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GSE53960: rat RNA-Seq transcriptomic Bodymap
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Results for Rad21_Smc3
Z-value: 1.83
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Transcription factors associated with Rad21_Smc3
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| Rad21 | rn6_v1_chr7_-_91538673_91538673 | 0.29 | 7.7e-08 | Click! |
| Smc3 | rn6_v1_chr1_+_274309758_274309758 | 0.29 | 1.3e-07 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| chr15_+_32244416 Show fit | 74.36 |
ENSRNOT00000012019
ENSRNOT00000060254 |
|
|
| chr6_-_138662365 Show fit | 70.04 |
ENSRNOT00000066209
ENSRNOT00000084892 |
immunoglobulin heavy constant mu |
|
| chr1_+_82480195 Show fit | 68.99 |
ENSRNOT00000028051
|
transforming growth factor, beta 1 |
|
| chr15_+_57241968 Show fit | 65.57 |
ENSRNOT00000082191
|
lymphocyte cytosolic protein 1 |
|
| chr15_+_31948035 Show fit | 62.57 |
ENSRNOT00000071627
|
|
|
| chr13_+_51958834 Show fit | 58.92 |
ENSRNOT00000007833
|
protein tyrosine phosphatase, non-receptor type 7 |
|
| chr6_-_139041654 Show fit | 57.00 |
ENSRNOT00000075664
|
|
|
| chr6_-_138900915 Show fit | 56.93 |
ENSRNOT00000075363
|
|
|
| chr15_+_30270740 Show fit | 55.37 |
ENSRNOT00000070991
|
|
|
| chr15_+_31950986 Show fit | 54.10 |
ENSRNOT00000080233
|
|
Network of associatons between targets according to the STRING database.
First level regulatory network of Rad21_Smc3
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.7 | 82.1 | GO:0035335 | peptidyl-tyrosine dephosphorylation(GO:0035335) |
| 23.0 | 69.0 | GO:1900126 | negative regulation of hyaluronan biosynthetic process(GO:1900126) |
| 5.5 | 65.6 | GO:0051639 | actin filament network formation(GO:0051639) |
| 10.8 | 54.1 | GO:0002483 | antigen processing and presentation of endogenous peptide antigen(GO:0002483) antigen processing and presentation of endogenous peptide antigen via MHC class I(GO:0019885) |
| 17.2 | 51.5 | GO:0046967 | antigen processing and presentation of exogenous peptide antigen via MHC class Ib(GO:0002477) antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent(GO:0002481) antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway(GO:0002488) antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent(GO:0002489) positive regulation of antigen processing and presentation of peptide antigen(GO:0002585) regulation of antigen processing and presentation of peptide antigen via MHC class I(GO:0002589) cytosol to ER transport(GO:0046967) peptide antigen transport(GO:0046968) |
| 1.3 | 49.4 | GO:0035458 | cellular response to interferon-beta(GO:0035458) |
| 9.4 | 47.2 | GO:0060741 | prostate gland stromal morphogenesis(GO:0060741) |
| 0.8 | 45.0 | GO:0002181 | cytoplasmic translation(GO:0002181) |
| 2.6 | 44.5 | GO:0002504 | antigen processing and presentation of peptide or polysaccharide antigen via MHC class II(GO:0002504) |
| 7.1 | 42.3 | GO:0042997 | negative regulation of low-density lipoprotein particle clearance(GO:0010989) negative regulation of Golgi to plasma membrane protein transport(GO:0042997) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 15.1 | 105.6 | GO:0042825 | TAP complex(GO:0042825) |
| 0.2 | 88.1 | GO:0000785 | chromatin(GO:0000785) |
| 0.9 | 84.0 | GO:0022625 | cytosolic large ribosomal subunit(GO:0022625) |
| 0.7 | 74.4 | GO:0005902 | microvillus(GO:0005902) |
| 4.6 | 74.1 | GO:0042613 | MHC class II protein complex(GO:0042613) |
| 1.9 | 54.1 | GO:0001891 | phagocytic cup(GO:0001891) |
| 0.7 | 49.2 | GO:0022627 | cytosolic small ribosomal subunit(GO:0022627) |
| 0.2 | 47.3 | GO:0005681 | spliceosomal complex(GO:0005681) |
| 0.3 | 47.1 | GO:0005840 | ribosome(GO:0005840) |
| 0.1 | 43.0 | GO:0005730 | nucleolus(GO:0005730) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.6 | 149.6 | GO:0003735 | structural constituent of ribosome(GO:0003735) |
| 21.1 | 105.6 | GO:0015440 | peptide-transporting ATPase activity(GO:0015440) |
| 0.4 | 69.9 | GO:0051015 | actin filament binding(GO:0051015) |
| 13.8 | 69.0 | GO:0034714 | type III transforming growth factor beta receptor binding(GO:0034714) |
| 1.8 | 56.7 | GO:0070064 | proline-rich region binding(GO:0070064) |
| 3.1 | 53.2 | GO:0036312 | phosphatidylinositol 3-kinase regulatory subunit binding(GO:0036312) |
| 4.7 | 47.2 | GO:0003680 | AT DNA binding(GO:0003680) |
| 2.1 | 44.9 | GO:0023026 | MHC class II protein complex binding(GO:0023026) |
| 7.1 | 42.6 | GO:0004726 | non-membrane spanning protein tyrosine phosphatase activity(GO:0004726) |
| 1.3 | 39.9 | GO:0004129 | cytochrome-c oxidase activity(GO:0004129) heme-copper terminal oxidase activity(GO:0015002) oxidoreductase activity, acting on a heme group of donors, oxygen as acceptor(GO:0016676) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 2.2 | 127.1 | PID CD8 TCR PATHWAY | TCR signaling in naïve CD8+ T cells |
| 3.8 | 69.0 | SA MMP CYTOKINE CONNECTION | Cytokines can induce activation of matrix metalloproteinases, which degrade extracellular matrix. |
| 1.6 | 64.7 | SIG PIP3 SIGNALING IN B LYMPHOCYTES | Genes related to PIP3 signaling in B lymphocytes |
| 3.5 | 56.3 | PID TCR RAS PATHWAY | Ras signaling in the CD4+ TCR pathway |
| 0.9 | 48.7 | PID ILK PATHWAY | Integrin-linked kinase signaling |
| 0.7 | 38.4 | PID P53 REGULATION PATHWAY | p53 pathway |
| 0.4 | 31.2 | PID MYC ACTIV PATHWAY | Validated targets of C-MYC transcriptional activation |
| 1.4 | 29.8 | ST WNT CA2 CYCLIC GMP PATHWAY | Wnt/Ca2+/cyclic GMP signaling. |
| 0.8 | 26.6 | PID BARD1 PATHWAY | BARD1 signaling events |
| 0.1 | 26.1 | NABA SECRETED FACTORS | Genes encoding secreted soluble factors |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 1.6 | 158.0 | REACTOME PEPTIDE CHAIN ELONGATION | Genes involved in Peptide chain elongation |
| 3.4 | 60.4 | REACTOME ANTIGEN PRESENTATION FOLDING ASSEMBLY AND PEPTIDE LOADING OF CLASS I MHC | Genes involved in Antigen Presentation: Folding, assembly and peptide loading of class I MHC |
| 3.0 | 56.1 | REACTOME TGF BETA RECEPTOR SIGNALING IN EMT EPITHELIAL TO MESENCHYMAL TRANSITION | Genes involved in TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) |
| 0.9 | 47.7 | REACTOME INTERFERON GAMMA SIGNALING | Genes involved in Interferon gamma signaling |
| 3.8 | 42.3 | REACTOME PHOSPHORYLATION OF CD3 AND TCR ZETA CHAINS | Genes involved in Phosphorylation of CD3 and TCR zeta chains |
| 3.0 | 38.4 | REACTOME IL 6 SIGNALING | Genes involved in Interleukin-6 signaling |
| 1.2 | 37.1 | REACTOME GPVI MEDIATED ACTIVATION CASCADE | Genes involved in GPVI-mediated activation cascade |
| 1.4 | 36.9 | REACTOME ACTIVATION OF THE PRE REPLICATIVE COMPLEX | Genes involved in Activation of the pre-replicative complex |
| 0.6 | 34.3 | REACTOME METABOLISM OF NON CODING RNA | Genes involved in Metabolism of non-coding RNA |
| 0.4 | 28.0 | REACTOME LATE PHASE OF HIV LIFE CYCLE | Genes involved in Late Phase of HIV Life Cycle |