WormMine: Gene WBGene00003180

• WormBase Gene ID: WBGene00003180
• Gene Name: med-1
• Sequence Name: T24D3.1
• Brief Description: med-1 encodes a GATA-type transcription factor; med-1 is an immediate target of maternal SKN-1 and, in the early embryo, participates in specifying the mesendoderm; MED-1 functions upstream of the END-1 and END-3 GATA-type transcription factors in endodermal cell fate specification.
• Organism: Caenorhabditis elegans
• Automated Description: Enables sequence-specific DNA binding activity. Involved in endodermal cell fate specification and pharynx development. Located in nucleus. Expressed in several structures, including MSaaaap; MSaapap; MSappp; MSppapa; and MSppapp.
• Biotype: SO:0001217
• Genetic Position: X :7.07152 ±0.012789
• Length (nt): 525

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003180

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:T24D3.1.1	T24D3.1.1	525	X: 12430609-12431133

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:T24D3.1	T24D3.1	525	X: 12430609-12431133

24 RNAi Result

• WBRNAi00049893
• WBRNAi00054050
• WBRNAi00079040
• WBRNAi00019151
• WBRNAi00079038
• WBRNAi00079047
• WBRNAi00079049
• WBRNAi00079066
• WBRNAi00079065
• WBRNAi00079039
• WBRNAi00077701
• WBRNAi00079845
• WBRNAi00098988
• WBRNAi00079052
• WBRNAi00098990
• WBRNAi00098989
• WBRNAi00079053
• WBRNAi00098992
• WBRNAi00079055
• WBRNAi00098991
• WBRNAi00079057
• WBRNAi00079060
• WBRNAi00079059
• WBRNAi00079061

15 Allele

• gk964260
• gk964029
• gk962707
• gk964028
• gk963810
• tm881
• ok3216
• WBVar01787184
• WBVar01571447
• gk661607
• gk849188
• tm10390
• gk604627
• ok804
• otn3757

1 Chromosome

• WormBase ID: X
• Organism: Caenorhabditis elegans
• Length (nt): 17718942

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003180
• Start: 12430609
• End: 12431133
• Strand: 1

4 Data Sets

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

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrX_12431134..12434096
• Length (nt): 2963
• Chromosome Location: X: 12431134-12434096
• Organism: Caenorhabditis elegans

22 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
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
	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
Reduced humidity (98% relative humidity).	Genes that were down-regulated after one day exposure to reduced humidity (98% relative humidity) according to microarray analysis.	Multiple hypothesis testing with the Benjamini-Hochberg correction was applied on calculated p-values. A change in the expression level was considered to be significant if the adjusted p-value was less than 0.001.	WBPaper00044578:reduced-humidity_downregulated_microarray
	Transcripts that showed significantly increased expression in set-2(tm1630) animals at embryo stage, comparing to in N2 animals.	DESeq2 (v2.1.8.3) was used to determine DE genes and to generate principal component and scatter plots. DE genes with FDR < 0.05 were analysed using g:Profiler with Bonferroni correction.	WBPaper00060014:set-2(tm1630)_upregulated
	Genes expressed in N2.	Expressed transcripts were identified on the basis of a Present call in 3 out of 4 N2 experiments as determined by Affymetrix MAS 5.0.	WBPaper00025141:N2_Expressed_Genes
control(maintained under normal lab light (mostly dark, in incubators).) vs UVC-EtBr-exposed(exposed to 7.5 J/m2 UVC radiation 3 times, 24 h apart (48 h total) and exposed to EtBr (5ug/mL in agar).) at just prior to the third UVC dose (48h).	Genes differentially expressed in control vs after UVC exposure and EtBr treatment at the -1h timepoint (just prior to the third UVC dose (48h)).	Transcripts were defined as fold-change >1.2, p < 0.05 based on Rosetta Resolver analysis for all pairwise treatment comparisons. The fold-change refers to the second intensity over the first.	WBPaper00041939:control_vs_UVC-EtBr-exposed_48h
	Genes found to be regulated in daf-16(mgDf50) by resveratrol treatment with p < 0.01.	N.A.	WBPaper00026929:Resveratrol_regulated_daf-16
Bacteria infection: Photorhabdus luminescens	Genes with increased expression after 24 hours of infection by P.lumniescens 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:P.lumniescens_24hr_upregulated_TilingArray
	Transcripts that showed differential expression in dauer N2 vs dauer mir-34(gk437) animals at 20C.	N.A.	WBPaper00050488:N2_vs_mir-34(gk437)_regulated_dauer_20C
	Transcripts that showed significantly decreased expression in mex-1(or286) comparing to in N2 at early embryo when there were only 3 -5 eggs in the adult.	RPKM fold change > 2.	WBPaper00058598:mex-1(or286)_downregulated
	Transcripts that showed significantly decreased expression in ogt-1(ok1474) neuronal cells isolated by FACs comparing to in FACs isolated neuronal cells from wild type.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00066485:ogt-1(ok1474)_downregulated_neuron
	Genome-wide analysis of developmental and sex-regulated gene expression profile.	self-organizing map	cgc4489_group_9
	Genes that showed significantly increased expression level in rsr-2(RNAi) animals comparing to in gfp(RNAi) control.	Fold change > 1.2 or < 0.8.	WBPaper00042477:rsr-2(RNAi)_upregulated_TilingArray
	Transcripts that showed significantly increased expression in natural variant RC301(that showed resistance towards bacteria infection) vs. natural variant DA650, after 4 hour of infection by P. aeruginosa PA14.	Fold change > 2, p-value < 0.05.	WBPaper00050712:RC301_vs_DA650_4h-PA_upregulated
	Transcripts that showed significantly decreased expression in mex-3(eu149) comparing to in N2 at early embryo when there were only 3 -5 eggs in the adult.	RPKM fold change > 2.	WBPaper00058598:mex-3(eu149)_downregulated
	Transcripts that showed significantly increased expression in drh-3(rrr2) comparing to in N2.	edgeR, log2 fold change > 2 or < -2.	WBPaper00053888:drh-3(rrr2)_upregulated
	Transcripts that showed significantly decreased expression in sin-3(tm1276) comparing to in N2.	DESeq2, fold change > 2, p-value < 0.01.	WBPaper00061203:sin-3(tm1276)_downregulated
	Transcripts that showed significantly decreased expression in spr-1(ok2144) comparing to in N2.	DESeq2, fold change > 2, p-value < 0.01.	WBPaper00061203:spr-1(ok2144)_downregulated
	Transcripts that showed significantly increased 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)_upregulated
	Coexpression clique No. 282, srj-21-srh-32, on the genome-wide coexpression clique map for the nematode GPL200 platform.	All available microarray datasets for the GPL200 platform (Affymetrix C. elegans Genome Array) were obtained from the GEO repository. This included 2243 individual microarray experiments. These were normalized against each other with the software RMAexpress (Bolstad, 2014). Based on these normalized values, Pearsons correlation coefficients were obtained for each probe-probe pair of the 22,620 probes represented on this array type. The resulting list of correlation coefficients was then ranked to generate the ranked coexpression database with information on each probe represented on the GPL200 platform.	WBPaper00061527:srj-21-srh-32
	Transcripts that showed significantly increased expression in ASER neuron cells comparing to in whole animal, according to dissected single neuron RNASeq analysis.	Fold change >= 4.	WBPaper00050344:ASER-neuron_enriched
	Single-cell RNA-Seq cell group 92_0 expressed in neuron.	scVI 0.6.0	WBPaper00065841:92_0

10 Expression Patterns

• Primary Identifier: Expr7680
• Remark: Clone: pUL#JS9D4
• Pattern: Expression is seen in the early/mid embryo in many cells. Expression is clearly seen in the embryos within the hermaphrodite. From hatched stages onwards expression is restricted to two nerves of the head. There is also some occasional expression in the posterior intestine of adult nematodes.

• Primary Identifier: Expr883
• Pattern: med-1 expression is first detectable in EMS at the six-cell stage. Thereafter, expression becomes weaker and persists in all EMS daughters until there are 8 E and 20 MS descendants. As transgenes are generally not expressed in the germline, these patterns are likely to reflect zygotic expression of med-1.

• Primary Identifier: Expr4000
• Remark: In the related nematode, C. briggsae, in situ hybridization with a Cb-med-1 probe reveals gonadal as well as embryonic signal in EMS.
• Pattern: Embryonic med transcripts accumulate in the EMS nucleus at the 4-cell stage, become cytoplasmic in MS and E, and are undetectable thereafter. Signal was also observed in the gonads of all adults, with 68% (174/257) showing very strong staining, while very little or no gonadal signal was observed using sense probes. Authors did not detect significant levels of med transcripts in very early embryos or late oocytes.
• Subcellular Localization: Embryonic med transcripts accumulate in the EMS nucleus at the 4-cell stage, become cytoplasmic in MS and E.

• Primary Identifier: Chronogram191
• Remark: Original chronogram file: chronogram.1220.xml
• Reporter Gene: [T24D3.1:gfp] transcriptional fusion.

• Primary Identifier: Expr2013505
• 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: Expr884
• Remark: Data source: S. Robertson and R. Lin, personal communication.
• Pattern: med-1 transcripts are reproducibly detected in 4-cell (EMS stage) embryos by RTPCR and become largely undetectable by the 12-cell stage, after E and MS are born.

• Primary Identifier: Expr3977
• Pattern: Nascent Ce-med-1 mRNA transcripts was detected in the EMS nucleus.
• Subcellular Localization: nucleus

• Primary Identifier: Expr1157591
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1200359
• Pattern: Data from the TransgeneOme project

• Primary Identifier: Expr2031739
• 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).

16 GO Annotation

24 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003180
• Start: 12430609
• End: 12431133
• Strand: 1

16 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 525

1 Sequence Ontology Term

• Name: gene

7 Strains

• WBStrain00022752
• WBStrain00022739
• WBStrain00031641
• WBStrain00035070
• WBStrain00035084
• WBStrain00037381
• WBStrain00001575

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrX_12426631..12430608
• Length (nt): 3978
• Chromosome Location: X: 12426631-12430608
• Organism: Caenorhabditis elegans