GSE49485: Hypoxia transcriptome sequencing of rat brain.

• Motif significance table
• Sample table
• Mean activities
• All promoters sorted by FOV

• Activity table
• Activity delta table
• Regulatory interactions
• Motifs sorted by significance
• Expression table
• Download the whole report

Gene Symbol	Gene ID	Gene Info
Smad4 Links NCBI RGD Ensembl	ENSRNOG00000051965	SMAD family member 4

Gene	Promoter	Pearson corr. coef.	P-value	Plot
Smad4	rn6_v1_chr18_-_69657301_69657301	0.26	6.7e-01	Click!

Promoter	Log-likelihood	Transcript	Gene	Gene Info
chr10_-_88670430 Show fit	1.25	ENSRNOT00000025547	Hcrt Links NCBI RGD Ensembl Show fit	hypocretin neuropeptide precursor
chr8_-_98738446 Show fit	0.41	ENSRNOT00000019860	Zic1 Links NCBI RGD Ensembl Show fit	Zic family member 1
chr17_-_9695292 Show fit	0.41	ENSRNOT00000036162	Prr7 Links NCBI RGD Ensembl Show fit	proline rich 7 (synaptic)
chr4_+_84194347 Show fit	0.36	ENSRNOT00000084256	Chn2 Links NCBI RGD Ensembl Show fit	chimerin 2
chr12_-_41671437 Show fit	0.34	ENSRNOT00000001883	Lhx5 Links NCBI RGD Ensembl Show fit	LIM homeobox 5
chr2_-_198360678 Show fit	0.27	ENSRNOT00000051917	Hist2h2ac Links NCBI RGD Ensembl Show fit	histone cluster 2 H2A family member c
chr5_-_152473868 Show fit	0.25	ENSRNOT00000022130	Fam110d Links NCBI RGD Ensembl Show fit	family with sequence similarity 110, member D
chr7_-_70842405 Show fit	0.20	ENSRNOT00000047449	Nxph4 Links NCBI RGD Ensembl Show fit	neurexophilin 4
chr7_+_123168811 Show fit	0.18	ENSRNOT00000007091	Csdc2 Links NCBI RGD Ensembl Show fit	cold shock domain containing C2
chr17_-_43821536 Show fit	0.17	ENSRNOT00000072286	RGD1562378 Links NCBI RGD Ensembl Show fit	histone H4 variant H4-v.1
chr1_-_101856881 Show fit	0.17	ENSRNOT00000028615	Grin2d Links NCBI RGD Ensembl Show fit	glutamate ionotropic receptor NMDA type subunit 2D
chr10_-_45297385 Show fit	0.16	ENSRNOT00000041187	Hist3h2bb Links NCBI RGD Ensembl Show fit	histone cluster 3 H2B family member b
chr4_+_153774486 Show fit	0.16	ENSRNOT00000074096	Tuba8 Links NCBI RGD Ensembl Show fit	tubulin, alpha 8
chr5_-_152464850 Show fit	0.15	ENSRNOT00000021937	Zfp593 Links NCBI RGD Ensembl Show fit	zinc finger protein 593
chr17_-_44744902 Show fit	0.14	ENSRNOT00000085381	RGD1562378 Links NCBI RGD Ensembl Show fit	histone H4 variant H4-v.1
chr3_+_56862691 Show fit	0.10	ENSRNOT00000087712	Gad1 Links NCBI RGD Ensembl Show fit	glutamate decarboxylase 1
chr8_+_58347736 Show fit	0.09	ENSRNOT00000080227 ENSRNOT00000066222	Slc35f2 Links NCBI RGD Ensembl Show fit	solute carrier family 35, member F2
chr14_-_35149608 Show fit	0.08	ENSRNOT00000003050 ENSRNOT00000090654	Kit Links NCBI RGD Ensembl Show fit	KIT proto-oncogene receptor tyrosine kinase
chr13_-_91872954 Show fit	0.08	ENSRNOT00000004613 ENSRNOT00000079263	Cadm3 Links NCBI RGD Ensembl Show fit	cell adhesion molecule 3
chr17_+_78739389 Show fit	0.08	ENSRNOT00000020384	LOC102547897 Links NCBI RGD Ensembl Show fit	uncharacterized LOC102547897
chr12_+_37668369 Show fit	0.08	ENSRNOT00000001419	Cdk2ap1 Links NCBI RGD Ensembl Show fit	cyclin-dependent kinase 2 associated protein 1
chr14_-_34218961 Show fit	0.07	ENSRNOT00000072588	LOC686911 Links NCBI RGD Ensembl Show fit	similar to Exocyst complex component 1 (Exocyst complex component Sec3)
chr4_-_170145262 Show fit	0.07	ENSRNOT00000074526	Hist1h4b Links NCBI RGD Ensembl Show fit	histone cluster 1, H4b
chr10_-_107539658 Show fit	0.07	ENSRNOT00000089346	Rbfox3 Links NCBI RGD Ensembl Show fit	RNA binding protein, fox-1 homolog 3
chr1_+_72636959 Show fit	0.07	ENSRNOT00000023489	Il11 Links NCBI RGD Ensembl Show fit	interleukin 11
chr1_+_219345918 Show fit	0.07	ENSRNOT00000025018	Cdk2ap2 Links NCBI RGD Ensembl Show fit	cyclin-dependent kinase 2 associated protein 2
chr13_+_106463368 Show fit	0.06	ENSRNOT00000003489	Esrrg Links NCBI RGD Ensembl Show fit	estrogen-related receptor gamma
chr1_+_14224393 Show fit	0.06	ENSRNOT00000016037	Perp Links NCBI RGD Ensembl Show fit	PERP, TP53 apoptosis effector
chr17_-_43689311 Show fit	0.06	ENSRNOT00000028779	Hist1h2bcl1 Links NCBI RGD Ensembl Show fit	histone cluster 1, H2bc-like 1
chr4_+_51553454 Show fit	0.06	ENSRNOT00000073466	LOC100909784 Links NCBI RGD Ensembl Show fit	leiomodin-2-like
chr13_+_48287873 Show fit	0.06	ENSRNOT00000068223	Fam72a Links NCBI RGD Ensembl Show fit	family with sequence similarity 72, member A
chr9_+_94562839 Show fit	0.05	ENSRNOT00000022308	RGD1311447 Links NCBI RGD Ensembl Show fit	LOC363276
chr10_-_107539465 Show fit	0.05	ENSRNOT00000004524	Rbfox3 Links NCBI RGD Ensembl Show fit	RNA binding protein, fox-1 homolog 3
chr1_-_101514547 Show fit	0.05	ENSRNOT00000079633	Ppp1r15a Links NCBI RGD Ensembl Show fit	protein phosphatase 1, regulatory subunit 15A
chr16_+_61758917 Show fit	0.05	ENSRNOT00000084858	Leprotl1 Links NCBI RGD Ensembl Show fit	leptin receptor overlapping transcript-like 1
chr10_+_56453877 Show fit	0.05	ENSRNOT00000031640	Plscr3 Links NCBI RGD Ensembl Show fit	phospholipid scramblase 3
chr17_-_44520240 Show fit	0.05	ENSRNOT00000086538	Hist1h2bh Links NCBI RGD Ensembl Show fit	histone cluster 1 H2B family member h
chr15_+_48327461 Show fit	0.05	ENSRNOT00000018071	Ints9 Links NCBI RGD Ensembl Show fit	integrator complex subunit 9
chr17_-_43770561 Show fit	0.04	ENSRNOT00000088408	RGD1562378 Links NCBI RGD Ensembl Show fit	histone H4 variant H4-v.1
chr12_+_21767606 Show fit	0.04	ENSRNOT00000059602	LOC103691013 Links NCBI RGD Ensembl Show fit	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adapter 1-like
chr3_+_148541909 Show fit	0.04	ENSRNOT00000012187	Ccm2l Links NCBI RGD Ensembl Show fit	CCM2 like scaffolding protein
chr9_-_16647458 Show fit	0.04	ENSRNOT00000024380	Mrpl2 Links NCBI RGD Ensembl Show fit	mitochondrial ribosomal protein L2
chrX_+_106823491 Show fit	0.04	ENSRNOT00000045997	Bex3 Links NCBI RGD Ensembl Show fit	brain expressed X-linked 3
chr7_-_14418950 Show fit	0.03	ENSRNOT00000066722	Rasal3 Links NCBI RGD Ensembl Show fit	RAS protein activator like 3
chr7_+_119647375 Show fit	0.03	ENSRNOT00000046563	Kctd17 Links NCBI RGD Ensembl Show fit	potassium channel tetramerization domain containing 17
chr8_+_117280705 Show fit	0.03	ENSRNOT00000085038	Usp19 Links NCBI RGD Ensembl Show fit	ubiquitin specific peptidase 19
chr10_-_90265017 Show fit	0.03	ENSRNOT00000064283 ENSRNOT00000048418	Ubtf Links NCBI RGD Ensembl Show fit	upstream binding transcription factor, RNA polymerase I
chr17_+_44520537 Show fit	0.03	ENSRNOT00000077985	hist1h2ail2 Links NCBI RGD Ensembl Show fit	histone cluster 1, H2ai-like2
chr15_-_88622413 Show fit	0.03	ENSRNOT00000092174	Pou4f1 Links NCBI RGD Ensembl Show fit	POU class 4 homeobox 1
chr9_+_66335492 Show fit	0.03	ENSRNOT00000037555	RGD1562029 Links NCBI RGD Ensembl Show fit	similar to KIAA2012 protein
chr17_+_23135985 Show fit	0.03	ENSRNOT00000090794	Nedd9 Links NCBI RGD Ensembl Show fit	neural precursor cell expressed, developmentally down-regulated 9
chr14_+_91557601 Show fit	0.03	ENSRNOT00000038733	RGD1309870 Links NCBI RGD Ensembl Show fit	hypothetical LOC289778
chr9_+_117583610 Show fit	0.03	ENSRNOT00000088647 ENSRNOT00000049426	Epb41l3 Links NCBI RGD Ensembl Show fit	erythrocyte membrane protein band 4.1-like 3
chr6_+_108745895 Show fit	0.02	ENSRNOT00000061786	LOC108348062 Links NCBI RGD Ensembl Show fit	eukaryotic translation initiation factor 3 subunit H
chr9_+_16647598 Show fit	0.02	ENSRNOT00000087413	Klc4 Links NCBI RGD Ensembl Show fit	kinesin light chain 4
chr9_+_16647922 Show fit	0.02	ENSRNOT00000031625	Klc4 Links NCBI RGD Ensembl Show fit	kinesin light chain 4
chr12_+_4546287 Show fit	0.02	ENSRNOT00000001416	Higd2al1 Links NCBI RGD Ensembl Show fit	HIG1 hypoxia inducible domain family, member 2A-like 1
chr2_+_209839299 Show fit	0.02	ENSRNOT00000092450	Kcna2 Links NCBI RGD Ensembl Show fit	potassium voltage-gated channel subfamily A member 2
chr7_-_143217535 Show fit	0.02	ENSRNOT00000088316	Kb15 Links NCBI RGD Ensembl Show fit	type II keratin Kb15
chr20_-_2211995 Show fit	0.01	ENSRNOT00000077201	Trim26 Links NCBI RGD Ensembl Show fit	tripartite motif-containing 26
chr15_+_23792931 Show fit	0.01	ENSRNOT00000092091	Samd4a Links NCBI RGD Ensembl Show fit	sterile alpha motif domain containing 4A
chr10_-_34333305 Show fit	0.01	ENSRNOT00000071365	Olr1384 Links NCBI RGD Ensembl Show fit	olfactory receptor gene Olr1384
chrX_+_107370431 Show fit	0.01	ENSRNOT00000044372	Tceal1 Links NCBI RGD Ensembl Show fit	transcription elongation factor A like 1
chrX_+_21696772 Show fit	0.01	ENSRNOT00000043559	Hsd17b10 Links NCBI RGD Ensembl Show fit	hydroxysteroid (17-beta) dehydrogenase 10
chr2_+_209838869 Show fit	0.01	ENSRNOT00000092365	Kcna2 Links NCBI RGD Ensembl Show fit	potassium voltage-gated channel subfamily A member 2
chr3_-_113342675 Show fit	0.01	ENSRNOT00000020130	Strc Links NCBI RGD Ensembl Show fit	stereocilin
chr3_-_8979889 Show fit	0.00	ENSRNOT00000065128	Crat Links NCBI RGD Ensembl Show fit	carnitine O-acetyltransferase
chr10_+_46940965 Show fit	0.00	ENSRNOT00000005366	Llgl1 Links NCBI RGD Ensembl Show fit	LLGL1, scribble cell polarity complex component
chr7_-_120403523 Show fit	0.00	ENSRNOT00000015283	Sox10 Links NCBI RGD Ensembl Show fit	SRY box 10
chr7_+_144623555 Show fit	0.00	ENSRNOT00000022217	Hoxc6 Links NCBI RGD Ensembl Show fit	homeo box C6

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Gene overrepresentation in biological process category:

Log-likelihood per target	Total log-likelihood	Term	Description
0.2	1.2	GO:0051970	negative regulation of transmission of nerve impulse(GO:0051970)
0.0	0.3	GO:0021937	cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation(GO:0021937)
0.0	0.4	GO:0045653	negative regulation of megakaryocyte differentiation(GO:0045653)
0.0	0.4	GO:0001675	acrosome assembly(GO:0001675)
0.0	0.1	GO:1905065	Kit signaling pathway(GO:0038109) melanocyte migration(GO:0097324) positive regulation of vascular smooth muscle cell differentiation(GO:1905065)
0.0	0.1	GO:0009449	gamma-aminobutyric acid biosynthetic process(GO:0009449)
0.0	0.1	GO:1903026	negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding(GO:1903026)
0.0	0.1	GO:1902310	regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation(GO:0060734) response to methyl methanesulfonate(GO:0072702) cellular response to methyl methanesulfonate(GO:0072703) response to environmental enrichment(GO:0090648) positive regulation of peptidyl-serine dephosphorylation(GO:1902310)
0.0	0.0	GO:0090271	positive regulation of fibroblast growth factor production(GO:0090271)
0.0	0.1	GO:0006362	transcription elongation from RNA polymerase I promoter(GO:0006362)
0.0	0.0	GO:0051140	regulation of NK T cell proliferation(GO:0051140) positive regulation of NK T cell proliferation(GO:0051142)
0.0	0.1	GO:1903659	regulation of complement-dependent cytotoxicity(GO:1903659)

Gene overrepresentation in cellular component category:

Log-likelihood per target	Total log-likelihood	Term	Description
0.0	0.4	GO:0000788	nuclear nucleosome(GO:0000788)
0.0	1.2	GO:0005791	rough endoplasmic reticulum(GO:0005791)

Gene overrepresentation in molecular function category:

Log-likelihood per target	Total log-likelihood	Term	Description
0.1	0.4	GO:0001565	phorbol ester receptor activity(GO:0001565)
0.0	0.1	GO:0031177	phosphopantetheine binding(GO:0031177)
0.0	1.2	GO:0005184	neuropeptide hormone activity(GO:0005184)
0.0	0.1	GO:0004351	glutamate decarboxylase activity(GO:0004351)
0.0	0.2	GO:0004972	NMDA glutamate receptor activity(GO:0004972)
0.0	0.1	GO:0050682	AF-2 domain binding(GO:0050682)

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target	Total log-likelihood	Term	Description
0.0	0.6	REACTOME RNA POL I PROMOTER OPENING	Genes involved in RNA Polymerase I Promoter Opening