496831 | Female | breast cancer subtype: Lum A | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 120.4276316 | Alive | |
| GSM496833 | Female | breast cancer subtype: Lum A | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 47.13815789 | Dead of other disease than BC | |
| GSM496834 | Female | breast cancer subtype: ERBB2 | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 10.26315789 | dead but cause not registered | |
| GSM496835 | Female | breast cancer subtype: Lum A | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 80.65789474 | Dead of BC | |
| GSM496837 | Female | breast cancer subtype: Lum A | tp53 mutation status: Mut | Negative | Positive | Breast Primary Tumor | 89.07894737 | Dead of BC | |
| GSM496838 | Female | breast cancer subtype: Lum B | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 118.6842105 | Alive | |
| GSM496839 | Female | breast cancer subtype: ERBB2 | tp53 mutation status: Mut | Negative | Positive | Breast Primary Tumor | 19.83552632 | Dead of other disease than BC | |
| GSM496840 | Female | breast cancer subtype: Lum B | tp53 mutation status: Mut | Positive | Positive | Breast Primary Tumor | 118.6184211 | Alive | |
| GSM496841 | Female | breast cancer subtype: Lum A | tp53 mutation status: WT | Positive | Positive | Breast Primary Tumor | 118.4210526 | Alive | |
| GSM496843 | Female | breast cancer subtype: Lum A | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 117.8618421 | Alive | |
| GSM496845 | Female | breast cancer subtype: Basal | tp53 mutation status: Mut | Negative | Negative | Breast Primary Tumor | 23.05921053 | Dead of BC | |
| GSM496848 | Female | breast cancer subtype: Lum A | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 116.7434211 | Alive | |
| GSM496849 | Female | breast cancer subtype: Normal-like | tp53 mutation status: Mut | Negative | Positive | Breast Primary Tumor | 54.63815789 | Dead of BC | |
| GSM496851 | Female | tp53 mutation status: Mut | death status: Alive | - | Negative | Breast Primary Tumor | 115.4276316 | Alive | |
| GSM496852 | Female | breast cancer subtype: Lum A | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 115.1973684 | Alive | |
| GSM496853 | Female | breast cancer subtype: Basal | tp53 mutation status: Mut | Negative | Negative | Breast Primary Tumor | 115.1973684 | Alive | |
| GSM496854 | Female | breast cancer subtype: not classified | tp53 mutation status: WT | Positive | Negative | Breast Primary Tumor | 115.1973684 | Alive | |
| GSM496855 | Female | breast cancer subtype: Lum A | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 115.1315789 | Alive | |
| GSM496856 | Female | breast cancer subtype: Lum B | tp53 mutation status: WT | Positive | Positive | Breast Primary Tumor | 114.5065789 | Alive | |
| GSM496857 | Female | breast cancer subtype: Lum A | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 114.4407895 | Alive | |
| GSM496858 | Female | breast cancer subtype: Basal | tp53 mutation status: WT | - | - | Breast Primary Tumor | 114.2434211 | Alive | |
| GSM496859 | Female | breast cancer subtype: Lum A | tp53 mutation status: WT | - | - | Breast Primary Tumor | - | - | |
| GSM496860 | Female | breast cancer subtype: Basal | tp53 mutation status: Mut | Negative | Negative | Breast Primary Tumor | 114.0460526 | Alive | |
| GSM496861 | Female | breast cancer subtype: Basal | tp53 mutation status: Mut | Negative | Negative | Breast Primary Tumor | 114.0131579 | Alive | |
| GSM496862 | Female | breast cancer subtype: Lum A | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 50.42763158 | Dead of BC | |
| GSM496863 | Female | breast cancer subtype: Lum A | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 59.04605263 | dead but cause not registered | |
| GSM496864 | Female | breast cancer subtype: Basal | tp53 mutation status: Mut | Negative | Negative | Breast Primary Tumor | 92.43421053 | dead but cause not registered | |
| GSM496865 | Female | tp53 mutation status: WT | death status: Alive | - | Positive | Breast Primary Tumor | 112.9276316 | Alive | |
| GSM496866 | Female | breast cancer subtype: Lum A | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 112.8618421 | Alive | |
| GSM496867 | Female | breast cancer subtype: not classified | tp53 mutation status: Mut | Negative | Positive | Breast Primary Tumor | 112.7960526 | Alive | |
| GSM496868 | Female | breast cancer subtype: Lum B | tp53 mutation status: Mut | Positive | Negative | Breast Primary Tumor | 28.02631579 | Dead of BC | |
| GSM496870 | Female | breast cancer subtype: Basal | tp53 mutation status: WT | Negative | Negative | Breast Primary Tumor | 111.7105263 | Alive | |
| GSM496871 | Female | breast cancer subtype: Normal-like | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 111.6776316 | Alive | |
| GSM496872 | Female | breast cancer subtype: Lum A | tp53 mutation status: Mut | Negative | Positive | Breast Primary Tumor | 27.13815789 | Dead of other disease than BC | |
| GSM496873 | Female | breast cancer subtype: Lum A | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 79.83552632 | Dead of BC | |
| GSM496875 | Female | breast cancer subtype: ERBB2 | tp53 mutation status: WT | Positive | Negative | Breast Primary Tumor | 110.5263158 | Alive | |
| GSM496876 | Female | breast cancer subtype: Basal | tp53 mutation status: Mut | Negative | Negative | Breast Primary Tumor | 110.5263158 | Alive | |
| GSM496879 | Female | breast cancer subtype: Lum A | tp53 mutation status: WT | Negative | Negative | Breast Primary Tumor | 109.9013158 | Alive | |
| GSM496880 | Female | breast cancer subtype: Lum A | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 109.9013158 | Alive | |
| GSM496881 | Female | breast cancer subtype: Normal-like | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 43.19078947 | Dead of other disease than BC | |
| GSM496882 | Female | breast cancer subtype: Lum A | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 109.4407895 | Alive | |
| GSM496883 | Female | breast cancer subtype: ERBB2 | tp53 mutation status: WT | Positive | Positive | Breast Primary Tumor | 109.2434211 | Alive | |
| GSM496884 | Female | breast cancer subtype: not classified | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 109.2105263 | Alive | |
| GSM496885 | Female | breast cancer subtype: ERBB2 | tp53 mutation status: WT | Positive | Negative | Breast Primary Tumor | 64.47368421 | Dead of BC | |
| GSM496886 | Female | breast cancer subtype: Normal-like | tp53 mutation status: WT | Negative | Negative | Breast Primary Tumor | 108.4868421 | Alive | |
| GSM496887 | Female | breast cancer subtype: Lum A | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 108.2894737 | Alive | |
| GSM496888 | Female | breast cancer subtype: Lum A | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 108.2565789 | Alive | |
| GSM496889 | Female | breast cancer subtype: Lum A | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 107.9934211 | Alive | |
| GSM496890 | Female | breast cancer subtype: ERBB2 | tp53 mutation status: Mut | Positive | Negative | Breast Primary Tumor | 107.8618421 | Alive | |
| GSM496891 | Female | breast cancer subtype: Lum A | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 106.9078947 | Alive | |
| GSM496892 | Female | breast cancer subtype: Lum A | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 95.88815789 | dead but cause not registered | |
| GSM496893 | Female | breast cancer subtype: Normal-like | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 105.2631579 | Alive | |
| GSM496894 | Female | breast cancer subtype: ERBB2 | tp53 mutation status: WT | Positive | Positive | Breast Primary Tumor | 105.0657895 | Alive | |
| GSM496895 | Female | breast cancer subtype: Lum A | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 104.8355263 | Alive | |
| GSM496896 | Female | breast cancer subtype: Lum B | tp53 mutation status: Mut | Positive | Negative | Breast Primary Tumor | 29.40789474 | Dead of BC | |
| GSM496897 | Female | breast cancer subtype: Lum A | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 55.16447368 | Dead of BC | |
| GSM496898 | Female | breast cancer subtype: Lum A | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 104.0460526 | Alive | |
| GSM496899 | Female | breast cancer subtype: Lum B | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 102.8947368 | Alive | |
| GSM496901 | Female | breast cancer subtype: ERBB2 | tp53 mutation status: Mut | Positive | Negative | Breast Primary Tumor | 27.82894737 | Dead of other disease than BC | |
| GSM496902 | Female | breast cancer subtype: Lum A | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 101.0855263 | Alive | |
| GSM496903 | Female | breast cancer subtype: ERBB2 | tp53 mutation status: Mut | Negative | Negative | Breast Primary Tumor | 100.5921053 | Alive | |
| GSM496904 | Female | breast cancer subtype: Normal-like | tp53 mutation status: Mut | Negative | Negative | Breast Primary Tumor | 34.53947368 | Dead of BC | |
| GSM496905 | Female | breast cancer subtype: Basal | tp53 mutation status: WT | Negative | Negative | Breast Primary Tumor | 98.61842105 | Alive | |
| GSM496906 | Female | breast cancer subtype: Lum A | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 98.61842105 | Alive | |
| GSM496907 | Female | breast cancer subtype: Basal | tp53 mutation status: Mut | Negative | Negative | Breast Primary Tumor | 15.29605263 | Dead of BC | |
| GSM496908 | Female | breast cancer subtype: Lum B | tp53 mutation status: WT | Negative | Positive | Breast Primary Tumor | 94.44078947 | Alive |