2.1 Top 1%

• Noonan:
  • http://www.uniprot.org/uniprot/P19419 - neuronal cell body
  • http://www.uniprot.org/uniprot/P32519 - weakly expressed in fetal brain
  • http://www.uniprot.org/uniprot/Q9BQA5 - Highly expressed in brain
  • http://www.uniprot.org/uniprot/P50549 - Very highly expressed in brain
  • http://www.uniprot.org/uniprot/P11161 - brain development (genome browser)
  • http://www.uniprot.org/uniprot/Q02446 - Abundant in brain
• E081:
  • http://www.uniprot.org/uniprot/P48985 - Developing nervous system, and in adult epithelial cells of the gastrointestinal tract. (in Mus musculus (Mouse))
  • http://www.uniprot.org/uniprot/Q9NVV9 - Weaker expression in brain and placenta
  • http://www.uniprot.org/uniprot/P70660 - Expression restricted to the embryonic nervous system. (in Mus musculus (Mouse))
  • http://www.uniprot.org/uniprot/Q7RTU3 - May determine the distinct specification program of class A neurons in the dorsal part of the spinal cord and suppress specification of class B neurons.
  • http://www.uniprot.org/uniprot/Q9H2A3 - Transcriptional regulator. Involved in neuronal differentiation. Activates transcription by binding to the E box (5’-CANNTG-3’).
  • http://www.uniprot.org/uniprot/Q99592 - Transcriptional repressor that plays a role in various developmental processes such as myogenesis and brain development.
  • http://www.uniprot.org/uniprot/Q8TAK6 - Expressed in the brain, in oligodendrocytes. Strongly expressed in oligodendrogliomas, while expression is weak to moderate in astrocytomas. Expression in glioblastomas is highly variable.
  • http://www.uniprot.org/uniprot/Q02575 - May serve as DNA-binding protein and may be involved in the control of cell-type determination, possibly within the developing nervous system.
  • http://www.uniprot.org/uniprot/Q61286 - Abundantly expressed during development of the central nervous system, in particular in proliferating neuroblasts and in cells at the initial stages of differentiation. (in Mus musculus (Mouse))
  • http://www.uniprot.org/uniprot/P15923 - Involved in the initiation of neuronal differentiation.
  • http://www.uniprot.org/uniprot/Q15583 - Links the nodal signaling pathway to the bifurcation of the forebrain and the establishment of ventral midline structures.
  • http://www.uniprot.org/uniprot/P15806 - Expressed during the development of the nervous system.
  • http://www.uniprot.org/uniprot/O14770 - Isoform 3 and isoform 4 can bind to a EPHA8 promoter sequence containing the DNA motif 5’-CGGTCA-3’; in cooperation with a PBX protein (such as PBX2) is proposed to be involved in the transcriptional activation of EPHA8 in the developing midbrain.
  • http://www.uniprot.org/uniprot/O00470 - Also expressed at high levels in the cerebellum.
  • http://www.uniprot.org/uniprot/O35885 - AS-C proteins are involved in the determination of the neuronal precursors in the peripheral nervous system and the central nervous system.
  • http://www.uniprot.org/uniprot/P15884 - Involved in the initiation of neuronal differentiation.
  • http://www.uniprot.org/uniprot/Q96JB3 - Highest levels in cerebellum. Transcriptional repressor.
  • http://www.uniprot.org/uniprot/Q15784 - Transcriptional regulator implicated in neuronal determination.
  • http://www.uniprot.org/uniprot/Q8NDY6 - May function as transcriptional repressor. May modulate the expression of genes required for the differentiation and/or maintenance of pancreatic and neuronal cell types.
  • http://www.uniprot.org/uniprot/P61244 - High levels found in the brain
  • http://www.uniprot.org/uniprot/Q5TA89 - Plays an important role as neurogenesis negative regulator (By similarity).
  • http://www.uniprot.org/uniprot/O15178 - neural plate morphogenesis, neural tube closure
  • http://www.uniprot.org/uniprot/Q13485 - neural crest cell differentiation, neuron fate commitment
  • http://www.uniprot.org/uniprot/Q8NFJ8 - Forms with PRDM8 a transcriptional repressor complex controlling genes involved in neural development and neuronal differentiation.
  • http://www.uniprot.org/uniprot/Q15915 - Acts as a transcriptional activator. Involved in neurogenesis. Plays important roles in the early stage of organogenesis of the CNS, as well as during dorsal spinal cord development and maturation of the cerebellum.
  • http://www.uniprot.org/uniprot/Q13516 - Required for oligodendrocyte and motor neuron specification in the spinal cord, as well as for the development of somatic motor neurons in the hindbrain.
  • http://www.uniprot.org/uniprot/O43889 - neuronal cell body
  • http://www.uniprot.org/uniprot/P03966 - Expressed in the proliferating cells of the developing CNS and the epidermis.
  • http://www.uniprot.org/uniprot/P61244 - neuron apoptotic process
  • http://www.uniprot.org/uniprot/A8MYZ6 - positive regulation of dendritic spine development
  • http://www.uniprot.org/uniprot/Q9R1E0 - regulation of neural precursor cell proliferation
• Both:
  • http://www.uniprot.org/uniprot/P41212 - neurogenesis
  • http://www.uniprot.org/uniprot/Q99581 - In brain, exclusively expressed in the major serotonergic neurons of the dorsal and median raphe nuclei located in the midbrain and pons
  • http://www.uniprot.org/uniprot/P40763 - brain, nervous system development

2.2 Random windows

• Noonan:
  • http://www.uniprot.org/uniprot/P40763 - brain, nervous system development (both) http://www.uniprot.org/uniprot/P50549 - Very highly expressed in brain (Noonan)
  • http://www.uniprot.org/uniprot/P14921 - hypothalamus development (new)
• E081
  • http://www.uniprot.org/uniprot/O15409 - Plays a role in synapse formation by regulating SRPX2 levels. Involved in neural mechanisms mediating the development of speech and language. Expressed in the brain at 15 and 22 weeks of gestation, with a pattern of strong cortical, basal ganglia, thalamic and cerebellar expression. (new)
  • http://www.uniprot.org/uniprot/Q99592 - Transcriptional repressor that plays a role in various developmental processes such as myogenesis and brain development. (E081)
  • http://www.uniprot.org/uniprot/Q02575 - May serve as DNA-binding protein and may be involved in the control of cell-type determination, possibly within the developing nervous system. (E081)
• Both
  • http://www.uniprot.org/uniprot/P41212 - neurogenesis (both)
  • http://www.uniprot.org/uniprot/P32519 - weakly expressed in fetal brain (Noonan)
  • http://www.uniprot.org/uniprot/Q99581 - In brain, exclusively expressed in the major serotonergic neurons of the dorsal and median raphe nuclei located in the midbrain and pons (both)

3.1 Overview

library(pander)
pandoc.table(tf.count)

3.2 Top 1%

e081.allRes

##         GO.ID                                        Term Annotated Significant Expected classicFisher
## 1  GO:0019722                  calcium-mediated signaling         5           4     0.81        0.0028
## 2  GO:0014904                    myotube cell development         3           3     0.49        0.0041
## 3  GO:0048708                   astrocyte differentiation         9           5     1.46        0.0072
## 4  GO:0006357 regulation of transcription from RNA pol...       303          56    49.20        0.0141
## 5  GO:0033173          calcineurin-NFAT signaling cascade         4           3     0.65        0.0145
## 6  GO:0048016       inositol phosphate-mediated signaling         4           3     0.65        0.0145
## 7  GO:0097720              calcineurin-mediated signaling         4           3     0.65        0.0145
## 8  GO:0019932         second-messenger-mediated signaling         7           4     1.14        0.0152
## 9  GO:0009890 negative regulation of biosynthetic proc...       171          36    27.77        0.0162
## 10 GO:0010558 negative regulation of macromolecule bio...       171          36    27.77        0.0162
## 11 GO:0031327 negative regulation of cellular biosynth...       171          36    27.77        0.0162
## 12 GO:0045934 negative regulation of nucleobase-contai...       171          36    27.77        0.0162
## 13 GO:0051172 negative regulation of nitrogen compound...       171          36    27.77        0.0162
## 14 GO:0051253 negative regulation of RNA metabolic pro...       171          36    27.77        0.0162
## 15 GO:1902679 negative regulation of RNA biosynthetic ...       171          36    27.77        0.0162
## 16 GO:1903507 negative regulation of nucleic acid-temp...       171          36    27.77        0.0162
## 17 GO:0031324 negative regulation of cellular metaboli...       172          36    27.93        0.0182
## 18 GO:0000082       G1/S transition of mitotic cell cycle        11           5     1.79        0.0203
## 19 GO:0044843            cell cycle G1/S phase transition        11           5     1.79        0.0203
## 20 GO:0009892    negative regulation of metabolic process       175          36    28.41        0.0252
## 21 GO:0010605 negative regulation of macromolecule met...       175          36    28.41        0.0252
## 22 GO:0048519 negative regulation of biological proces...       219          43    35.56        0.0260
## 23 GO:0000429 carbon catabolite regulation of transcri...         2           2     0.32        0.0260
## 24 GO:0000430 regulation of transcription from RNA pol...         2           2     0.32        0.0260
## 25 GO:0000432 positive regulation of transcription fro...         2           2     0.32        0.0260
## 26 GO:0000436 carbon catabolite activation of transcri...         2           2     0.32        0.0260
## 27 GO:0006816                       calcium ion transport         2           2     0.32        0.0260
## 28 GO:0007520                             myoblast fusion         2           2     0.32        0.0260
## 29 GO:0019086                    late viral transcription         2           2     0.32        0.0260
## 30 GO:0048710     regulation of astrocyte differentiation         2           2     0.32        0.0260
## 31 GO:0048712 negative regulation of astrocyte differe...         2           2     0.32        0.0260
## 32 GO:0048715 negative regulation of oligodendrocyte d...         2           2     0.32        0.0260
## 33 GO:0048741           skeletal muscle fiber development         2           2     0.32        0.0260
## 34 GO:0051924         regulation of calcium ion transport         2           2     0.32        0.0260
## 35 GO:0060074                          synapse maturation         2           2     0.32        0.0260
## 36 GO:0070838                divalent metal ion transport         2           2     0.32        0.0260
## 37 GO:0071157    negative regulation of cell cycle arrest         2           2     0.32        0.0260
## 38 GO:0072511         divalent inorganic cation transport         2           2     0.32        0.0260
## 39 GO:1901739               regulation of myoblast fusion         2           2     0.32        0.0260
## 40 GO:1901741      positive regulation of myoblast fusion         2           2     0.32        0.0260
## 41 GO:0006260                             DNA replication         8           4     1.30        0.0266
## 42 GO:0000083 regulation of transcription involved in ...         5           3     0.81        0.0321
## 43 GO:0032924          activin receptor signaling pathway         5           3     0.81        0.0321
## 44 GO:0038092                     nodal signaling pathway         5           3     0.81        0.0321
## 45 GO:0051302                 regulation of cell division         5           3     0.81        0.0321
## 46 GO:0048523     negative regulation of cellular process       215          42    34.91        0.0331
## 47 GO:0045666 positive regulation of neuron differenti...        17           6     2.76        0.0413
## 48 GO:0019058                            viral life cycle         9           4     1.46        0.0421
## 49 GO:0055088                           lipid homeostasis         9           4     1.46        0.0421
## 50 GO:0006366 transcription from RNA polymerase II pro...       313          56    50.82        0.0463

noonan.allRes

##         GO.ID                                        Term Annotated Significant Expected classicFisher
## 1  GO:0033173          calcineurin-NFAT signaling cascade         4           3     0.34        0.0021
## 2  GO:0034698                    response to gonadotropin         4           3     0.34        0.0021
## 3  GO:0048016       inositol phosphate-mediated signaling         4           3     0.34        0.0021
## 4  GO:0071320                   cellular response to cAMP         4           3     0.34        0.0021
## 5  GO:0071371 cellular response to gonadotropin stimul...         4           3     0.34        0.0021
## 6  GO:0097720              calcineurin-mediated signaling         4           3     0.34        0.0021
## 7  GO:0030154                        cell differentiation       243          28    20.67        0.0035
## 8  GO:0048869              cellular developmental process       246          28    20.92        0.0046
## 9  GO:0000083 regulation of transcription involved in ...         5           3     0.43        0.0050
## 10 GO:0019722                  calcium-mediated signaling         5           3     0.43        0.0050
## 11 GO:0002429 immune response-activating cell surface ...        10           4     0.85        0.0064
## 12 GO:0007268              chemical synaptic transmission        10           4     0.85        0.0064
## 13 GO:0098916        anterograde trans-synaptic signaling        10           4     0.85        0.0064
## 14 GO:0099536                          synaptic signaling        10           4     0.85        0.0064
## 15 GO:0099537                    trans-synaptic signaling        10           4     0.85        0.0064
## 16 GO:0007274         neuromuscular synaptic transmission         2           2     0.17        0.0070
## 17 GO:0048168 regulation of neuronal synaptic plastici...         2           2     0.17        0.0070
## 18 GO:0060396 growth hormone receptor signaling pathwa...         2           2     0.17        0.0070
## 19 GO:0060397 JAK-STAT cascade involved in growth horm...         2           2     0.17        0.0070
## 20 GO:0060416                  response to growth hormone         2           2     0.17        0.0070
## 21 GO:0060762 regulation of branching involved in mamm...         2           2     0.17        0.0070
## 22 GO:0071378 cellular response to growth hormone stim...         2           2     0.17        0.0070
## 23 GO:0071480        cellular response to gamma radiation         2           2     0.17        0.0070
## 24 GO:0072203 cell proliferation involved in metanephr...         2           2     0.17        0.0070
## 25 GO:0002220 innate immune response activating cell s...         6           3     0.51        0.0094
## 26 GO:0002223 stimulatory C-type lectin receptor signa...         6           3     0.51        0.0094
## 27 GO:0002253               activation of immune response        17           5     1.45        0.0097
## 28 GO:0002757 immune response-activating signal transd...        17           5     1.45        0.0097
## 29 GO:0045088        regulation of innate immune response        17           5     1.45        0.0097
## 30 GO:0006357 regulation of transcription from RNA pol...       303          31    25.77        0.0119
## 31 GO:0019932         second-messenger-mediated signaling         7           3     0.60        0.0155
## 32 GO:0045087                      innate immune response        26           6     2.21        0.0159
## 33 GO:0050776               regulation of immune response        26           6     2.21        0.0159
## 34 GO:0002764 immune response-regulating signaling pat...        19           5     1.62        0.0160
## 35 GO:0046683                response to organophosphorus        13           4     1.11        0.0180
## 36 GO:0051591                            response to cAMP        13           4     1.11        0.0180
## 37 GO:0007259                            JAK-STAT cascade         3           2     0.26        0.0200
## 38 GO:0014904                    myotube cell development         3           2     0.26        0.0200
## 39 GO:0016925                         protein sumoylation         3           2     0.26        0.0200
## 40 GO:0072111 cell proliferation involved in kidney de...         3           2     0.26        0.0200
## 41 GO:0072215       regulation of metanephros development         3           2     0.26        0.0200
## 42 GO:0097696                                STAT cascade         3           2     0.26        0.0200
## 43 GO:0050778      positive regulation of immune response        20           5     1.70        0.0200
## 44 GO:0071417 cellular response to organonitrogen comp...        20           5     1.70        0.0200
## 45 GO:0006952                            defense response        44           8     3.74        0.0224
## 46 GO:0044763            single-organism cellular process       295          30    25.09        0.0231
## 47 GO:0002218        activation of innate immune response        14           4     1.19        0.0237
## 48 GO:0002758 innate immune response-activating signal...        14           4     1.19        0.0237
## 49 GO:0003013                  circulatory system process        14           4     1.19        0.0237
## 50 GO:0008015                           blood circulation        14           4     1.19        0.0237

3.3 Randomly selected windows

e081.random.allRes

##         GO.ID                                        Term Annotated Significant Expected classicFisher
## 1  GO:0006357 regulation of transcription from RNA pol...       303          22    17.18        0.0036
## 2  GO:0006366 transcription from RNA polymerase II pro...       313          22    17.75        0.0076
## 3  GO:0030154                        cell differentiation       243          19    13.78        0.0123
## 4  GO:0048869              cellular developmental process       246          19    13.95        0.0148
## 5  GO:0044763            single-organism cellular process       295          21    16.73        0.0168
## 6  GO:0033173          calcineurin-NFAT signaling cascade         4           2     0.23        0.0172
## 7  GO:0048016       inositol phosphate-mediated signaling         4           2     0.23        0.0172
## 8  GO:0097720              calcineurin-mediated signaling         4           2     0.23        0.0172
## 9  GO:0019722                  calcium-mediated signaling         5           2     0.28        0.0277
## 10 GO:0046677                      response to antibiotic         5           2     0.28        0.0277
## 11 GO:0060795 cell fate commitment involved in formati...         5           2     0.28        0.0277
## 12 GO:1904018 positive regulation of vasculature devel...         5           2     0.28        0.0277
## 13 GO:0044699                     single-organism process       334          22    18.94        0.0335
## 14 GO:0021761                   limbic system development        15           3     0.85        0.0462
## 15 GO:0019932         second-messenger-mediated signaling         7           2     0.40        0.0542
## 16 GO:0050851 antigen receptor-mediated signaling path...         7           2     0.40        0.0542
## 17 GO:0060428                 lung epithelium development         7           2     0.40        0.0542
## 18 GO:0070555                   response to interleukin-1         7           2     0.40        0.0542
## 19 GO:0009612             response to mechanical stimulus        16           3     0.91        0.0548
## 20 GO:0001705                          ectoderm formation         1           1     0.06        0.0567
## 21 GO:0001712             ectodermal cell fate commitment         1           1     0.06        0.0567
## 22 GO:0001787           natural killer cell proliferation         1           1     0.06        0.0567
## 23 GO:0001866                     NK T cell proliferation         1           1     0.06        0.0567
## 24 GO:0001941          postsynaptic membrane organization         1           1     0.06        0.0567
## 25 GO:0006997                        nucleus organization         1           1     0.06        0.0567
## 26 GO:0007501          mesodermal cell fate specification         1           1     0.06        0.0567
## 27 GO:0007528          neuromuscular junction development         1           1     0.06        0.0567
## 28 GO:0008356                    asymmetric cell division         1           1     0.06        0.0567
## 29 GO:0010668             ectodermal cell differentiation         1           1     0.06        0.0567
## 30 GO:0010715 regulation of extracellular matrix disas...         1           1     0.06        0.0567
## 31 GO:0010996               response to auditory stimulus         1           1     0.06        0.0567
## 32 GO:0021756                        striatum development         1           1     0.06        0.0567
## 33 GO:0021757                 caudate nucleus development         1           1     0.06        0.0567
## 34 GO:0021758                         putamen development         1           1     0.06        0.0567
## 35 GO:0022617            extracellular matrix disassembly         1           1     0.06        0.0567
## 36 GO:0030575                   nuclear body organization         1           1     0.06        0.0567
## 37 GO:0030578                       PML body organization         1           1     0.06        0.0567
## 38 GO:0031223                           auditory behavior         1           1     0.06        0.0567
## 39 GO:0032354    response to follicle-stimulating hormone         1           1     0.06        0.0567
## 40 GO:0034465                 response to carbon monoxide         1           1     0.06        0.0567
## 41 GO:0042078                germ-line stem cell division         1           1     0.06        0.0567
## 42 GO:0042220                         response to cocaine         1           1     0.06        0.0567
## 43 GO:0042297                              vocal learning         1           1     0.06        0.0567
## 44 GO:0043113                         receptor clustering         1           1     0.06        0.0567
## 45 GO:0044849                               estrous cycle         1           1     0.06        0.0567
## 46 GO:0045601 regulation of endothelial cell different...         1           1     0.06        0.0567
## 47 GO:0045603 positive regulation of endothelial cell ...         1           1     0.06        0.0567
## 48 GO:0048133 male germ-line stem cell asymmetric divi...         1           1     0.06        0.0567
## 49 GO:0048169 regulation of long-term neuronal synapti...         1           1     0.06        0.0567
## 50 GO:0050854 regulation of antigen receptor-mediated ...         1           1     0.06        0.0567

noonan.random.allRes

##         GO.ID                                        Term Annotated Significant Expected classicFisher
## 1  GO:0060396 growth hormone receptor signaling pathwa...         2           2     0.10        0.0025
## 2  GO:0060397 JAK-STAT cascade involved in growth horm...         2           2     0.10        0.0025
## 3  GO:0060416                  response to growth hormone         2           2     0.10        0.0025
## 4  GO:0071378 cellular response to growth hormone stim...         2           2     0.10        0.0025
## 5  GO:0031328 positive regulation of cellular biosynth...       244          18    12.58        0.0063
## 6  GO:0045893 positive regulation of transcription, DN...       244          18    12.58        0.0063
## 7  GO:0045935 positive regulation of nucleobase-contai...       244          18    12.58        0.0063
## 8  GO:0051173 positive regulation of nitrogen compound...       244          18    12.58        0.0063
## 9  GO:0051254 positive regulation of RNA metabolic pro...       244          18    12.58        0.0063
## 10 GO:1902680 positive regulation of RNA biosynthetic ...       244          18    12.58        0.0063
## 11 GO:1903508 positive regulation of nucleic acid-temp...       244          18    12.58        0.0063
## 12 GO:0009891 positive regulation of biosynthetic proc...       245          18    12.63        0.0067
## 13 GO:0010557 positive regulation of macromolecule bio...       245          18    12.63        0.0067
## 14 GO:0007259                            JAK-STAT cascade         3           2     0.15        0.0074
## 15 GO:0097696                                STAT cascade         3           2     0.15        0.0074
## 16 GO:0031325 positive regulation of cellular metaboli...       248          18    12.78        0.0081
## 17 GO:0010628      positive regulation of gene expression       249          18    12.84        0.0086
## 18 GO:0010604 positive regulation of macromolecule met...       252          18    12.99        0.0104
## 19 GO:0045944 positive regulation of transcription fro...       228          17    11.75        0.0104
## 20 GO:0009893    positive regulation of metabolic process       253          18    13.04        0.0110
## 21 GO:0000768 syncytium formation by plasma membrane f...         4           2     0.21        0.0143
## 22 GO:0006949                         syncytium formation         4           2     0.21        0.0143
## 23 GO:0033173          calcineurin-NFAT signaling cascade         4           2     0.21        0.0143
## 24 GO:0048016       inositol phosphate-mediated signaling         4           2     0.21        0.0143
## 25 GO:0060142 regulation of syncytium formation by pla...         4           2     0.21        0.0143
## 26 GO:0097720              calcineurin-mediated signaling         4           2     0.21        0.0143
## 27 GO:0019722                  calcium-mediated signaling         5           2     0.26        0.0230
## 28 GO:0032355                       response to estradiol         5           2     0.26        0.0230
## 29 GO:0060795 cell fate commitment involved in formati...         5           2     0.26        0.0230
## 30 GO:0048522     positive regulation of cellular process       266          18    13.71        0.0236
## 31 GO:0030154                        cell differentiation       243          17    12.53        0.0249
## 32 GO:0044763            single-organism cellular process       295          19    15.21        0.0275
## 33 GO:0048518 positive regulation of biological proces...       269          18    13.87        0.0279
## 34 GO:0048869              cellular developmental process       246          17    12.68        0.0292
## 35 GO:0006357 regulation of transcription from RNA pol...       303          19    15.62        0.0431
## 36 GO:0019932         second-messenger-mediated signaling         7           2     0.36        0.0454
## 37 GO:0050851 antigen receptor-mediated signaling path...         7           2     0.36        0.0454
## 38 GO:0001659                     temperature homeostasis         1           1     0.05        0.0515
## 39 GO:0001705                          ectoderm formation         1           1     0.05        0.0515
## 40 GO:0001712             ectodermal cell fate commitment         1           1     0.05        0.0515
## 41 GO:0001787           natural killer cell proliferation         1           1     0.05        0.0515
## 42 GO:0001866                     NK T cell proliferation         1           1     0.05        0.0515
## 43 GO:0001937 negative regulation of endothelial cell ...         1           1     0.05        0.0515
## 44 GO:0003337 mesenchymal to epithelial transition inv...         1           1     0.05        0.0515
## 45 GO:0003339 regulation of mesenchymal to epithelial ...         1           1     0.05        0.0515
## 46 GO:0003340 negative regulation of mesenchymal to ep...         1           1     0.05        0.0515
## 47 GO:0006164      purine nucleotide biosynthetic process         1           1     0.05        0.0515
## 48 GO:0006754                    ATP biosynthetic process         1           1     0.05        0.0515
## 49 GO:0006997                        nucleus organization         1           1     0.05        0.0515
## 50 GO:0007501          mesodermal cell fate specification         1           1     0.05        0.0515

3.4 Summary

E081 hits in enriched in neuron development process but there is no brain related function enriched in Noonan hits.