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GSE49485: Hypoxia transcriptome sequencing of rat brain.
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Results for Chd1_Pml
Z-value: 3.78
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Transcription factors associated with Chd1_Pml
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| Pml | rn6_v1_chr8_-_63034226_63034226 | 0.88 | 4.8e-02 | Click! |
| Chd1 | rn6_v1_chr1_+_57692836_57692983 | 0.80 | 1.1e-01 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| chr9_+_49479023 Show fit | 5.47 |
ENSRNOT00000050922
ENSRNOT00000077111 |
POU class 3 homeobox 3 |
|
| chr7_+_70364813 Show fit | 4.49 |
ENSRNOT00000084012
ENSRNOT00000031230 |
ArfGAP with GTPase domain, ankyrin repeat and PH domain 2 |
|
| chr7_+_130474279 Show fit | 4.46 |
ENSRNOT00000092388
|
SH3 and multiple ankyrin repeat domains 3 |
|
| chr7_+_130474508 Show fit | 4.22 |
ENSRNOT00000085191
|
SH3 and multiple ankyrin repeat domains 3 |
|
| chr19_-_19832812 Show fit | 4.01 |
ENSRNOT00000084657
|
poly(A) RNA polymerase D5, non-canonical |
|
| chr3_+_147585947 Show fit | 3.68 |
ENSRNOT00000006833
|
scratch family transcriptional repressor 2 |
|
| chr14_-_78902063 Show fit | 3.63 |
ENSRNOT00000088469
|
protein phosphatase 2, regulatory subunit B, gamma |
|
| chr15_+_51756978 Show fit | 3.45 |
ENSRNOT00000024067
|
early growth response 3 |
|
| chr8_+_114866768 Show fit | 3.34 |
ENSRNOT00000076731
|
WD repeat domain 82 |
|
| chr3_-_164095878 Show fit | 3.13 |
ENSRNOT00000079414
|
beta-1,4-galactosyltransferase 5 |
Network of associatons between targets according to the STRING database.
First level regulatory network of Chd1_Pml
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 2.5 | 12.6 | GO:1904717 | regulation of AMPA glutamate receptor clustering(GO:1904717) |
| 1.5 | 6.1 | GO:0072218 | ascending thin limb development(GO:0072021) metanephric ascending thin limb development(GO:0072218) |
| 0.3 | 5.1 | GO:0080182 | histone H3-K4 trimethylation(GO:0080182) |
| 0.6 | 4.9 | GO:0060024 | rhythmic synaptic transmission(GO:0060024) |
| 0.3 | 4.7 | GO:0071044 | histone mRNA catabolic process(GO:0071044) |
| 0.2 | 4.7 | GO:0000301 | retrograde transport, vesicle recycling within Golgi(GO:0000301) |
| 0.4 | 4.4 | GO:0033601 | positive regulation of mammary gland epithelial cell proliferation(GO:0033601) |
| 0.1 | 4.2 | GO:0006182 | cGMP biosynthetic process(GO:0006182) |
| 0.1 | 4.1 | GO:2000300 | regulation of synaptic vesicle exocytosis(GO:2000300) |
| 0.3 | 3.6 | GO:0045586 | regulation of gamma-delta T cell differentiation(GO:0045586) regulation of gamma-delta T cell activation(GO:0046643) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.2 | 13.3 | GO:0060170 | ciliary membrane(GO:0060170) |
| 0.1 | 6.9 | GO:0017053 | transcriptional repressor complex(GO:0017053) |
| 0.0 | 6.4 | GO:0005578 | proteinaceous extracellular matrix(GO:0005578) |
| 0.0 | 6.1 | GO:0030027 | lamellipodium(GO:0030027) |
| 0.3 | 5.6 | GO:0048188 | Set1C/COMPASS complex(GO:0048188) |
| 0.1 | 5.0 | GO:0032590 | dendrite membrane(GO:0032590) |
| 0.0 | 4.9 | GO:0005802 | trans-Golgi network(GO:0005802) |
| 0.3 | 4.2 | GO:0031588 | nucleotide-activated protein kinase complex(GO:0031588) |
| 0.1 | 4.0 | GO:0060077 | inhibitory synapse(GO:0060077) |
| 0.2 | 3.9 | GO:0008074 | guanylate cyclase complex, soluble(GO:0008074) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 2.1 | 14.4 | GO:0030160 | GKAP/Homer scaffold activity(GO:0030160) |
| 0.0 | 8.8 | GO:0005096 | GTPase activator activity(GO:0005096) |
| 0.1 | 7.6 | GO:0005089 | Rho guanyl-nucleotide exchange factor activity(GO:0005089) |
| 0.1 | 7.3 | GO:0005546 | phosphatidylinositol-4,5-bisphosphate binding(GO:0005546) |
| 0.0 | 6.9 | GO:0061659 | ubiquitin protein ligase activity(GO:0061630) ubiquitin-like protein ligase activity(GO:0061659) |
| 0.3 | 6.8 | GO:0042800 | histone methyltransferase activity (H3-K4 specific)(GO:0042800) |
| 0.2 | 6.6 | GO:0046875 | ephrin receptor binding(GO:0046875) |
| 0.1 | 6.5 | GO:0017124 | SH3 domain binding(GO:0017124) |
| 0.2 | 6.0 | GO:0008139 | nuclear localization sequence binding(GO:0008139) |
| 0.2 | 5.4 | GO:0017091 | AU-rich element binding(GO:0017091) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.3 | 16.8 | PID RET PATHWAY | Signaling events regulated by Ret tyrosine kinase |
| 0.2 | 6.7 | ST DIFFERENTIATION PATHWAY IN PC12 CELLS | Differentiation Pathway in PC12 Cells; this is a specific case of PAC1 Receptor Pathway. |
| 0.2 | 6.4 | PID NETRIN PATHWAY | Netrin-mediated signaling events |
| 0.1 | 5.7 | PID KIT PATHWAY | Signaling events mediated by Stem cell factor receptor (c-Kit) |
| 0.0 | 4.4 | NABA ECM AFFILIATED | Genes encoding proteins affiliated structurally or functionally to extracellular matrix proteins |
| 0.2 | 4.0 | PID S1P S1P2 PATHWAY | S1P2 pathway |
| 0.1 | 4.0 | PID BMP PATHWAY | BMP receptor signaling |
| 0.1 | 3.8 | NABA COLLAGENS | Genes encoding collagen proteins |
| 0.2 | 3.6 | PID LPA4 PATHWAY | LPA4-mediated signaling events |
| 0.1 | 3.3 | PID CD8 TCR DOWNSTREAM PATHWAY | Downstream signaling in naïve CD8+ T cells |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.2 | 8.4 | REACTOME SYNTHESIS OF PIPS AT THE PLASMA MEMBRANE | Genes involved in Synthesis of PIPs at the plasma membrane |
| 0.3 | 5.8 | REACTOME ADENYLATE CYCLASE INHIBITORY PATHWAY | Genes involved in Adenylate cyclase inhibitory pathway |
| 0.1 | 5.3 | REACTOME NRAGE SIGNALS DEATH THROUGH JNK | Genes involved in NRAGE signals death through JNK |
| 0.2 | 5.2 | REACTOME GABA SYNTHESIS RELEASE REUPTAKE AND DEGRADATION | Genes involved in GABA synthesis, release, reuptake and degradation |
| 0.2 | 4.8 | REACTOME DOWNREGULATION OF SMAD2 3 SMAD4 TRANSCRIPTIONAL ACTIVITY | Genes involved in Downregulation of SMAD2/3:SMAD4 transcriptional activity |
| 0.1 | 4.5 | REACTOME NCAM1 INTERACTIONS | Genes involved in NCAM1 interactions |
| 0.2 | 4.3 | REACTOME CRMPS IN SEMA3A SIGNALING | Genes involved in CRMPs in Sema3A signaling |
| 0.2 | 4.0 | REACTOME OTHER SEMAPHORIN INTERACTIONS | Genes involved in Other semaphorin interactions |
| 0.2 | 3.9 | REACTOME SIGNALING BY HIPPO | Genes involved in Signaling by Hippo |
| 0.1 | 3.9 | REACTOME MYOGENESIS | Genes involved in Myogenesis |