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GSE53960: rat RNA-Seq transcriptomic Bodymap

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Results for Gcm1

Z-value: 0.82

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Transcription factors associated with Gcm1

Gene Symbol Gene ID Gene Info
ENSRNOG00000007932 glial cells missing homolog 1

Activity-expression correlation:

GenePromoterPearson corr. coef.P-valuePlot
Gcm1rn6_v1_chr8_+_85355766_85355766-0.172.7e-03Click!

Activity profile of Gcm1 motif

Sorted Z-values of Gcm1 motif

Promoter Log-likelihood Transcript Gene Gene Info
chr3_-_16537433 28.14 ENSRNOT00000048523

chr11_+_85508300 26.59 ENSRNOT00000038646

chr4_-_103369224 26.24 ENSRNOT00000075709

chr11_+_85532526 26.01 ENSRNOT00000036565

chr17_-_31813716 24.70 ENSRNOT00000074147

chr11_+_85561460 23.13 ENSRNOT00000075455

chr11_+_85618714 22.95 ENSRNOT00000074614

chr3_+_19141133 20.40 ENSRNOT00000058323

chr14_-_78377825 19.26 ENSRNOT00000068104

chr3_+_19128400 16.35 ENSRNOT00000074272

chr14_-_20953095 15.57 ENSRNOT00000004440
deoxycytidine kinase
chr14_-_3389943 14.71 ENSRNOT00000037101
epoxide hydrolase 4
chr5_+_154522119 12.66 ENSRNOT00000072618
E2F transcription factor 2
chr11_+_85633243 12.08 ENSRNOT00000045807
Ig lambda chain V-VI region AR-like
chr16_+_81616604 11.77 ENSRNOT00000026392
ENSRNOT00000057740
ADP-ribosylhydrolase like 1
growth hormone regulated TBC protein 1
chr1_+_221773254 11.16 ENSRNOT00000028646
RAS guanyl releasing protein 2
chr3_+_19174027 10.64 ENSRNOT00000074445

chr3_+_33440191 9.81 ENSRNOT00000034632
ENSRNOT00000092907
methyl-CpG binding domain protein 5
chr5_-_75676584 9.51 ENSRNOT00000044348
lysophosphatidic acid receptor 1
chr7_-_115910522 9.39 ENSRNOT00000076998
ENSRNOT00000067442
activity-regulated cytoskeleton-associated protein
chr7_-_12346475 9.12 ENSRNOT00000060708
melanoma associated antigen (mutated) 1
chr10_+_105861743 8.76 ENSRNOT00000064410
mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isozyme B
chr1_-_259674425 8.53 ENSRNOT00000091116
delta-1-pyrroline-5-carboxylate synthase
chr1_-_259089632 8.43 ENSRNOT00000020940
ENSRNOT00000091297
aldehyde dehydrogenase 18 family, member A1
chr1_+_53360157 7.30 ENSRNOT00000017809
ribosomal protein S6 kinase A2
chr15_+_34187223 7.29 ENSRNOT00000024978
copine 6
chr8_+_7128656 7.16 ENSRNOT00000038313
progesterone receptor
chr16_+_81089292 7.07 ENSRNOT00000087192
ENSRNOT00000026150
transcription factor Dp-1
chr11_-_86276430 7.00 ENSRNOT00000075164
histone cell cycle regulator
chr7_-_122247139 6.95 ENSRNOT00000064515
megakaryoblastic leukemia (translocation) 1
chr8_+_96551245 6.94 ENSRNOT00000039850
BCL2-related protein A1
chr20_+_50394650 5.84 ENSRNOT00000076010
ENSRNOT00000077065
ENSRNOT00000073259
popeye domain containing 3
chr1_+_137799185 5.64 ENSRNOT00000083590
ENSRNOT00000092778
ATP/GTP binding protein-like 1
chr2_-_166255302 5.12 ENSRNOT00000016012
beta-1,3-N-acetylgalactosaminyltransferase 1 (globoside blood group)
chr5_-_173233188 5.05 ENSRNOT00000055343
transmembrane protein 88B
chr9_+_47386626 4.95 ENSRNOT00000021270
solute carrier family 9 member A2
chr7_-_126913585 4.58 ENSRNOT00000036025
cadherin, EGF LAG seven-pass G-type receptor 1
chr5_+_157165341 4.54 ENSRNOT00000087072
phospholipase A2, group IIC
chr4_-_163649637 4.52 ENSRNOT00000080873
similar to killer cell lectin-like receptor, subfamily A, member 17
chrX_+_62363757 4.50 ENSRNOT00000091240
aristaless related homeobox
chr1_-_101131413 4.42 ENSRNOT00000093729
fms-related tyrosine kinase 3 ligand
chr14_-_104523297 4.39 ENSRNOT00000039523
centrosomal protein 68
chr10_-_11878792 3.82 ENSRNOT00000064964
clusterin associated protein 1
chr7_-_12424367 3.53 ENSRNOT00000060698
midnolin
chr8_-_55696601 3.44 ENSRNOT00000016127
RGD1562914
chr5_+_139468546 3.43 ENSRNOT00000013193
schlafen-like 1
chr1_-_101131012 3.38 ENSRNOT00000082283
ENSRNOT00000093498
ENSRNOT00000093559
fms-related tyrosine kinase 3 ligand
ribosomal protein L13A
chr16_+_8823872 3.14 ENSRNOT00000027186
dorsal root ganglia homeobox
chr11_+_86276616 3.11 ENSRNOT00000071159
mitochondrial ribosomal protein L40
chr4_+_38240728 3.09 ENSRNOT00000047029
PHD finger protein 14
chr8_+_119121669 2.91 ENSRNOT00000028479
protease, serine, 46
chrX_+_18998532 2.86 ENSRNOT00000004213

chr16_+_34795971 2.66 ENSRNOT00000043510
myeloid-associated differentiation marker-like
chr9_+_118586179 2.62 ENSRNOT00000022351
DLG associated protein 1
chrX_+_62363953 2.53 ENSRNOT00000083362
aristaless related homeobox
chr1_+_220423426 2.51 ENSRNOT00000072647
breast cancer metastasis-suppressor 1
chr3_-_122947075 2.51 ENSRNOT00000082369
PC-esterase domain containing 1A
chr6_-_137084739 2.34 ENSRNOT00000060943
transmembrane protein 179
chr3_-_8924032 2.22 ENSRNOT00000023527
ENSRNOT00000085042
SH3 domain-containing GRB2-like endophilin B2
chr13_-_111849653 2.21 ENSRNOT00000006395
digestive organ expansion factor homolog (zebrafish)
chr4_-_113764532 2.18 ENSRNOT00000009269
ssemaphorin 4F
chr6_+_135610743 2.17 ENSRNOT00000010906
Tnf receptor-associated factor 3
chr8_-_48736506 2.16 ENSRNOT00000016227
coiled-coil domain containing 84
chr3_+_108944141 2.06 ENSRNOT00000034950
family with sequence similarity 98, member B
chr2_+_204886202 2.00 ENSRNOT00000022200
nerve growth factor
chr10_+_61685645 1.79 ENSRNOT00000003933
MAX network transcriptional repressor
chr19_-_17346808 1.76 ENSRNOT00000017361
RB transcriptional corepressor like 2
chr2_+_266141581 1.65 ENSRNOT00000078187
ENSRNOT00000051951
RPE65, retinoid isomerohydrolase
chr2_+_57206613 1.62 ENSRNOT00000082694
ENSRNOT00000046069
nucleoporin 155
chr19_+_37127508 1.51 ENSRNOT00000019656
core-binding factor, beta subunit
chr5_-_153252021 1.40 ENSRNOT00000023221
transmembrane protein 50A
chr2_-_157066781 1.30 ENSRNOT00000001187
similar to RalA binding protein 1
chr15_+_36897999 1.15 ENSRNOT00000076030
poly (ADP-ribose) polymerase family, member 4
chr14_+_104191517 1.12 ENSRNOT00000006573
sprouty-related, EVH1 domain containing 2
chr7_-_60988124 1.05 ENSRNOT00000038294
transmembrane protein 186-like
chr7_-_14217778 1.04 ENSRNOT00000038961
epoxide hydrolase 3
chr9_+_49479023 1.04 ENSRNOT00000050922
ENSRNOT00000077111
POU class 3 homeobox 3
chr4_-_38240848 0.92 ENSRNOT00000007567
NADH:ubiquinone oxidoreductase subunit A4
chr3_-_95954983 0.88 ENSRNOT00000006385

chr4_+_1459363 0.70 ENSRNOT00000082919
olfactory receptor 1234
chr11_-_87158597 0.70 ENSRNOT00000002517
pre-B lymphocyte gene 2
chr6_-_147172022 0.58 ENSRNOT00000080675
integrin subunit beta 8
chr3_-_21061070 0.45 ENSRNOT00000044461
olfactory receptor 422
chrX_-_25628272 0.39 ENSRNOT00000086414
midline 1
chr15_+_33885106 0.29 ENSRNOT00000024483
dehydrogenase/reductase 2
chr20_+_1110773 0.20 ENSRNOT00000041697
olfactory receptor 1702
chr11_+_88376256 0.19 ENSRNOT00000081776
pre-B lymphocyte 1

Network of associatons between targets according to the STRING database.

First level regulatory network of Gcm1

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
3.3 9.8 GO:0060399 positive regulation of growth hormone receptor signaling pathway(GO:0060399)
2.9 11.8 GO:0051725 protein de-ADP-ribosylation(GO:0051725)
2.6 15.6 GO:0046125 pyrimidine deoxyribonucleoside metabolic process(GO:0046125)
2.4 7.2 GO:1904700 granulosa cell apoptotic process(GO:1904700) regulation of granulosa cell apoptotic process(GO:1904708)
2.1 12.7 GO:1990086 lens fiber cell apoptotic process(GO:1990086)
1.9 7.8 GO:0090290 positive regulation of osteoclast proliferation(GO:0090290)
1.9 9.5 GO:0071673 positive regulation of smooth muscle cell chemotaxis(GO:0071673)
1.7 17.0 GO:0006561 proline biosynthetic process(GO:0006561)
1.5 4.6 GO:0060490 orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis(GO:0060488) planar dichotomous subdivision of terminal units involved in lung branching morphogenesis(GO:0060489) lateral sprouting involved in lung morphogenesis(GO:0060490)
1.3 3.8 GO:0021508 floor plate formation(GO:0021508)
1.2 9.4 GO:2000969 positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity(GO:2000969)
1.2 7.0 GO:0021759 globus pallidus development(GO:0021759)
1.0 7.3 GO:0002035 brain renin-angiotensin system(GO:0002035)
1.0 7.1 GO:0070345 negative regulation of fat cell proliferation(GO:0070345)
0.9 5.6 GO:0035609 C-terminal protein deglutamylation(GO:0035609)
0.9 7.0 GO:0010735 positive regulation of transcription via serum response element binding(GO:0010735)
0.7 3.5 GO:1903300 negative regulation of glucokinase activity(GO:0033132) negative regulation of hexokinase activity(GO:1903300)
0.6 3.1 GO:2000584 regulation of platelet-derived growth factor receptor-alpha signaling pathway(GO:2000583) negative regulation of platelet-derived growth factor receptor-alpha signaling pathway(GO:2000584) regulation of mesenchymal cell proliferation involved in lung development(GO:2000790) negative regulation of mesenchymal cell proliferation involved in lung development(GO:2000791)
0.5 1.6 GO:0007468 regulation of rhodopsin gene expression(GO:0007468)
0.4 5.0 GO:1990118 sodium ion import across plasma membrane(GO:0098719) sodium ion import into cell(GO:1990118)
0.4 4.4 GO:0010457 centriole-centriole cohesion(GO:0010457)
0.4 5.1 GO:0009312 oligosaccharide biosynthetic process(GO:0009312)
0.3 2.6 GO:0070842 aggresome assembly(GO:0070842)
0.3 2.5 GO:2000210 positive regulation of anoikis(GO:2000210)
0.3 1.0 GO:0072021 ascending thin limb development(GO:0072021) metanephric ascending thin limb development(GO:0072218)
0.3 18.4 GO:0071277 cellular response to calcium ion(GO:0071277)
0.3 2.0 GO:0051388 positive regulation of neurotrophin TRK receptor signaling pathway(GO:0051388)
0.2 3.1 GO:0021559 trigeminal nerve development(GO:0021559)
0.2 7.0 GO:0031935 regulation of chromatin silencing(GO:0031935)
0.2 2.2 GO:0008063 Toll signaling pathway(GO:0008063)
0.2 1.6 GO:0000972 transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery(GO:0000972)
0.1 4.5 GO:0050482 arachidonic acid secretion(GO:0050482) arachidonate transport(GO:1903963)
0.1 8.8 GO:0006487 protein N-linked glycosylation(GO:0006487)
0.1 2.2 GO:0031290 retinal ganglion cell axon guidance(GO:0031290)
0.1 1.1 GO:0043517 positive regulation of DNA damage response, signal transduction by p53 class mediator(GO:0043517)
0.1 1.5 GO:0060216 definitive hemopoiesis(GO:0060216)
0.1 2.2 GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)(GO:0000462)
0.0 0.4 GO:0035372 protein localization to microtubule(GO:0035372)
0.0 1.8 GO:0043550 regulation of lipid kinase activity(GO:0043550)
0.0 1.2 GO:0006278 RNA-dependent DNA biosynthetic process(GO:0006278) telomere maintenance via telomerase(GO:0007004)
0.0 8.7 GO:0006281 DNA repair(GO:0006281)
0.0 2.1 GO:0021987 cerebral cortex development(GO:0021987)
0.0 0.3 GO:0043011 myeloid dendritic cell differentiation(GO:0043011)
0.0 0.9 GO:0042100 B cell proliferation(GO:0042100)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
0.5 1.6 GO:0044611 nuclear pore inner ring(GO:0044611)
0.4 9.8 GO:0010369 chromocenter(GO:0010369)
0.4 3.4 GO:0097452 GAIT complex(GO:0097452)
0.3 3.8 GO:0097542 ciliary tip(GO:0097542)
0.3 2.1 GO:0072669 tRNA-splicing ligase complex(GO:0072669)
0.2 7.3 GO:0045334 clathrin-coated endocytic vesicle(GO:0045334)
0.2 4.4 GO:0031233 intrinsic component of external side of plasma membrane(GO:0031233)
0.2 2.2 GO:0035631 CD40 receptor complex(GO:0035631)
0.2 2.0 GO:0005796 Golgi lumen(GO:0005796)
0.1 2.5 GO:0070822 Sin3-type complex(GO:0070822)
0.1 26.1 GO:0043197 dendritic spine(GO:0043197)
0.1 11.2 GO:0032587 ruffle membrane(GO:0032587)
0.1 2.2 GO:0032040 small-subunit processome(GO:0032040)
0.1 0.9 GO:0005751 mitochondrial respiratory chain complex IV(GO:0005751)
0.1 21.5 GO:0005667 transcription factor complex(GO:0005667)
0.0 2.0 GO:0000315 organellar large ribosomal subunit(GO:0000315) mitochondrial large ribosomal subunit(GO:0005762)
0.0 8.4 GO:0005819 spindle(GO:0005819)
0.0 4.8 GO:0045211 postsynaptic membrane(GO:0045211)
0.0 7.0 GO:0000790 nuclear chromatin(GO:0000790)
0.0 5.1 GO:0000139 Golgi membrane(GO:0000139)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
3.9 15.6 GO:0019136 pyrimidine nucleoside binding(GO:0001884) deoxynucleoside kinase activity(GO:0019136)
2.8 17.0 GO:0016774 phosphotransferase activity, carboxyl group as acceptor(GO:0016774)
2.4 9.5 GO:0035727 lysophosphatidic acid binding(GO:0035727) lysophosphatidic acid receptor activity(GO:0070915)
2.2 8.8 GO:0030144 alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity(GO:0030144)
1.8 7.3 GO:0004711 ribosomal protein S6 kinase activity(GO:0004711)
1.0 5.1 GO:0008499 UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity(GO:0008499)
0.5 4.5 GO:0047498 calcium-dependent phospholipase A2 activity(GO:0047498)
0.5 7.0 GO:0001206 transcriptional repressor activity, RNA polymerase II distal enhancer sequence-specific binding(GO:0001206)
0.5 2.0 GO:0005163 nerve growth factor receptor binding(GO:0005163)
0.5 5.0 GO:0015386 potassium:proton antiporter activity(GO:0015386)
0.5 7.0 GO:0043522 leucine zipper domain binding(GO:0043522)
0.5 11.8 GO:0016799 hydrolase activity, hydrolyzing N-glycosyl compounds(GO:0016799)
0.4 6.9 GO:0051400 BH domain binding(GO:0051400)
0.3 16.1 GO:0031491 nucleosome binding(GO:0031491)
0.2 1.6 GO:1901612 cardiolipin binding(GO:1901612)
0.2 2.2 GO:0034511 U3 snoRNA binding(GO:0034511)
0.2 5.6 GO:0004181 metallocarboxypeptidase activity(GO:0004181)
0.2 2.6 GO:0098919 structural constituent of postsynaptic specialization(GO:0098879) structural constituent of synapse(GO:0098918) structural constituent of postsynaptic density(GO:0098919)
0.2 1.1 GO:0005173 stem cell factor receptor binding(GO:0005173)
0.1 5.8 GO:0030552 cAMP binding(GO:0030552)
0.1 7.3 GO:0001786 phosphatidylserine binding(GO:0001786)
0.1 7.8 GO:0030971 receptor tyrosine kinase binding(GO:0030971)
0.1 2.2 GO:0031996 thioesterase binding(GO:0031996)
0.1 7.2 GO:0004879 RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding(GO:0004879) transcription factor activity, direct ligand regulated sequence-specific DNA binding(GO:0098531)
0.1 2.5 GO:0004407 histone deacetylase activity(GO:0004407)
0.1 1.6 GO:0017056 structural constituent of nuclear pore(GO:0017056)
0.1 0.3 GO:0004090 carbonyl reductase (NADPH) activity(GO:0004090)
0.1 1.8 GO:1990841 promoter-specific chromatin binding(GO:1990841)
0.1 1.2 GO:0003950 NAD+ ADP-ribosyltransferase activity(GO:0003950)
0.0 11.2 GO:0005085 guanyl-nucleotide exchange factor activity(GO:0005085)
0.0 1.0 GO:0071837 HMG box domain binding(GO:0071837)
0.0 8.6 GO:0003713 transcription coactivator activity(GO:0003713)
0.0 5.9 GO:0001047 core promoter binding(GO:0001047)
0.0 0.9 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)
0.0 11.2 GO:0003682 chromatin binding(GO:0003682)
0.0 4.5 GO:0030246 carbohydrate binding(GO:0030246)

Gene overrepresentation in curated gene sets: canonical pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.7 12.7 SA REG CASCADE OF CYCLIN EXPR Expression of cyclins regulates progression through the cell cycle by activating cyclin-dependent kinases.
0.4 7.2 PID ANTHRAX PATHWAY Cellular roles of Anthrax toxin
0.3 9.5 ST ERK1 ERK2 MAPK PATHWAY ERK1/ERK2 MAPK Pathway
0.3 11.2 PID RAS PATHWAY Regulation of Ras family activation
0.2 2.0 SA TRKA RECEPTOR The TrkA receptor binds nerve growth factor to activate MAP kinase pathways and promote cell growth.
0.1 7.0 PID RHOA PATHWAY RhoA signaling pathway
0.1 6.9 PID BCR 5PATHWAY BCR signaling pathway
0.1 9.5 PID LYSOPHOSPHOLIPID PATHWAY LPA receptor mediated events
0.1 1.8 SA PTEN PATHWAY PTEN is a tumor suppressor that dephosphorylates the lipid messenger phosphatidylinositol triphosphate.
0.1 7.1 PID RB 1PATHWAY Regulation of retinoblastoma protein
0.1 1.6 PID RHODOPSIN PATHWAY Visual signal transduction: Rods
0.0 3.4 WNT SIGNALING Genes related to Wnt-mediated signal transduction
0.0 1.1 PID KIT PATHWAY Signaling events mediated by Stem cell factor receptor (c-Kit)
0.0 1.5 PID AP1 PATHWAY AP-1 transcription factor network

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
1.0 15.6 REACTOME PURINE SALVAGE Genes involved in Purine salvage
0.7 12.7 REACTOME CDC6 ASSOCIATION WITH THE ORC ORIGIN COMPLEX Genes involved in CDC6 association with the ORC:origin complex
0.7 11.2 REACTOME RAP1 SIGNALLING Genes involved in Rap1 signalling
0.5 7.1 REACTOME INHIBITION OF REPLICATION INITIATION OF DAMAGED DNA BY RB1 E2F1 Genes involved in Inhibition of replication initiation of damaged DNA by RB1/E2F1
0.5 8.4 REACTOME AMINO ACID SYNTHESIS AND INTERCONVERSION TRANSAMINATION Genes involved in Amino acid synthesis and interconversion (transamination)
0.3 7.3 REACTOME ERK MAPK TARGETS Genes involved in ERK/MAPK targets
0.2 2.2 REACTOME ACTIVATION OF IRF3 IRF7 MEDIATED BY TBK1 IKK EPSILON Genes involved in Activation of IRF3/IRF7 mediated by TBK1/IKK epsilon
0.2 2.0 REACTOME NFKB IS ACTIVATED AND SIGNALS SURVIVAL Genes involved in NF-kB is activated and signals survival
0.1 7.2 REACTOME NUCLEAR SIGNALING BY ERBB4 Genes involved in Nuclear signaling by ERBB4
0.1 1.8 REACTOME G0 AND EARLY G1 Genes involved in G0 and Early G1
0.1 1.6 REACTOME TRANSPORT OF RIBONUCLEOPROTEINS INTO THE HOST NUCLEUS Genes involved in Transport of Ribonucleoproteins into the Host Nucleus
0.0 9.5 REACTOME G ALPHA Q SIGNALLING EVENTS Genes involved in G alpha (q) signalling events
0.0 3.4 REACTOME PEPTIDE CHAIN ELONGATION Genes involved in Peptide chain elongation
0.0 0.9 REACTOME RESPIRATORY ELECTRON TRANSPORT Genes involved in Respiratory electron transport