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PRJNA438478: RNAseq of wild type zebrafish germline
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Results for gcm2
Z-value: 0.60
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Transcription factors associated with gcm2
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| gcm2 | dr11_v1_chr24_-_8831866_8831912 | 0.79 | 1.1e-04 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| chr25_+_1732838 Show fit | 1.52 |
ENSDART00000159555
ENSDART00000168161 |
fibulin 1 |
|
| chr15_-_20939579 Show fit | 1.47 |
ENSDART00000152371
|
ubiquitin specific peptidase 2a |
|
| chr5_-_34185115 Show fit | 1.29 |
ENSDART00000192771
|
fibrinogen C domain containing 1 |
|
| chr2_-_32505091 Show fit | 1.24 |
ENSDART00000141884
ENSDART00000056639 |
Fas apoptotic inhibitory molecule 2a |
|
| chr3_-_57425961 Show fit | 1.24 |
ENSDART00000033716
|
suppressor of cytokine signaling 3a |
|
| chr21_-_43117327 Show fit | 1.20 |
ENSDART00000122352
|
procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide 2 |
|
| chr16_+_41517188 Show fit | 1.07 |
ENSDART00000049976
|
si:dkey-11p23.7 |
|
| chr20_+_30725778 Show fit | 1.02 |
ENSDART00000062532
|
NHS-like 1b |
|
| chr21_-_3452683 Show fit | 1.01 |
ENSDART00000009740
|
SMAD family member 7 |
|
| chr1_-_20928772 Show fit | 1.00 |
ENSDART00000078277
|
methylsterol monooxygenase 1 |
Network of associatons between targets according to the STRING database.
First level regulatory network of gcm2
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.2 | 1.2 | GO:0048681 | negative regulation of axon regeneration(GO:0048681) negative regulation of neuron projection regeneration(GO:0070571) |
| 0.1 | 1.2 | GO:0019471 | peptidyl-proline hydroxylation to 4-hydroxy-L-proline(GO:0018401) 4-hydroxyproline metabolic process(GO:0019471) |
| 0.2 | 1.1 | GO:0045124 | regulation of bone resorption(GO:0045124) |
| 0.1 | 1.1 | GO:0030878 | thyroid gland development(GO:0030878) |
| 0.1 | 1.0 | GO:0097475 | motor neuron migration(GO:0097475) |
| 0.0 | 1.0 | GO:0016126 | sterol biosynthetic process(GO:0016126) |
| 0.0 | 1.0 | GO:0050773 | regulation of dendrite development(GO:0050773) |
| 0.0 | 1.0 | GO:0060395 | SMAD protein signal transduction(GO:0060395) |
| 0.0 | 1.0 | GO:0016573 | histone acetylation(GO:0016573) |
| 0.3 | 0.9 | GO:0072344 | rescue of stalled ribosome(GO:0072344) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 1.3 | GO:0005788 | endoplasmic reticulum lumen(GO:0005788) |
| 0.0 | 1.2 | GO:0005942 | phosphatidylinositol 3-kinase complex(GO:0005942) |
| 0.1 | 1.0 | GO:0071144 | SMAD2-SMAD3 protein complex(GO:0071144) |
| 0.0 | 1.0 | GO:0000123 | histone acetyltransferase complex(GO:0000123) |
| 0.0 | 0.9 | GO:0001518 | voltage-gated sodium channel complex(GO:0001518) sodium channel complex(GO:0034706) |
| 0.1 | 0.7 | GO:0061617 | MICOS complex(GO:0061617) |
| 0.1 | 0.7 | GO:0045009 | melanosome membrane(GO:0033162) chitosome(GO:0045009) |
| 0.0 | 0.6 | GO:0043195 | terminal bouton(GO:0043195) |
| 0.0 | 0.6 | GO:0032040 | small-subunit processome(GO:0032040) |
| 0.0 | 0.6 | GO:0000421 | autophagosome membrane(GO:0000421) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 1.2 | GO:0004656 | procollagen-proline 4-dioxygenase activity(GO:0004656) |
| 0.0 | 1.2 | GO:0046935 | 1-phosphatidylinositol-3-kinase regulator activity(GO:0046935) |
| 0.0 | 1.1 | GO:0005112 | Notch binding(GO:0005112) |
| 0.1 | 1.0 | GO:0000254 | C-4 methylsterol oxidase activity(GO:0000254) |
| 0.1 | 1.0 | GO:0070411 | I-SMAD binding(GO:0070411) |
| 0.0 | 1.0 | GO:0004402 | histone acetyltransferase activity(GO:0004402) |
| 0.1 | 0.9 | GO:0008332 | low voltage-gated calcium channel activity(GO:0008332) |
| 0.1 | 0.9 | GO:0004459 | L-lactate dehydrogenase activity(GO:0004459) |
| 0.0 | 0.9 | GO:0004181 | metallocarboxypeptidase activity(GO:0004181) |
| 0.0 | 0.9 | GO:0004869 | cysteine-type endopeptidase inhibitor activity(GO:0004869) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 2.2 | NABA ECM REGULATORS | Genes encoding enzymes and their regulators involved in the remodeling of the extracellular matrix |
| 0.0 | 1.8 | NABA ECM GLYCOPROTEINS | Genes encoding structural ECM glycoproteins |
| 0.0 | 1.2 | PID ALK1 PATHWAY | ALK1 signaling events |
| 0.0 | 0.5 | PID WNT SIGNALING PATHWAY | Wnt signaling network |
| 0.0 | 0.5 | PID NCADHERIN PATHWAY | N-cadherin signaling events |
| 0.0 | 0.4 | SA CASPASE CASCADE | Apoptosis is mediated by caspases, cysteine proteases arranged in a proteolytic cascade. |
| 0.0 | 0.4 | PID ARF6 TRAFFICKING PATHWAY | Arf6 trafficking events |
| 0.0 | 0.3 | PID HEDGEHOG 2PATHWAY | Signaling events mediated by the Hedgehog family |
| 0.0 | 0.2 | PID LPA4 PATHWAY | LPA4-mediated signaling events |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 1.0 | REACTOME SIGNALING BY BMP | Genes involved in Signaling by BMP |
| 0.0 | 1.0 | REACTOME CHOLESTEROL BIOSYNTHESIS | Genes involved in Cholesterol biosynthesis |
| 0.0 | 0.9 | REACTOME MHC CLASS II ANTIGEN PRESENTATION | Genes involved in MHC class II antigen presentation |
| 0.0 | 0.5 | REACTOME ADHERENS JUNCTIONS INTERACTIONS | Genes involved in Adherens junctions interactions |
| 0.0 | 0.4 | REACTOME DOWNREGULATION OF SMAD2 3 SMAD4 TRANSCRIPTIONAL ACTIVITY | Genes involved in Downregulation of SMAD2/3:SMAD4 transcriptional activity |
| 0.0 | 0.4 | REACTOME INSULIN SYNTHESIS AND PROCESSING | Genes involved in Insulin Synthesis and Processing |
| 0.0 | 0.4 | REACTOME PTM GAMMA CARBOXYLATION HYPUSINE FORMATION AND ARYLSULFATASE ACTIVATION | Genes involved in PTM: gamma carboxylation, hypusine formation and arylsulfatase activation |
| 0.0 | 0.3 | REACTOME IONOTROPIC ACTIVITY OF KAINATE RECEPTORS | Genes involved in Ionotropic activity of Kainate Receptors |
| 0.0 | 0.2 | REACTOME RECRUITMENT OF NUMA TO MITOTIC CENTROSOMES | Genes involved in Recruitment of NuMA to mitotic centrosomes |
| 0.0 | 0.2 | REACTOME ADENYLATE CYCLASE ACTIVATING PATHWAY | Genes involved in Adenylate cyclase activating pathway |