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GSE53960: rat RNA-Seq transcriptomic Bodymap

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Results for Hoxa3

Z-value: 0.30

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Transcription factors associated with Hoxa3

Gene Symbol Gene ID Gene Info
Hoxa3
ENSRNOG00000006281 homeobox A3

Activity-expression correlation:

GenePromoterPearson corr. coef.P-valuePlot
Hoxa3rn6_v1_chr4_-_82141385_821413850.132.4e-02Click!

Activity profile of Hoxa3 motif

Sorted Z-values of Hoxa3 motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
chr4_-_170740274 10.32 ENSRNOT00000012212
Gucy2c
guanylate cyclase 2C
chr9_-_119190698 7.89 ENSRNOT00000021534
Tgif1
TGFB-induced factor homeobox 1
chr16_+_2634603 7.03 ENSRNOT00000019113
Hesx1
HESX homeobox 1
chr17_-_84247038 6.45 ENSRNOT00000068553
Nebl
nebulette
chr8_+_22648323 5.77 ENSRNOT00000013165
Smarca4
SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4
chr12_-_45801842 5.76 ENSRNOT00000078837
AABR07036513.1

chr1_-_101095594 5.63 ENSRNOT00000027944
Fcgrt
Fc fragment of IgG receptor and transporter
chr3_-_165537940 5.07 ENSRNOT00000071119
ENSRNOT00000070964
Sall4
spalt-like transcription factor 4
chr7_-_73130740 4.58 ENSRNOT00000075584
9430069I07Rik
RIKEN cDNA 9430069I07 gene
chr12_-_47142852 3.97 ENSRNOT00000001591
Pop5
POP5 homolog, ribonuclease P/MRP subunit
chr2_+_266315036 3.74 ENSRNOT00000055245
Wls
wntless Wnt ligand secretion mediator
chr10_+_61685645 3.64 ENSRNOT00000003933
Mnt
MAX network transcriptional repressor
chr7_-_143016040 3.59 ENSRNOT00000029697
Krt80
keratin 80
chr3_-_90751055 3.45 ENSRNOT00000040741
LOC499843
LRRGT00091
chr20_+_45458558 2.80 ENSRNOT00000000713
Cdk19
cyclin-dependent kinase 19
chr20_+_42966140 2.51 ENSRNOT00000000707
Marcks
myristoylated alanine rich protein kinase C substrate
chr10_-_87468711 2.27 ENSRNOT00000039983
Krtap3-3
keratin associated protein 3-3
chr5_-_102743417 2.27 ENSRNOT00000067389
Bnc2
basonuclin 2
chr7_-_126382449 2.18 ENSRNOT00000085540
7530416G11Rik
RIKEN cDNA 7530416G11 gene
chr6_+_80108655 2.12 ENSRNOT00000006137
Gemin2
gem (nuclear organelle) associated protein 2
chr4_+_147832136 1.96 ENSRNOT00000064603
Rho
rhodopsin
chr4_-_88684415 1.80 ENSRNOT00000009001
LOC500148
similar to 40S ribosomal protein S7 (S8)
chr14_+_23405717 1.72 ENSRNOT00000029805
Tmprss11c
transmembrane protease, serine 11C
chr1_-_220938814 1.57 ENSRNOT00000028081
Ovol1
ovo like transcriptional repressor 1
chr6_-_108660063 1.43 ENSRNOT00000006240
Arel1
apoptosis resistant E3 ubiquitin protein ligase 1
chr2_-_158133861 1.17 ENSRNOT00000090700
Veph1
ventricular zone expressed PH domain-containing 1
chr1_-_276228574 1.08 ENSRNOT00000021746
Gucy2g
guanylate cyclase 2G
chr2_-_185852759 0.69 ENSRNOT00000049461
Mab21l2
mab-21 like 2
chr10_-_88000423 0.63 ENSRNOT00000076787
ENSRNOT00000046751
ENSRNOT00000091394
Krt32
keratin 32
chr3_-_104018861 0.52 ENSRNOT00000008387
Chrm5
cholinergic receptor, muscarinic 5
chr1_+_167758636 0.39 ENSRNOT00000024957
Olr46
olfactory receptor 46
chr2_-_33025271 0.37 ENSRNOT00000074941
NEWGENE_1310139
microtubule associated serine/threonine kinase family member 4
chr2_-_170301348 0.33 ENSRNOT00000088131
Si
sucrase-isomaltase
chr11_-_32550539 0.29 ENSRNOT00000002715
Rcan1
regulator of calcineurin 1
chr18_+_16544508 0.23 ENSRNOT00000020601
Elp2
elongator acetyltransferase complex subunit 2

Network of associatons between targets according to the STRING database.

First level regulatory network of Hoxa3

PNG image of the network

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Gene Ontology Analysis

Gene overrepresentation in biological process category:

Log-likelihood per target  Total log-likelihood Term Description
2.1 6.4 GO:0071691 cardiac muscle thin filament assembly(GO:0071691)
1.9 5.8 GO:1902659 regulation of glucose mediated signaling pathway(GO:1902659)
1.2 3.7 GO:0061357 positive regulation of Wnt protein secretion(GO:0061357)
1.0 7.0 GO:0030916 otic vesicle formation(GO:0030916)
0.9 7.9 GO:0048387 negative regulation of retinoic acid receptor signaling pathway(GO:0048387)
0.4 5.6 GO:0038094 Fc-gamma receptor signaling pathway(GO:0038094)
0.4 2.5 GO:0031584 activation of phospholipase D activity(GO:0031584) regulation of protein kinase C activity(GO:1900019) positive regulation of protein kinase C activity(GO:1900020)
0.3 1.6 GO:1901994 negative regulation of meiotic cell cycle phase transition(GO:1901994)
0.3 5.1 GO:0001833 inner cell mass cell proliferation(GO:0001833)
0.2 2.0 GO:0016056 rhodopsin mediated signaling pathway(GO:0016056)
0.2 11.4 GO:0006182 cGMP biosynthetic process(GO:0006182)
0.2 1.7 GO:0097264 self proteolysis(GO:0097264)
0.1 0.5 GO:0007197 adenylate cyclase-inhibiting G-protein coupled acetylcholine receptor signaling pathway(GO:0007197) phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway(GO:0007207)
0.1 2.3 GO:0003416 endochondral bone growth(GO:0003416)
0.1 2.1 GO:0000387 spliceosomal snRNP assembly(GO:0000387)
0.1 4.0 GO:0090502 RNA phosphodiester bond hydrolysis, endonucleolytic(GO:0090502)
0.0 3.4 GO:0006334 nucleosome assembly(GO:0006334)
0.0 3.6 GO:0007569 cell aging(GO:0007569)
0.0 0.7 GO:0010172 embryonic body morphogenesis(GO:0010172)
0.0 0.3 GO:0034285 response to sucrose(GO:0009744) response to disaccharide(GO:0034285)
0.0 2.8 GO:0050729 positive regulation of inflammatory response(GO:0050729)
0.0 0.3 GO:0007614 short-term memory(GO:0007614)
0.0 0.2 GO:0043248 proteasome assembly(GO:0043248)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
1.0 5.8 GO:0005726 perichromatin fibrils(GO:0005726)
0.7 4.0 GO:0005655 nucleolar ribonuclease P complex(GO:0005655) ribonuclease P complex(GO:0030677) multimeric ribonuclease P complex(GO:0030681)
0.6 2.5 GO:0042585 germinal vesicle(GO:0042585) dendritic branch(GO:0044307)
0.5 11.4 GO:0008074 guanylate cyclase complex, soluble(GO:0008074)
0.3 2.1 GO:0097504 Gemini of coiled bodies(GO:0097504)
0.2 3.6 GO:0030057 desmosome(GO:0030057)
0.1 2.0 GO:0042622 photoreceptor outer segment membrane(GO:0042622)
0.1 3.7 GO:0032839 dendrite cytoplasm(GO:0032839)
0.1 6.4 GO:0001725 stress fiber(GO:0001725) contractile actin filament bundle(GO:0097517)
0.1 2.8 GO:0016592 mediator complex(GO:0016592)
0.0 5.1 GO:0000792 heterochromatin(GO:0000792)
0.0 0.2 GO:0033588 Elongator holoenzyme complex(GO:0033588)
0.0 2.3 GO:0045095 keratin filament(GO:0045095)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
1.1 5.6 GO:0019770 IgG receptor activity(GO:0019770)
0.7 5.8 GO:0001163 RNA polymerase I regulatory region sequence-specific DNA binding(GO:0001163) RNA polymerase I CORE element sequence-specific DNA binding(GO:0001164)
0.5 10.3 GO:0015643 toxic substance binding(GO:0015643)
0.5 3.7 GO:0031852 mu-type opioid receptor binding(GO:0031852)
0.5 7.9 GO:0070410 co-SMAD binding(GO:0070410)
0.4 4.0 GO:0004526 ribonuclease P activity(GO:0004526)
0.4 6.4 GO:0005523 tropomyosin binding(GO:0005523)
0.2 2.0 GO:0009881 photoreceptor activity(GO:0009881)
0.1 0.3 GO:0004574 oligo-1,6-glucosidase activity(GO:0004574)
0.1 0.5 GO:0016907 G-protein coupled acetylcholine receptor activity(GO:0016907)
0.1 2.8 GO:0004693 cyclin-dependent protein serine/threonine kinase activity(GO:0004693)
0.1 0.3 GO:0008597 calcium-dependent protein serine/threonine phosphatase regulator activity(GO:0008597)
0.1 8.6 GO:0001078 transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding(GO:0001078)
0.0 3.6 GO:0001227 transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding(GO:0001227)
0.0 1.1 GO:0004383 guanylate cyclase activity(GO:0004383)
0.0 2.5 GO:0001786 phosphatidylserine binding(GO:0001786)
0.0 0.2 GO:0061133 endopeptidase activator activity(GO:0061133)
0.0 8.3 GO:0005198 structural molecule activity(GO:0005198)

Gene overrepresentation in curated gene sets: canonical pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.3 5.8 PID ERB GENOMIC PATHWAY Validated nuclear estrogen receptor beta network
0.1 7.9 PID AR PATHWAY Coregulation of Androgen receptor activity
0.1 2.0 PID RHODOPSIN PATHWAY Visual signal transduction: Rods
0.1 5.1 PID BETA CATENIN NUC PATHWAY Regulation of nuclear beta catenin signaling and target gene transcription
0.0 0.2 ST INTERFERON GAMMA PATHWAY Interferon gamma pathway.

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.3 7.9 REACTOME DOWNREGULATION OF SMAD2 3 SMAD4 TRANSCRIPTIONAL ACTIVITY Genes involved in Downregulation of SMAD2/3:SMAD4 transcriptional activity
0.3 2.5 REACTOME REGULATION OF INSULIN SECRETION BY ACETYLCHOLINE Genes involved in Regulation of Insulin Secretion by Acetylcholine
0.2 2.0 REACTOME OPSINS Genes involved in Opsins
0.1 0.3 REACTOME DIGESTION OF DIETARY CARBOHYDRATE Genes involved in Digestion of dietary carbohydrate
0.0 2.1 REACTOME METABOLISM OF NON CODING RNA Genes involved in Metabolism of non-coding RNA
0.0 2.8 REACTOME TRANSCRIPTIONAL REGULATION OF WHITE ADIPOCYTE DIFFERENTIATION Genes involved in Transcriptional Regulation of White Adipocyte Differentiation
0.0 0.5 REACTOME AMINE LIGAND BINDING RECEPTORS Genes involved in Amine ligand-binding receptors