Mllt11 UP in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: IncreasedDifferentialExpressionRatio
fold change: 1.20088536203901
p value: 6.94105102761163E-8
refers to: Mllt11
refers to: 1416313_at
t statistic: 15.6157698207832

Cdh6 UP in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: IncreasedDifferentialExpressionRatio
fold change: 1.47407771890269
p value: 5.69173516755767E-7
refers to: Cdh6
refers to: 1438989_s_at
t statistic: 12.6259744137281

Fam102b
type: EnsemblDatabaseReference

Fam102b
type: EnsemblDatabaseReference

1416149_at
type: EFO_0005072
part of: A-AFFY-45

Slit2 UP in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: IncreasedDifferentialExpressionRatio
fold change: 1.05257695831319
p value: 3.14772838558687E-5
refers to: Slit2
refers to: 1458140_at
t statistic: 8.75461610047368

Foxa2
type: EnsemblDatabaseReference

Nefl
type: EnsemblDatabaseReference

Prnp
type: EnsemblDatabaseReference

1448201_at
type: EFO_0005072
part of: A-AFFY-45

Pax6 DOWN in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: DecreasedDifferentialExpressionRatio
fold change: -1.22851383494541
p value: 1.95175948344884E-8
refers to: 1452526_a_at
refers to: Pax6
t statistic: -17.3851963322745

Sulf1
type: EnsemblDatabaseReference

Elavl4
type: EnsemblDatabaseReference

Sulf1 UP in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: IncreasedDifferentialExpressionRatio
fold change: 1.33056124563959
p value: 5.70429166674473E-7
refers to: Sulf1
refers to: 1438200_at
t statistic: 12.5937237209623

Nefl UP in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: IncreasedDifferentialExpressionRatio
fold change: 1.75463663094925
p value: 2.03577677324416E-9
refers to: Nefl
refers to: 1426255_at
t statistic: 21.3584530014559

Analysis of '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: MicroarrayDifferentialExpressionAnalysis

Elavl4
type: EnsemblDatabaseReference

(Sample) developmental stage/embryoid bodies
type: EFO_0004988
property type: developmental stage
property value: embryoid bodies

Nefm
type: EnsemblDatabaseReference

Sfrp2 DOWN in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: DecreasedDifferentialExpressionRatio
fold change: -1.46262723453386
p value: 9.50077048638063E-8
refers to: Sfrp2
refers to: 1448201_at
t statistic: -14.9737191104776

Irx3
type: EnsemblDatabaseReference

Crmp1
type: EnsemblDatabaseReference

Rgs4
type: EnsemblDatabaseReference

Crmp1
type: EnsemblDatabaseReference

Spon1 UP in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: IncreasedDifferentialExpressionRatio
fold change: 1.84406571923895
p value: 6.94105102761163E-8
refers to: Spon1
refers to: 1451342_at
t statistic: 15.5623240265158

Dbx1
type: EnsemblDatabaseReference

Gja1
type: EnsemblDatabaseReference

1450723_at
type: EFO_0005072
part of: A-AFFY-45

1436319_at
type: EFO_0005072
part of: A-AFFY-45

Elavl4 UP in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: IncreasedDifferentialExpressionRatio
fold change: 1.02270824399869
p value: 2.23923546385968E-4
refers to: Elavl4
refers to: 1428741_at
t statistic: 7.14249669113745

Insm1
type: EnsemblDatabaseReference

1425828_at
type: EFO_0005072
part of: A-AFFY-45

Ntn1
type: EnsemblDatabaseReference

Gja1 DOWN in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: DecreasedDifferentialExpressionRatio
fold change: -1.25709947003547
p value: 1.29761772280801E-6
refers to: Gja1
refers to: 1437992_x_at
t statistic: -11.6785706202664

Insm1 UP in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: IncreasedDifferentialExpressionRatio
fold change: 1.07952946400839
p value: 2.67907293724713E-6
refers to: Insm1
refers to: 1455865_at
t statistic: 10.9824248871278

(Factor value) COMPOUND/500 nanomolar retinoic acid
type: CHEBI 6067
property type: COMPOUND
property value: 500 nanomolar retinoic acid

1423537_at
type: EFO_0005072
part of: A-AFFY-45

Tubb3
type: EnsemblDatabaseReference

(Sample) cell type/embryonic stem cell
type: CL_0002322
property type: cell type
property value: embryonic stem cell

Slit2
type: EnsemblDatabaseReference

Mllt11
type: EnsemblDatabaseReference

Fam102b UP in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: IncreasedDifferentialExpressionRatio
fold change: 1.00285209794033
p value: 2.47371856456586E-7
refers to: Fam102b
refers to: 1455033_at
t statistic: 13.5342673650831

(Assay) 03_RA_EB
type: Assay
has participant: A-AFFY-45

(Assay) 08_RAHh_EB
type: Assay
has participant: A-AFFY-45

1416286_at
type: EFO_0005072
part of: A-AFFY-45

1418517_at
type: EFO_0005072
part of: A-AFFY-45

Ndnf DOWN in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: DecreasedDifferentialExpressionRatio
fold change: -1.23217725230201
p value: 2.15194097599993E-7
refers to: Ndnf
refers to: 1460465_at
t statistic: -13.8132793472696

Cdh6
type: EnsemblDatabaseReference

Ntn1 UP in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: IncreasedDifferentialExpressionRatio
fold change: 1.09704723127823
p value: 1.40643778307408E-7
refers to: Ntn1
refers to: 1454974_at
t statistic: 14.3861852506383

1422720_at
type: EFO_0005072
part of: A-AFFY-45

1419549_at
type: EFO_0005072
part of: A-AFFY-45

Pax6
type: EnsemblDatabaseReference

Arg1
type: EnsemblDatabaseReference

Gja1 DOWN in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: DecreasedDifferentialExpressionRatio
fold change: -1.40638192535177
p value: 9.92366046131499E-7
refers to: Gja1
refers to: 1415800_at
t statistic: -12.0642784118832

Nefm UP in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: IncreasedDifferentialExpressionRatio
fold change: 1.8735157200109
p value: 2.03577677324416E-9
refers to: Nefm
refers to: 1422520_at
t statistic: 21.0938674471584

Pax6 DOWN in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: DecreasedDifferentialExpressionRatio
fold change: -1.18913897640095
p value: 5.26648250116372E-4
refers to: Pax6
refers to: 1419271_at
t statistic: -6.49952402929694

Olig1
type: EnsemblDatabaseReference

Ndnf
type: EnsemblDatabaseReference

1448233_at
type: EFO_0005072
part of: A-AFFY-45

Nkx6-1
type: EnsemblDatabaseReference

Gap43
type: EnsemblDatabaseReference

1452526_a_at
type: EFO_0005072
part of: A-AFFY-45

Isl1 UP in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: IncreasedDifferentialExpressionRatio
fold change: 1.99966024967647
p value: 1.02960383824003E-6
refers to: Isl1
refers to: 1422720_at
t statistic: 11.9523864554322

1415885_at
type: EFO_0005072
part of: A-AFFY-45

1450258_a_at
type: EFO_0005072
part of: A-AFFY-45

Nnat
type: EnsemblDatabaseReference

1422833_at
type: EFO_0005072
part of: A-AFFY-45

1447886_at
type: EFO_0005072
part of: A-AFFY-45

1438989_s_at
type: EFO_0005072
part of: A-AFFY-45

Isl1 UP in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: IncreasedDifferentialExpressionRatio
fold change: 3.10339288341119
p value: 1.27950780993904E-11
refers to: Isl1
refers to: 1450723_at
t statistic: 33.765459707014

1426255_at
type: EFO_0005072
part of: A-AFFY-45

1457012_at
type: EFO_0005072
part of: A-AFFY-45

1437992_x_at
type: EFO_0005072
part of: A-AFFY-45

1455033_at
type: EFO_0005072
part of: A-AFFY-45

Nkx2-9 UP in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: IncreasedDifferentialExpressionRatio
fold change: 1.53713107708249
p value: 1.13830191050692E-7
refers to: Nkx2-9
refers to: 1422284_at
t statistic: 14.7164494657535

Chgb
type: EnsemblDatabaseReference

(Assay) 01_RA_EB
type: Assay
has participant: A-AFFY-45

Foxa2
type: EnsemblDatabaseReference

Stmn2
type: EnsemblDatabaseReference

Elavl4 UP in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: IncreasedDifferentialExpressionRatio
fold change: 1.88499882544813
p value: 1.21860684443063E-6
refers to: Elavl4
refers to: 1452894_at
t statistic: 11.7561797559972

Nefl
type: EnsemblDatabaseReference

Prnp
type: EnsemblDatabaseReference

1419271_at
type: EFO_0005072
part of: A-AFFY-45

Sulf1
type: EnsemblDatabaseReference

(Assay) 07_RAHh_EB
type: Assay
has participant: A-AFFY-45

Spon1
type: EnsemblDatabaseReference

Isl1
type: EnsemblDatabaseReference

1451342_at
type: EFO_0005072
part of: A-AFFY-45

Nnat UP in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: IncreasedDifferentialExpressionRatio
fold change: 1.22486340239266
p value: 1.40993259575967E-8
refers to: Nnat
refers to: 1423506_a_at
t statistic: 17.9187753889995

Isl1
type: EnsemblDatabaseReference

Gap43 UP in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: IncreasedDifferentialExpressionRatio
fold change: 1.64780414903174
p value: 2.03577677324416E-9
refers to: Gap43
refers to: 1423537_at
t statistic: 21.8146377242333

Sfrp2
type: EnsemblDatabaseReference

1448289_at
type: EFO_0005072
part of: A-AFFY-45

Sfrp2
type: EnsemblDatabaseReference

1423281_at
type: EFO_0005072
part of: A-AFFY-45

1454974_at
type: EFO_0005072
part of: A-AFFY-45

Gja1
type: EnsemblDatabaseReference

1438200_at
type: EFO_0005072
part of: A-AFFY-45

(Factor value) COMPOUND/500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist
type: EFO_0000001
property type: COMPOUND
property value: 500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist

Stmn2 UP in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: IncreasedDifferentialExpressionRatio
fold change: 1.28390828333405
p value: 1.61126841951244E-7
refers to: Stmn2
refers to: 1423280_at
t statistic: 14.1966399683589

(Assay) 06_RAHh_EB
type: Assay
has participant: A-AFFY-45

1428741_at
type: EFO_0005072
part of: A-AFFY-45

Olig1 UP in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: IncreasedDifferentialExpressionRatio
fold change: 2.06968717773375
p value: 2.03577677324416E-9
refers to: Olig1
refers to: 1416149_at
t statistic: 21.1046498284883

1416313_at
type: EFO_0005072
part of: A-AFFY-45

Dbx1 DOWN in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: DecreasedDifferentialExpressionRatio
fold change: -1.91792593874024
p value: 2.46875229479649E-7
refers to: 1457012_at
refers to: Dbx1
t statistic: -13.5949250779367

Chgb UP in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: IncreasedDifferentialExpressionRatio
fold change: 1.05974377962634
p value: 2.03157863216614E-5
refers to: Chgb
refers to: 1415885_at
t statistic: 9.14009500088976

Nefm
type: EnsemblDatabaseReference

E-GEOD-4936
type: microarray 1colour mrna differential
RO_0002162: Mus musculus
description: This experiment was specifically designed to measure neural targets of Shh signaling, we sought to profile the genes upregulated by Hh signaling in the ventral neural tube to obtain a valid dataset. To obtain ventral-specific markers, we generated retinoic acid-treated EBs grown in the presence or absence of HH-Ag. We did not observe induction of ventral Hh markers in RA-treated constitutive Gli1FLAG EBs and used these for the control, baseline set. The presence of FoxA2, Nkx2.9 and Nkx6.1 amongst the top 10 genes based on expression levels suggests that profiling significantly enriches for Hh-dependent cell types. As expected, the benchmark standard Gli1 was not up-regulated in our array, since it is constitutively expressed in the control as well. Experiment Overall Design: There are a total of 8 samples. Four biological replicates of Retinoic-acid treated EBs (Baseline) and 4 additional biological samples of retinoic acid + Hh-Ag treated EBs (induced sample).
uses data from: http://identifiers.org/pubmed/17442700

Irx3 DOWN in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: DecreasedDifferentialExpressionRatio
fold change: -1.44088958276666
p value: 7.83864946538975E-8
refers to: 1418517_at
refers to: Irx3
t statistic: -15.3114113770612

(Assay) 02_RA_EB
type: Assay
has participant: A-AFFY-45

Nefl UP in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: IncreasedDifferentialExpressionRatio
fold change: 1.46752271295071
p value: 1.47256564443376E-6
refers to: Nefl
refers to: 1454672_at
t statistic: 11.5256408024473

1415978_at
type: EFO_0005072
part of: A-AFFY-45

Cdh6
type: EnsemblDatabaseReference

Irx3
type: EnsemblDatabaseReference

Rgs4
type: EnsemblDatabaseReference

Sulf1 UP in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: IncreasedDifferentialExpressionRatio
fold change: 1.11254570764598
p value: 1.97874829329101E-5
refers to: Sulf1
refers to: 1436319_at
t statistic: 9.18284102315198

Hoxb5os DOWN in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: DecreasedDifferentialExpressionRatio
fold change: -1.57040379530453
p value: 1.16315893994901E-5
refers to: Hoxb5os
refers to: 1447886_at
t statistic: -9.69369121105803

1454672_at
type: EFO_0005072
part of: A-AFFY-45

1423506_a_at
type: EFO_0005072
part of: A-AFFY-45

Dbx1
type: EnsemblDatabaseReference

A-AFFY-45
type: EFO_0000269

Crmp1 UP in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: IncreasedDifferentialExpressionRatio
fold change: 1.07705161505117
p value: 2.41665902077947E-7
refers to: Crmp1
refers to: 1448289_at
t statistic: 13.6561035159279

Pax6
type: EnsemblDatabaseReference

(Assay) 04_RA_EB
type: Assay
has participant: A-AFFY-45

Arg1
type: EnsemblDatabaseReference

Insm1
type: EnsemblDatabaseReference

Hoxb5os
type: EnsemblDatabaseReference

1422520_at
type: EFO_0005072
part of: A-AFFY-45

Ntn1
type: EnsemblDatabaseReference

Hoxb5os
type: EnsemblDatabaseReference

Stmn2 UP in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: IncreasedDifferentialExpressionRatio
fold change: 1.90254263934706
p value: 6.60065926473362E-10
refers to: 1423281_at
refers to: Stmn2
t statistic: 24.5948967621304

Tubb3
type: EnsemblDatabaseReference

Mus musculus
type: OBI_0100026

Prnp UP in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: IncreasedDifferentialExpressionRatio
fold change: 1.07730962346223
p value: 9.50077048638063E-8
refers to: 1448233_at
refers to: Prnp
t statistic: 14.9687654858596

Elavl4 UP in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: IncreasedDifferentialExpressionRatio
fold change: 1.82597013292944
p value: 1.38399431138927E-8
refers to: Elavl4
refers to: 1450258_a_at
t statistic: 18.0908556776479

1455865_at
type: EFO_0005072
part of: A-AFFY-45

1422284_at
type: EFO_0005072
part of: A-AFFY-45

Slit2
type: EnsemblDatabaseReference

Nkx6-1 UP in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: IncreasedDifferentialExpressionRatio
fold change: 1.91540790802975
p value: 2.47371856456586E-7
refers to: 1425828_at
refers to: Nkx6-1
t statistic: 13.5175277210534

Ndnf
type: EnsemblDatabaseReference

Mllt11
type: EnsemblDatabaseReference

Nkx6-1
type: EnsemblDatabaseReference

Arg1 UP in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: IncreasedDifferentialExpressionRatio
fold change: 1.49331559457371
p value: 1.16504397317017E-7
refers to: 1419549_at
refers to: Arg1
t statistic: 14.6352900596195

Nnat
type: EnsemblDatabaseReference

Rgs4 UP in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: IncreasedDifferentialExpressionRatio
fold change: 2.10358556898196
p value: 8.42901268069328E-9
refers to: 1416286_at
refers to: Rgs4
t statistic: 18.9050815042351

Nkx2-9
type: EnsemblDatabaseReference

1415800_at
type: EFO_0005072
part of: A-AFFY-45

Nkx2-9
type: EnsemblDatabaseReference

1460465_at
type: EFO_0005072
part of: A-AFFY-45

1458140_at
type: EFO_0005072
part of: A-AFFY-45

Olig1
type: EnsemblDatabaseReference

1452894_at
type: EFO_0005072
part of: A-AFFY-45

(Sample) organism/Mus musculus
type: Mus musculus
property type: organism
property value: Mus musculus

Chgb
type: EnsemblDatabaseReference

1423280_at
type: EFO_0005072
part of: A-AFFY-45

Stmn2
type: EnsemblDatabaseReference

Gap43
type: EnsemblDatabaseReference

Foxa2 UP in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: IncreasedDifferentialExpressionRatio
fold change: 1.60872313142729
p value: 6.94105102761163E-8
refers to: 1422833_at
refers to: Foxa2
t statistic: 15.5204607893145

(Assay) 05_RAHh_EB
type: Assay
has participant: A-AFFY-45

Spon1
type: EnsemblDatabaseReference

Tubb3 UP in '500 nanomloar retinoic acid and 1 micromolar Hedgehog agonist' vs '500 nanomolar retinoic acid'
type: IncreasedDifferentialExpressionRatio
fold change: 1.33067948266126
p value: 3.94503077989111E-7
refers to: Tubb3
refers to: 1415978_at
t statistic: 13.0000295855485