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GSE53960: rat RNA-Seq transcriptomic Bodymap
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Results for Smad4
Z-value: 1.00
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Transcription factors associated with Smad4
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| Smad4 | rn6_v1_chr18_-_69657301_69657301 | 0.46 | 5.7e-18 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| chr3_+_56862691 Show fit | 39.59 |
ENSRNOT00000087712
|
glutamate decarboxylase 1 |
|
| chr16_-_39476384 Show fit | 28.64 |
ENSRNOT00000092968
|
glycoprotein m6a |
|
| chr13_-_91872954 Show fit | 27.80 |
ENSRNOT00000004613
ENSRNOT00000079263 |
cell adhesion molecule 3 |
|
| chr10_-_45297385 Show fit | 26.55 |
ENSRNOT00000041187
|
histone cluster 3 H2B family member b |
|
| chr10_-_107539658 Show fit | 25.72 |
ENSRNOT00000089346
|
RNA binding protein, fox-1 homolog 3 |
|
| chr1_+_196996581 Show fit | 25.64 |
ENSRNOT00000021690
|
interleukin 21 receptor |
|
| chr2_+_209839299 Show fit | 25.56 |
ENSRNOT00000092450
|
potassium voltage-gated channel subfamily A member 2 |
|
| chr2_+_209838869 Show fit | 25.51 |
ENSRNOT00000092365
|
potassium voltage-gated channel subfamily A member 2 |
|
| chr16_-_39476025 Show fit | 25.16 |
ENSRNOT00000014312
|
glycoprotein m6a |
|
| chr10_-_107539465 Show fit | 25.11 |
ENSRNOT00000004524
|
RNA binding protein, fox-1 homolog 3 |
Network of associatons between targets according to the STRING database.
First level regulatory network of Smad4
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 3.6 | 60.9 | GO:0045653 | negative regulation of megakaryocyte differentiation(GO:0045653) |
| 1.3 | 53.8 | GO:0051491 | positive regulation of filopodium assembly(GO:0051491) |
| 8.5 | 51.1 | GO:0021633 | optic nerve structural organization(GO:0021633) |
| 1.0 | 50.8 | GO:0000381 | regulation of alternative mRNA splicing, via spliceosome(GO:0000381) |
| 7.9 | 39.6 | GO:0009449 | gamma-aminobutyric acid biosynthetic process(GO:0009449) |
| 0.4 | 34.5 | GO:0006334 | nucleosome assembly(GO:0006334) |
| 0.5 | 27.8 | GO:0007157 | heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules(GO:0007157) |
| 1.3 | 26.3 | GO:0070831 | basement membrane assembly(GO:0070831) |
| 0.1 | 25.8 | GO:0019221 | cytokine-mediated signaling pathway(GO:0019221) |
| 1.7 | 21.5 | GO:0032808 | lacrimal gland development(GO:0032808) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 4.3 | 68.1 | GO:0044224 | juxtaparanode region of axon(GO:0044224) |
| 2.2 | 60.9 | GO:0000788 | nuclear nucleosome(GO:0000788) |
| 0.8 | 55.6 | GO:0000786 | nucleosome(GO:0000786) |
| 1.2 | 53.8 | GO:0044295 | axonal growth cone(GO:0044295) |
| 0.3 | 50.8 | GO:0043204 | perikaryon(GO:0043204) |
| 1.0 | 39.6 | GO:0060077 | inhibitory synapse(GO:0060077) |
| 0.2 | 27.8 | GO:0005913 | cell-cell adherens junction(GO:0005913) |
| 6.6 | 26.3 | GO:0005607 | laminin-2 complex(GO:0005607) |
| 3.3 | 16.7 | GO:0031315 | extrinsic component of mitochondrial outer membrane(GO:0031315) |
| 0.3 | 15.8 | GO:0005720 | nuclear heterochromatin(GO:0005720) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.3 | 66.3 | GO:0044822 | mRNA binding(GO:0003729) poly(A) RNA binding(GO:0044822) |
| 0.3 | 61.6 | GO:0042393 | histone binding(GO:0042393) |
| 0.1 | 55.1 | GO:0046982 | protein heterodimerization activity(GO:0046982) |
| 0.4 | 53.8 | GO:0005262 | calcium channel activity(GO:0005262) |
| 2.6 | 51.1 | GO:0015271 | outward rectifier potassium channel activity(GO:0015271) |
| 7.9 | 39.6 | GO:0004351 | glutamate decarboxylase activity(GO:0004351) |
| 0.3 | 37.7 | GO:0005200 | structural constituent of cytoskeleton(GO:0005200) |
| 0.1 | 26.3 | GO:0008201 | heparin binding(GO:0008201) |
| 0.2 | 25.6 | GO:0004896 | cytokine receptor activity(GO:0004896) |
| 3.0 | 21.3 | GO:0030160 | GKAP/Homer scaffold activity(GO:0030160) ankyrin repeat binding(GO:0071532) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 1.5 | 26.3 | PID INTEGRIN4 PATHWAY | Alpha6 beta4 integrin-ligand interactions |
| 0.2 | 15.8 | PID CASPASE PATHWAY | Caspase cascade in apoptosis |
| 0.1 | 14.4 | PID PDGFRB PATHWAY | PDGFR-beta signaling pathway |
| 0.2 | 11.4 | PID LKB1 PATHWAY | LKB1 signaling events |
| 0.2 | 7.8 | PID IL12 STAT4 PATHWAY | IL12 signaling mediated by STAT4 |
| 0.1 | 7.8 | NABA ECM AFFILIATED | Genes encoding proteins affiliated structurally or functionally to extracellular matrix proteins |
| 0.1 | 5.0 | PID BMP PATHWAY | BMP receptor signaling |
| 0.2 | 4.5 | PID HDAC CLASSIII PATHWAY | Signaling events mediated by HDAC Class III |
| 0.1 | 4.4 | PID RAC1 REG PATHWAY | Regulation of RAC1 activity |
| 0.1 | 3.8 | PID KIT PATHWAY | Signaling events mediated by Stem cell factor receptor (c-Kit) |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 2.0 | 52.1 | REACTOME PACKAGING OF TELOMERE ENDS | Genes involved in Packaging Of Telomere Ends |
| 1.0 | 51.1 | REACTOME VOLTAGE GATED POTASSIUM CHANNELS | Genes involved in Voltage gated Potassium channels |
| 1.5 | 39.6 | REACTOME GABA SYNTHESIS RELEASE REUPTAKE AND DEGRADATION | Genes involved in GABA synthesis, release, reuptake and degradation |
| 0.3 | 26.3 | REACTOME CELL JUNCTION ORGANIZATION | Genes involved in Cell junction organization |
| 0.3 | 15.8 | REACTOME APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS | Genes involved in Apoptotic cleavage of cellular proteins |
| 0.8 | 9.8 | REACTOME ANDROGEN BIOSYNTHESIS | Genes involved in Androgen biosynthesis |
| 0.4 | 7.8 | REACTOME OTHER SEMAPHORIN INTERACTIONS | Genes involved in Other semaphorin interactions |
| 0.3 | 7.8 | REACTOME DARPP 32 EVENTS | Genes involved in DARPP-32 events |
| 0.3 | 6.8 | REACTOME CLASS C 3 METABOTROPIC GLUTAMATE PHEROMONE RECEPTORS | Genes involved in Class C/3 (Metabotropic glutamate/pheromone receptors) |
| 0.2 | 5.0 | REACTOME DOWNREGULATION OF TGF BETA RECEPTOR SIGNALING | Genes involved in Downregulation of TGF-beta receptor signaling |