Baugh et al 2005, Supplymental Dataset, subclass ETmax_53min

Baugh et al 2005, Supplymental Dataset, class SE

Baugh et al 2005, Supplymental Dataset, subclass MDpd_PC32

Baugh et al 2005, Supplymental Dataset, subclass E_101min

Baugh et al 2005, Supplymental Dataset, subclass ETmax_41min

Baugh et al 2005, Supplymental Dataset, class ME

Baugh et al 2005, Supplymental Dataset, class MDET

Baugh et al 2005, Supplymental Dataset, subclass E_53min

Baugh et al 2005, Supplymental Dataset, subclass SE_186min

Baugh et al 2005, Supplymental Dataset, subclass MDpd_159min

Baugh et al 2005, Supplymental Dataset, subclass MDpd_41min

Baugh et al 2005, Supplymental Dataset, subclass E_425min

Baugh et al 2005, Supplymental Dataset, class MDE

Baugh et al 2005, Supplymental Dataset, subclass E_66min

Baugh et al 2005, Supplymental Dataset, subclass SE_143min

Baugh et al 2005, Supplymental Dataset, subclass ETmax_66min

Baugh et al 2005, Supplymental Dataset, subclass ETmax_143min

Baugh et al 2005, Supplymental Dataset, subclass E_23min

Baugh et al 2005, Supplymental Dataset, subclass E_143min

Baugh et al 2005, Supplymental Dataset, subclass ETmax_101min

Baugh et al 2005, Supplymental Dataset, class M

Baugh et al 2005, Supplymental Dataset, class MD

Baugh et al 2005, Supplymental Dataset, subclass SE_PC32

Baugh et al 2005, Supplymental Dataset, class SET

Baugh et al 2005, Supplymental Dataset, subclass SE_101min

Baugh et al 2005, Supplymental Dataset, class SMD

Baugh et al 2005, Supplymental Dataset, subclass E_41min

Baugh et al 2005, Supplymental Dataset, subclass ETmax_122min

Baugh et al 2005, Supplymental Dataset, class SM

Baugh et al 2005, Supplymental Dataset, subclass SE_41min

Baugh et al 2005, Supplymental Dataset, subclass SE_23min

Baugh et al 2005, Supplymental Dataset, subclass E_122min

Baugh et al 2005, Supplymental Dataset, subclass SE_93min

Baugh et al 2005, Supplymental Dataset, subclass ETmax_23min

Baugh et al 2005, Supplymental Dataset, class E

Baugh et al 2005, Supplymental Dataset, subclass SE_66min

Baugh et al 2005, Supplymental Dataset, class MET

Baugh et al 2005, Supplymental Dataset, subclass ETmax_83min

Baugh et al 2005, Supplymental Dataset, subclass SE_53min

Baugh et al 2005, Supplymental Dataset, subclass E_186min

Baugh et al 2005, Supplymental Dataset, subclass MDpd_53min

Baugh et al 2005, Supplymental Dataset, subclass MD_23min

Baugh et al 2005, Supplymental Dataset, subclass E_31min

Baugh et al 2005, Supplymental Dataset, subclass SE_83min

Baugh et al 2005, Supplymental Dataset, class ET

Baugh et al 2005, T1 PAL-1 target genes

Baugh et al 2005, T3 validated PAL-1 target genes

Baugh et al 2005, Supplymental Dataset, PAL-1 target genes, score 1

Baugh et al 2005, Supplymental Dataset, 308 PAL-1 target genes

Baugh et al 2005, Fig7 and Table4, 14 PAL-1 target genes that likely involved in patterning

Baugh et al 2005, Supplymental Dataset, PAL-1 target genes, score 5, 6, 7

Baugh et al 2005, Supplymental Dataset, PAL-1 target genes, score 2,3,4

Bishop et al 2004 Table2: 6 Egl-9 hif-1 pathway genes

Bishop et al 2004 Table4: 57 vhl-1 depend hif-1 independent genes

Bishop et al 2004 Table1: 30 genes Upregulated in vhl-1 vs WT

Blacque et al 2005 ST2 SAGE tag data for 42 genes known to be expressed in most ciliated cells (e.g., IFT-related genes) or in a subset of ciliated cells (e.g., tax-1, guanylate cyclases, receptors, and channels).

Blacque et al 2005 ST3 Putative X Box Sequences Used to Derive a Consensus X Box Sequence: Only genes with a restricted expression pattern in many, if not all, ciliated cells of C. elegans were considered.

Blacque et al 2005 S42 Full List of Putative X-Box-Containing Genes: Genes are ranked by X box score (homology to the consensus X box sequence). Only X boxes with scores >10.0 and within 1500 bp upstream of the gene start codons are included. Note also that only those genes with significant homology to a human gene are shown (Blast E-value < e.10).

Blacque et al 2005 T1 Shown are all genes (46 in total) that are enriched for SAGE tags in the ciliated-cell transcriptome (C), with R1.5-fold enrichment versus the pan-neural transcriptome (P) and R2.0-fold enrichment versus the muscle (M) and gut (G) transcriptomes, and with a canonically-positioned (Pos) putative X box (i.e., within 250 bp of the start codon). Only genes with homology to a human gene (Blast E-value < e?10) are represented.

Operon gene pairs with confirmed spacing

A supplimentary table showing the disease gene operons organized by disease with a short description of each gene

genes confirmed to be transpliced to SL2/SL12 from cDNA clone analysis, from the worm transcriptome project, lead by Y.Kohara.

Operons containing human disease gone orthologues, an expandedlist can be found in Blumenthal2002_suppDGO.txt, the Disease Gene Orthologue supplimentary file

Chen et al 2006 S2 X-box regulated genes

Chen et al 2006 C. elegans genes that contain X-box motifs in their promoters, are positively correlated with daf-19 in gene expression, and have reduced expression in daf-19(-) strains

Chi et al 2006 Summplement Table, 43 genes commonly down-regulated in all three mutants.

Chi et al 2006 Supplemental Table: lin-35/elf-1/dpl-1 regulated genes that not in group.

Chi et al 2006 Supplemental Table 42 genes variably up-regulated in all three mutants.

Chi et al 2006 Supplemental Table: 75 genes down-regulated in elf-1;dpl-1 mutant.

Chi et al 2006 Supplemental Table 88 genes up-regulated in lin-35 mutant.

Custodia et al 2001 Table2: Metallothionein

Custodia et al 2001 Table2: Glut-S-transferase

Custodia et al 2001 Table2: Yolk proteins

Custodia et al 2001 Table2: heat shock

Custodia et al 2001 Table2: Cytochrome P450

Denver et al 2005 Supplement Table 2: 123 genes that differentially expressed in NI(Natual Isolate) lines.

Denver et al 2005 Supplement Table 1: 662 genes that differentially expressed in MA(Mutation Accumulation) lines.

Dybbs2005 et al 2005, reduced expression in tom-1(nu468) compared with wt (fold-change <-0.5, p<0.01)

Dybbs2005 et al 2005, Supplymental Table1,List of Missense and Nonsense Alleles

Dybbs2005 et al 2005, Fig3, reduced expression in unc-43(n1186) compared with wt (fold-change <-0.5, p<0.01)

Fox et al 2005 Additional File 14/Table2: Summary of unc-4::GFP enriched and expressed (EGs) transcripts in selected categories. This file is an expanded version of Table 2 (see text) in which EGs are added to the list of enriched genes. Genes are organized as in Table 2 according to molecular function (KOG description, other description http://www.wormbase.org). Statistical rank is indicated for each enriched transcript and "EG" designates transcripts that are EGs.

Fox et al 2005 Additional File 14/Table2: Summary of unc-4::GFP enriched and expressed (EGs) transcripts in selected categories. This file is an expanded version of Table 2 (see text) in which EGs are added to the list of enriched genes. Genes are organized as in Table 2 according to molecular function (KOG description, other description http://www.wormbase.org). Statistical rank is indicated for each enriched transcript and "EG" designates transcripts that are EGs.

Fox et al 2005 Additional File 11: Genes previously known to be expressed in unc-4::GFP neurons. Published literature and wormbase http://www.wormbase.org were searched to identify 27 genes that are expressed in embryonic neurons that also express unc-4::GFP (I5, DA, SAB).

Fox et al 2005 Additional File 14/Table2: Summary of unc-4::GFP enriched and expressed (EGs) transcripts in selected categories. This file is an expanded version of Table 2 (see text) in which EGs are added to the list of enriched genes. Genes are organized as in Table 2 according to molecular function (KOG description, other description http://www.wormbase.org). Statistical rank is indicated for each enriched transcript and "EG" designates transcripts that are EGs.

Fox et al 2005 Additional File 10: genes are enriched 1.7fold (FDR .1%) in N2 cells compared to unc-4::GFP neurons.

Fox et al 2005 Additional File 14/Table2: Summary of unc-4::GFP enriched and expressed (EGs) transcripts in selected categories. This file is an expanded version of Table 2 (see text) in which EGs are added to the list of enriched genes. Genes are organized as in Table 2 according to molecular function (KOG description, other description http://www.wormbase.org). Statistical rank is indicated for each enriched transcript and "EG" designates transcripts that are EGs.

Fox et al 2005 Additional File 14/Table2: Summary of unc-4::GFP enriched and expressed (EGs) transcripts in selected categories. This file is an expanded version of Table 2 (see text) in which EGs are added to the list of enriched genes. Genes are organized as in Table 2 according to molecular function (KOG description, other description http://www.wormbase.org). Statistical rank is indicated for each enriched transcript and "EG" designates transcripts that are EGs.

Fox et al 2005 Additional File 14/Table2: Summary of unc-4::GFP enriched and expressed (EGs) transcripts in selected categories. This file is an expanded version of Table 2 (see text) in which EGs are added to the list of enriched genes. Genes are organized as in Table 2 according to molecular function (KOG description, other description http://www.wormbase.org). Statistical rank is indicated for each enriched transcript and "EG" designates transcripts that are EGs.

Fox et al 2005 Additional File 15: Genes Expressed only in unc-4::GFP neurons.

Fox et al 2005 Additional File 14/Table2: Summary of unc-4::GFP enriched and expressed (EGs) transcripts in selected categories. This file is an expanded version of Table 2 (see text) in which EGs are added to the list of enriched genes. Genes are organized as in Table 2 according to molecular function (KOG description, other description http://www.wormbase.org). Statistical rank is indicated for each enriched transcript and "EG" designates transcripts that are EGs.

Fox et al 2005 Additional File 14/Table2: Summary of unc-4::GFP enriched and expressed (EGs) transcripts in selected categories. This file is an expanded version of Table 2 (see text) in which EGs are added to the list of enriched genes. Genes are organized as in Table 2 according to molecular function (KOG description, other description http://www.wormbase.org). Statistical rank is indicated for each enriched transcript and "EG" designates transcripts that are EGs.

Fox et al 2005 Additional File 14/Table2: Summary of unc-4::GFP enriched and expressed (EGs) transcripts in selected categories. This file is an expanded version of Table 2 (see text) in which EGs are added to the list of enriched genes. Genes are organized as in Table 2 according to molecular function (KOG description, other description http://www.wormbase.org). Statistical rank is indicated for each enriched transcript and "EG" designates transcripts that are EGs.

Fox et al 2005 Additional File 14/Table2: Summary of unc-4::GFP enriched and expressed (EGs) transcripts in selected categories. This file is an expanded version of Table 2 (see text) in which EGs are added to the list of enriched genes. Genes are organized as in Table 2 according to molecular function (KOG description, other description http://www.wormbase.org). Statistical rank is indicated for each enriched transcript and "EG" designates transcripts that are EGs.

Fox et al 2005 Additional File 14/Table2: Summary of unc-4::GFP enriched and expressed (EGs) transcripts in selected categories. This file is an expanded version of Table 2 (see text) in which EGs are added to the list of enriched genes. Genes are organized as in Table 2 according to molecular function (KOG description, other description http://www.wormbase.org). Statistical rank is indicated for each enriched transcript and "EG" designates transcripts that are EGs.

Fox et al 2005 Additional File 14/Table2: Summary of unc-4::GFP enriched and expressed (EGs) transcripts in selected categories. This file is an expanded version of Table 2 (see text) in which EGs are added to the list of enriched genes. Genes are organized as in Table 2 according to molecular function (KOG description, other description http://www.wormbase.org). Statistical rank is indicated for each enriched transcript and "EG" designates transcripts that are EGs.

Fox et al 2005 Additional File 14/Table2: Summary of unc-4::GFP enriched and expressed (EGs) transcripts in selected categories. This file is an expanded version of Table 2 (see text) in which EGs are added to the list of enriched genes. Genes are organized as in Table 2 according to molecular function (KOG description, other description http://www.wormbase.org). Statistical rank is indicated for each enriched transcript and "EG" designates transcripts that are EGs.

Fox et al 2005 Supplement6: 1012 unc-4::GFP Enriched Genes Transcripts elevated 1.7 fold above baseline at a FDR .1%.

Fox et al 2005 Additional File 14/Table2: Summary of unc-4::GFP enriched and expressed (EGs) transcripts in selected categories. This file is an expanded version of Table 2 (see text) in which EGs are added to the list of enriched genes. Genes are organized as in Table 2 according to molecular function (KOG description, other description http://www.wormbase.org). Statistical rank is indicated for each enriched transcript and "EG" designates transcripts that are EGs.

Fox et al 2005 Additional File 14/Table2: Summary of unc-4::GFP enriched and expressed (EGs) transcripts in selected categories. This file is an expanded version of Table 2 (see text) in which EGs are added to the list of enriched genes. Genes are organized as in Table 2 according to molecular function (KOG description, other description http://www.wormbase.org). Statistical rank is indicated for each enriched transcript and "EG" designates transcripts that are EGs.

Fox et al 2005 Additional File 14/Table2: Summary of unc-4::GFP enriched and expressed (EGs) transcripts in selected categories. This file is an expanded version of Table 2 (see text) in which EGs are added to the list of enriched genes. Genes are organized as in Table 2 according to molecular function (KOG description, other description http://www.wormbase.org). Statistical rank is indicated for each enriched transcript and "EG" designates transcripts that are EGs.

Fox et al 2005 Additional File 14/Table2: Summary of unc-4::GFP enriched and expressed (EGs) transcripts in selected categories. This file is an expanded version of Table 2 (see text) in which EGs are added to the list of enriched genes. Genes are organized as in Table 2 according to molecular function (KOG description, other description http://www.wormbase.org). Statistical rank is indicated for each enriched transcript and "EG" designates transcripts that are EGs.

Fox et al 2005 Additional File 14/Table2: Summary of unc-4::GFP enriched and expressed (EGs) transcripts in selected categories. This file is an expanded version of Table 2 (see text) in which EGs are added to the list of enriched genes. Genes are organized as in Table 2 according to molecular function (KOG description, other description http://www.wormbase.org). Statistical rank is indicated for each enriched transcript and "EG" designates transcripts that are EGs.

Fox et al 2005 Additional File 14/Table2: Summary of unc-4::GFP enriched and expressed (EGs) transcripts in selected categories. This file is an expanded version of Table 2 (see text) in which EGs are added to the list of enriched genes. Genes are organized as in Table 2 according to molecular function (KOG description, other description http://www.wormbase.org). Statistical rank is indicated for each enriched transcript and "EG" designates transcripts that are EGs.

Fox et al 2005 Additional File 14/Table2: Summary of unc-4::GFP enriched and expressed (EGs) transcripts in selected categories. This file is an expanded version of Table 2 (see text) in which EGs are added to the list of enriched genes. Genes are organized as in Table 2 according to molecular function (KOG description, other description http://www.wormbase.org). Statistical rank is indicated for each enriched transcript and "EG" designates transcripts that are EGs.

Fox et al 2005 Additional File 14/Table2: Summary of unc-4::GFP enriched and expressed (EGs) transcripts in selected categories. This file is an expanded version of Table 2 (see text) in which EGs are added to the list of enriched genes. Genes are organized as in Table 2 according to molecular function (KOG description, other description http://www.wormbase.org). Statistical rank is indicated for each enriched transcript and "EG" designates transcripts that are EGs.

Fox et al 2005 Additional File 14/Table2: Summary of unc-4::GFP enriched and expressed (EGs) transcripts in selected categories. This file is an expanded version of Table 2 (see text) in which EGs are added to the list of enriched genes. Genes are organized as in Table 2 according to