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[188348_at]

Description F36A4.14 /REP_DB=WormBase Gene ID /WP=CE07187 /GEN=nhr-78 /TR=Q20097 /GB=AAA96165.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 76      6grp_high1_10_10 > 76      4grp_high_8_8 > 06      6grp_highest_nonorm > 90      6grp_total > 67      4grp_total > 02      6grp_highest_sub > Da      6grp_cgc > 38      6grp_high1_sub > Da      6grp_cgc_sub > Da      6grp_total_sub > Increase      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 950
1 2 3 4 range
A 95.7
(-3)
P 		144.8
(-2.7)
P 		113.4
(-2.9)
A 		1007.5
(3)
P 		912
B 154.6
(-2.7)
P 		114.5
(-3)
P 		126.6
(-2.9)
P 		1016
(3)
P 		902
C 119.7
(-2.6)
P 		65.8
(-3)
A 		127.9
(-2.5)
P 		883.9
(3)
P 		818
avr 123.3
(-2.9) 		108.4
(-3) 		122.6
(-2.9) 		969.1
(3) 		861

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 148
1 2 3 4 5 6 range
A 153.4
(-1)
P 		118.7
(-3)
P 		120.3
(-2.9)
P 		151.1
(-1.2)
P 		143.7
(-1.6)
P 		225.2
(3)
P 		107
B 122.5
(-1.9)
P 		161.3
(0.3)
P 		122.7
(-1.9)
P 		103.5
(-3)
P 		122.4
(-1.9)
P 		207.4
(3)
P 		104
C 97.7
(-2.1)
P 		123.1
(-0.9)
P 		132.4
(-0.5)
P 		88
(-2.5)
P 		77.5
(-3)
P 		210.3
(3)
P 		133
avr 124.5
(-2.4) 		134.4
(-1.8) 		125.1
(-2.3) 		114.2
(-3) 		114.5
(-3) 		214.3
(3) 		100
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 198
1 2 3 4 range
A 34.8
(-2.7)
P 		31.4
(-2.9)
P 		29.6
(-3)
A 		147.5
(3)
P 		118
B 49.3
(-2.3)
P 		28.3
(-3)
P 		29.3
(-3)
P 		216.5
(3)
P 		188
C 39.6
(-2)
P 		18.9
(-3)
A 		44.6
(-1.8)
P 		149
(3)
P 		130
avr 41.2
(-2.4) 		26.2
(-3) 		34.5
(-2.7) 		171
(3) 		145

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 60
1 2 3 4 5 6 range
A 28.3
(-2.6)
P 		42.2
(0.4)
P 		26.2
(-3)
P 		38.3
(-0.5)
P 		43.4
(0.6)
P 		54.8
(3)
P 		29
B 42.6
(-1.2)
P 		53.7
(0.2)
P 		29.8
(-2.7)
P 		27.4
(-3)
P 		49.7
(-0.3)
P 		77.3
(3)
P 		50
C 36.2
(-0.9)
P 		37.6
(-0.7)
P 		33.7
(-1.2)
P 		17.7
(-3)
P 		25.1
(-2.2)
P 		70.4
(3)
P 		53
avr 35.7
(-1.8) 		44.5
(-0.5) 		29.9
(-2.7) 		27.8
(-3) 		39.4
(-1.2) 		67.5
(3) 		40
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188348_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.10573
Sequence Type Exemplar sequence
Representative Public ID F36A4.14 NCBI
Target Description F36A4.14 /REP_DB=WormBase Gene ID /WP=CE07187 /GEN=nhr-78 /TR=Q20097 /GB=AAA96165.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation
Annotation Method Description
Annotation Description This probe set was annotated using the Matching Probes based pipeline to a RefSeq identifier using 1 transcript(s).
Annotation Grade This is a grade A annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_068129(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_068129 NCBI Caenorhabditis elegans Nuclear Hormone Receptor family member (nhr-78) (nhr-78) mRNA, complete cds. 11/11 None
SNAP00000033272 ENSEMBL cdna:SNAP chromosome:CEL140:IV:4274386:4277704:-1 10/11 None
GENEFINDER00000033281 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:4275107:4277704:-1 10/11 None
F36A4.14 ENSEMBL cdna:known chromosome:CEL140:IV:4275178:4277704:-1 gene:F36A4.14 11/11 None
Annotation Notes
There are no noteworthy cross hybridizing mRNAs found for this probe set.
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIV:4275183-4277710(-) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol nhr-78
Ensembl F36A4.14
Entrez Gene 191727 Entrez gene
SwissProt Q20097 EMBL-EBI
WormBase CE07187 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6355 regulation of transcription, DNA-dependent inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5634 nucleus inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3700 transcription factor activity inferred from electronic annotation QuickGO AmiGO
3707 steroid hormone receptor activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAA96165 Nuclear hormone receptor family protein 78 [Caenorhabditis elegans] ref|NP_500530.1| Nuclear Hormone Receptor family member (nhr-78) [Caenorhabditis elegans] 0.0
blast CAE61470 Hypothetical protein CBG05363 [Caenorhabditis briggsae] 1.0E-167
blast CAE61470 Hypothetical protein CBG05363 [Caenorhabditis briggsae] 1.0E-153
blast CAE61470 Hypothetical protein CBG05363 [Caenorhabditis briggsae] 1.0E-119
blast AAA96165 Nuclear hormone receptor family protein 78 [Caenorhabditis elegans] ref|NP_500530.1| Nuclear Hormone Receptor family member (nhr-78) [Caenorhabditis elegans] 1.0E-114
blast AAD03686 nuclear receptor NHR-13 [Caenorhabditis elegans] 7.0E-51
Protein Domains
Database ID Description E-Value
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 3.3E-18
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 5.5E-16
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 1.7E-20
Pfam IPR000536 EMBL-EBI Ligand-binding domain of nuclear hormone receptor 3.3E-18
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 1.1E-8
Sequence
Target Sequence 
>C. ELEGANS:188348_AT
tcaactatgcgaacacgctacccggcttccaagaactctcgaatgctagtcagaactttt
tattccgaatcgcttgtggtgtggattacgtgattagcagctcttattacacattgtgca
ttggtaccgaaagcaatttgctaattaatcaagatggtacctatatccaaatgatgcccc
ttcctctgatgggtgatgaacccggtactgagctaatgttcaccaggaaagaagagctgg
aaaagtaccggaacatcataaaaccccgtgtcaattcctggcttgagtttatcccgttgt
tcaagtccctggagttgagcttcgaagagaatgctattctaaaagcactgtgttgctggc
aaactgctcattttaagctggaagagtgtgataaggagaatgttagaaagcaaaagtctc
tattggttcaatgtctgttaaagttttgcatcgatacatatggagaggaagaggggcctg
cgagggctggaaatatcatcttgttctcttcgtctatcagtgtgagt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCAACTATGCGAACACGCTACCCGG 650 629 587 Antisense
CGGCTTCCAAGAACTCTCGAATGCT 226 243 609 Antisense
GGATTACGTGATTAGCAGCTCTTAT 566 509 669 Antisense
ACCTATATCCAAATGATGCCCCTTC 635 85 745 Antisense
TGCCCCTTCCTCTGATGGGTGATGA 587 583 761 Antisense
GATGAACCCGGTACTGAGCTAATGT 278 409 781 Antisense
CATAAAACCCCGTGTCAATTCCTGG 376 9 843 Antisense
ATTCCTGGCTTGAGTTTATCCCGTT 594 5 860 Antisense
AGTCCCTGGAGTTGAGCTTCGAAGA 104 61 890 Antisense
GTTGCTGGCAAACTGCTCATTTTAA 353 439 938 Antisense
GTTCTCTTCGTCTATCAGTGTGAGT 589 443 1089 Antisense
Sequence Source Affymetrix Proprietary Database