WormMine: Gene WBGene00000584

• WormBase Gene ID: WBGene00000584
• Gene Name: cog-1
• Sequence Name: R03C1.3
• Brief Description: cog-1 encodes the C. elegans ortholog of the vertebrate Nkx6 homeodomain proteins; cog-1 activity is required for multiple aspects of reproductive system development, including connection of uterus to the vulva and vulval cell specification, as well as for specification of left/right asymmetry in the ASE taste receptor sensory neurons where cog-1 acts in ASER to suppress the ASEL cell fate; cog-1 expression in ASEL is negatively regulated by the lsy-6 miRNA; a cog-1::gfp reporter fusion is expressed in neurons and in the hermaphrodite vulva and uterus; in males, cog-1::gfp expression is seen in proctodeal cells and occasionally in the rectal Rep cells and P11.pp progeny.
• Organism: Caenorhabditis elegans
• Automated Description: Enables DNA-binding transcription factor binding activity. Involved in several processes, including determination of left/right symmetry; neuron development involved in amphid sensory organ development; and regulation of gene expression. Predicted to be located in nucleus. Expressed in several structures, including body ganglion; egg-laying apparatus; head neurons; male-specific anatomical entity; and tail ganglion. Human ortholog(s) of this gene implicated in spastic ataxia 8. Is an ortholog of human NKX6-1 (NK6 homeobox 1) and NKX6-2 (NK6 homeobox 2).
• Biotype: SO:0001217
• Genetic Position: II :23.6958 ±0.059369
• Length (nt): 5041

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00000584

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:R03C1.3a.1	R03C1.3a.1	1191	II: 14902493-14907533
Transcript:R03C1.3b.1	R03C1.3b.1	836	II: 14903130-14907515

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:R03C1.3b	R03C1.3b	321	II: 14904810-14905001
CDS:R03C1.3a	R03C1.3a	771	II: 14902519-14902830

6 RNAi Result

• WBRNAi00107689
• WBRNAi00001218
• WBRNAi00051169
• WBRNAi00062927
• WBRNAi00017345
• WBRNAi00034550

136 Allele

• gk963801
• gk963053
• WBVar01321302
• WBVar01321303
• WBVar01321305
• WBVar01321307
• WBVar01321292
• WBVar01321294
• WBVar01321298
• gk962684
• gk963297
• WBVar00245753
• WBVar02068545
• sy275
• WBVar01696627
• WBVar01696628
• sy607
• WBVar01267995
• WBVar01268006
• WBVar01268017
• WBVar01548161
• WBVar01548160
• WBVar01548163
• WBVar01548162
• WBVar00001786
• WBVar01442619
• WBVar01442622
• WBVar01442620
• WBVar01253951
• WBVar01253950

1 Chromosome

• WormBase ID: II
• Organism: Caenorhabditis elegans
• Length (nt): 15279421

1 Chromosome Location

• Feature . Primary Identifier: WBGene00000584
• Start: 14902493
• End: 14907533
• Strand: 1

4 Data Sets

• WormBaseAcedbConverter
• GO Annotation data set
• C. elegans genomic annotations (GFF3 Gene)
• Panther orthologue and paralogue predictions

0 Downstream Intergenic Region

134 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly increased expression in L1 neural cells comparing to in adult neural cells.	DESeq2 (v1.18.1) fold change > 2, P-adj<0.05, using BenjaminiHochberg correction.	WBPaper00060811:L1_vs_adult_upregulated_neural
	Transcripts expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons.	DESeq. False discovry rate (FDR) < 0.1.	WBPaper00048988:neuron_expressed
adult vs dauer larva	Transcripts that showed differential expression in adult vs dauer lava in N2 animals at 20C.	N.A.	WBPaper00050488:adult_vs_dauer_regulated_N2_20C
	mRNAs that showed decreased expression in 1 cell mebryo comparing to in oocyte, according to RNAseq analysis.	Gaussian error propagation. As cutoff for the up-regulated genes authors used log2 fold change > 1 and P < 0.05 and as cutoff for the down-regulated genes authors used log2 fold change < -1 and P < 0.05.	WBPaper00045420:fertilization_downregulated_transcript
	Neuronally enriched transcripts according to a comparison of neuronal nuclei IP samples to total nuclei using isolation of nuclei from tagged specific cell types (INTACT) technology.	DESEQ2, fold change > 2 and FDR < 0.01.	WBPaper00062103:neuron_enriched
Bacteria infection: Enterococcus faecalis	Genes with increased expression after 24 hours of infection by E.faecalis Fold changes shown are pathogen vs OP50.	For RNA-seq and tiling arrays, log2 fold changes between gene expression values of infected versus uninfected nematodes were calculated. For log2 fold changes > 0.00001 the values > 81.25th percentile were defined as up-regulated and for log2 fold changes < -0.00001 the values < 18.75th percentile were defined as down-regulated.	WBPaper00038438:E.faecalis_24hr_upregulated_TilingArray
	Transcripts that showed significantly higher expression in somatic gonad precursor cells (SGP) vs. head mesodermal cells (hmc).	DESeq2, fold change >= 2, FDR <= 0.01.	WBPaper00056826:SGP_biased
	Transcripts expressed in the epithelial tissues surrounding the pharynx that includes the arcade and intestinal valve (AIV) cells, according to PAT-Seq analysis using Pbath-15-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:arcade_intestinal-valve_expressed
	Transcripts expressed in GABAergic neuron, according to PAT-Seq analysis using Punc-47-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:GABAergic-neuron_expressed
	Transcripts expressed in hypodermis, according to PAT-Seq analysis using Pdpy-7-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:hypodermis_expressed
	Transcripts expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:intestine_expressed
	Transcripts expressed in NMDA neuron, according to PAT-Seq analysis using Pnmr-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:NMDA-neuron_expressed
	Transcripts that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_downregulated_glp-1(e2141)
	Transcripts that showed significantly increased expression after four-day-old young adult worms were placed on NGM plates seeded with OP50 in the presence 5% Agaro-oligosaccharides(AGO) for 24 h, comparing to animals grown in the absence of AGO.	Fold change > 2.	WBPaper00064306:Agaro-oligosaccharides_upregulated
	Transcripts that showed significantly increased expression in sin-3(tm1276) comparing to in N2.	DESeq2, fold change > 2, p-value < 0.01.	WBPaper00061203:sin-3(tm1276)_upregulated
Bacteria infection: Staphylococcus aureus MW2. 4 hours of exposure.	Transcripts that showed significantly increased expression after N2 animals had 4 hours of infection by Staphylococcus aureus (MW2).	DEseq 1.18.0, adjusted p-value < 0.05.	WBPaper00056471:S.aureus-4h_upregulated_N2
	Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_regulated
	Transcripts that showed significantly decreased expression in sin-3(tm1276) comparing to in N2 at early embryo when there were only 3 -5 eggs in the adult.	DESeq2, fold change > 2, adjusted p-value < 0.01	WBPaper00058598:sin-3(tm1276)_downregulated
Gamma irradiation 100 mGY per hour for 72 hours since L1 larva.	Transcripts that showed significantly increased expression after exposure to 100mGy per hour gamma irradiation from L1 to day 1 adult hermaphrodite stage.	DESeq2, FDR <= 0.05, log2 fold change >= 0.3 or <= -0.3.	WBPaper00058958:100mGy-irradiation-72h_upregulated
	Genes that showed expression levels higher than the corresponding reference sample (L2 all cell reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:A-class-motor-neurons_L2-larva_expressed
	Transcripts that showed significantly increased expression in hda-1(ne4752[3xFLAG-Degron-HDA-1]) in gonads dissected from 1-day old adult animals.	Salmon was used to map the mRNA-seq reads with the worm database WS268, and its output files were imported to DESeq2 in R. The differentially expressed genes were filtered by fold change more than 2 and adjusted p-value < 0.05. The scatter plots were generated by the plot function in R.	WBPaper00061479:hda-1(ne4752)_upregulated
	Genes that showed expression levels higher than the corresponding reference sample (L2 all cell reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:glr-1(+)-neurons_L2-larva_expressed
	Transcripts that showed significantly increased expression in hda-2(ok1479) comparing to in N2 animals.	DESeq2 (version 1.28.1), FDR < 0.01, fold change > 2.	WBPaper00062159:hda-2(ok1479)_upregulated
	Transcripts that showed significantly increased expression in srbc-48(ac23);kyIs262;fer-1(b232ts) comparing to in kyIs262;fer-1(b232ts), 24h after infection with P.aeruginosa.	DESeq2, FDR <0.05, fold change > 2.	WBPaper00059664:srbc-48(ac23)_upregulated
	Transcripts that showed significantly decreased expression after animals were treated with 100uM Psora and 250uM Allantoin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Psora-Allantoin_downregulated
	Transcripts that showed significantly decreased expression after animals were treated with 100uM Psora from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Psora_downregulated
	Transcripts that showed significantly decreased expression after animals were treated with 100uM Rapamycin and 250uM Allantoin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rapamycin-Allantoin_downregulated
	Transcripts that showed significantly decreased expression after animals were treated with 100uM Rapamycin and 50mM Metformin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rapamycin-Metformin_downregulated
	Transcripts that showed significantly decreased expression after animals were treated with 50uM Rifampicin and 250uM Allantoin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rifampicin-Allantoin_downregulated
	Transcripts that showed significantly decreased expression after animals were treated with 50uM Rifampicin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rifampicin_downregulated

15 Expression Patterns

• Primary Identifier: Marker97
• Remark: Picture: Fig 2A.
• Pattern: Marker for ASER neuron.

• Primary Identifier: Expr1030344
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr2276
• Pattern: Neuronal expression. In the L1 stage cog-1::gfp is expressed in amphid neurons ADL(L/R), ASE(L/R), and ASJ(L/R). One additional pair of head neurons expresses cog-1::gfp in the L1. This pair is located between the excretory cell and the excretory pore, and is probably either AIA(L/R), SMBD(L/R), SIAD(L/R), or SIAV(L/R). In the tail, phasmid neurons PHB(L/R) express cog-1::gfp. The expression in amphid and phasmid neurons persists to the adult. Additional unidentified cells in the preanal ganglion express cog-1::gfp in late larvae and adults. Other cells in the tail region. The sphincter muscle (mu_sph) and phasmid sheath cells (PHshL, PHshR) express cog-1::gfp in all stages examined. Uterine expression. In the hermaphrodite gonad, cog-1::gfp is expressed exclusively in the dorsal uterine lineage. During the L3 stage, GFP is in the central four great-granddaughters of DU cells (DE4/DE5; DE, dorsal eight). The expression apparently persists in DE4/DE5 descendants, du, uv2, and uv3, until the adult stage, DE2 and DE7 lineages in the dorsal uterus also express cog-1::gfp starting from the early L4 stage. In the late L4, cog-1::gfp in this region is observed exclusively in sujc cells. Each core is surrounded by the spermathecaluterine valve and appears to form a plug which blocks the uterine lumen from the spermathecal lumen. None of the cog-1::gfp fusions, including the rescuing construct, was ever observed to express in any ventral uterine cells, including the anchor cell. Thus, the function of cog-1 in the connection is believed to be a consequence of abnormal gene regulation in the vulva, although a function in the dorsal uterine cells have not been ruled out. Vulval expression. In the vulva, cog-1::gfp is expressed from early L4 to the adult. Cells that express are vulC [P5.ppa(l/r), P7.pap(l/r)], vulD (P5.ppp, P7.paa), vulE(P6.pppl, P6.pppr, P6.paal, P6.paar), and vulF (P6.ppal, P6.ppar, P6.papl, P6.papr). The expression is considerably brighter in vulC and vulD than in vulE and vulF. Occasionally, expression in vulB and vulA was observed. Male expression. The expression of cog-1::gfp in the male was scored mostly in animals containing an extrachromosomal array containing the SmaI insertion. cog-1::gfp is expressed during proctodeal development. eL.aav and eR.aav express cog-1. In addition, proctodeal cells B.pap and B.pppa express cog-1::gfp. Additional expressing cells observed in occasional males include: rep, and P11.pp progeny. No gonadal cells in the male, including the linker cell, expressed cog-1::gfp in any stage of development.

• Primary Identifier: Expr15616

• Primary Identifier: Expr10660
• Pattern: cog-1::yfp is expressed in ASER from the 3- fold stage of embryogenesis.

• Primary Identifier: Expr12793
• Pattern: A fusion of 6 kb of sequences upstream of the cog-1 start codon to gfp shows expression in the sites previously reported to express cog-1, namely vulval cells and head neurons, including ASER.

• Primary Identifier: Expr14269
• Pattern: cog-1::GFP is expressed in the wild type dorsal uterus and Sp-Ut valve core, beginning from late-L3/early-L4 stage. cog-1::GFP was expressed in somatic gonadal tissues prior to the vulva in wild-type animals. cog-1::GFP is also expressed in the ventral hypodermis (vulval cell lineages) beginning in the mid L4 stage, which is after the onset of cog-1::GFP somatic gonadal expression.

• Primary Identifier: Marker114
• Pattern: Marker for PDA cell.

• Primary Identifier: Expr15875
• Pattern: cog-1::gfp transgene (PS3662 strain) localizes GFP expression to the PDA neuron.

• Primary Identifier: Expr2010289
• Pattern: Single cell embryonic expression. Only cell types with an expression fraction of greater 0.2 of the maximum expressed fraction are labeled (Full data can be downloaded from http://caltech.wormbase.org/pub/wormbase/datasets-published/packer2019/). The colors represent the broad cell class to which the cell type has been assigned. The size of the point is proportional to the log2 of the numbers of cells in the dataset of that cell type. Interactive visualizations are available as a web app (https://cello.shinyapps.io/celegans/) and can also be installed as an R package (https://github.com/qinzhu/VisCello.celegans).

• Primary Identifier: Expr16254
• Pattern: cog-1 is expressed in uterine and vulval cells.

• Primary Identifier: Expr1018090
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2028531
• Pattern: Single cell embryonic expression. Only cell types with an expression fraction of greater 0.2 of the maximum expressed fraction are labeled (Full data can be downloaded from http://caltech.wormbase.org/pub/wormbase/datasets-published/packer2019/). The colors represent the broad cell class to which the cell type has been assigned. The size of the point is proportional to the log2 of the numbers of cells in the dataset of that cell type. Interactive visualizations are available as a web app (https://cello.shinyapps.io/celegans/) and can also be installed as an R package (https://github.com/qinzhu/VisCello.celegans).

• Primary Identifier: Expr1154876
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1170047
• Pattern: Time-lapse fluorescence microscopy was performed, including DIC for morphology. Gene expression patterns were summarized in 4 manners: Average over time, Average over time and at different positions along the anterior-posterior (AP) axis, a voxelized representation over time, and on individual cells overlaid from a reference coordinate dataset (https://doi.org/10.1016/j.ydbio.2009.06.014). The analysis was done with a pipeline based on the multi-purpose image analysis software Endrov (https://doi.org/10.1038/nmeth.2478), which further is needed to browse the raw recording data. Thumbnail movies were also generated, using maximum Z projection for the 3D fluorescence channel. Raw recordings available in the Endrov OST-file format are available at https://www.ebi.ac.uk/biostudies/studies/S-BIAD191?query=S-BIAD191

20 GO Annotation

11 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00000584
• Start: 14902493
• End: 14907533
• Strand: 1

20 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 5041

1 Sequence Ontology Term

• Name: gene

15 Strains

• WBStrain00029285
• WBStrain00029298
• WBStrain00029435
• WBStrain00029387
• WBStrain00029369
• WBStrain00029374
• WBStrain00029370
• WBStrain00029386
• WBStrain00030960
• WBStrain00030961
• WBStrain00030904
• WBStrain00030905
• WBStrain00030922
• WBStrain00030864
• WBStrain00030887

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrII_14898232..14902492
• Length (nt): 4261
• Chromosome Location: II: 14898232-14902492
• Organism: Caenorhabditis elegans