WormMine: Gene WBGene00001820

• WormBase Gene ID: WBGene00001820
• Gene Name: ham-1
• Sequence Name: F53B2.6
• Brief Description: ham-1 encodes a novel protein with a winged helix DNA-binding motif; ham-1 is required for the asymmetric divisions of several neuroblasts in the developing embryo and may influence their spindle position; ham-1 mutations also exhibit HSN motor neuron migration defects; HAM-1 interacts with itself in a yeast two-hybrid screen and observations suggest that its multimerization is required for its proper localization; HAM-1 is cytoplasmic and is asymmetrically distributed to the posterior of the HSNPHB neuroblast.
• Organism: Caenorhabditis elegans
• Automated Description: Enables DNA-binding transcription activator activity, RNA polymerase II-specific. Involved in several processes, including generation of neurons; positive regulation of transcription by RNA polymerase II; and protein localization. Located in cell cortex and nucleus. Expressed in neuroblasts. Human ortholog(s) of this gene implicated in Alzheimer's disease and pre-eclampsia. Is an ortholog of human STOX1 (storkhead box 1).
• Biotype: SO:0001217
• Genetic Position: IV :6.01751 ±0.001346
• Length (nt): 3555

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00001820

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F53B2.6.1	F53B2.6.1	1685	IV: 12542183-12545737

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F53B2.6	F53B2.6	1245	IV: 12542216-12542316

33 RNAi Result

• WBRNAi00048080
• WBRNAi00015478
• WBRNAi00032670
• WBRNAi00070180
• WBRNAi00107357
• WBRNAi00106761
• WBRNAi00104566
• WBRNAi00104568
• WBRNAi00104567
• WBRNAi00104570
• WBRNAi00104569
• WBRNAi00104572
• WBRNAi00104571
• WBRNAi00104574
• WBRNAi00104573
• WBRNAi00104576
• WBRNAi00104575
• WBRNAi00104578
• WBRNAi00104577
• WBRNAi00104580
• WBRNAi00104579
• WBRNAi00104582
• WBRNAi00104581
• WBRNAi00104584
• WBRNAi00104583
• WBRNAi00104586
• WBRNAi00104585
• WBRNAi00104588
• WBRNAi00104587
• WBRNAi00104590

74 Allele

• otn10058
• gk964278
• gk964078
• gk964500
• gk962765
• gk962743
• gk964475
• WBVar02021357
• gt1984
• ot361
• ot364
• ot371
• cas27
• cas137
• otn16477
• WBVar02059414
• gk789667
• gk527789
• gk451123
• gk336070
• gk314403
• h5786
• gk485634
• snx3034
• gk702530
• gk600664
• gk353871
• gk528259
• gk341699
• gk801540

1 Chromosome

• WormBase ID: IV
• Organism: Caenorhabditis elegans
• Length (nt): 17493829

1 Chromosome Location

• Feature . Primary Identifier: WBGene00001820
• Start: 12542183
• End: 12545737
• Strand: 1

3 Data Sets

• WormBaseAcedbConverter
• GO Annotation data set
• C. elegans genomic annotations (GFF3 Gene)

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrIV_12545738..12547380
• Length (nt): 1643
• Chromosome Location: IV: 12545738-12547380
• Organism: Caenorhabditis elegans

272 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 of coding genes that showed significantly decreased expression in muscle.	DESeq2 (version 1.24.0). Transcripts with a false-discovery rate adjusted p-value less than 0.05 were considered significantly differentially expressed.	WBPaper00062325:muscle_depleted_coding-RNA
	Transcripts expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons.	DESeq. False discovry rate (FDR) < 0.1.	WBPaper00048988:neuron_expressed
	Genes significantly enriched (> 2x, FDR < 5%) in a particular cell-type versus a reference sample of all cells at the same stage.	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_larva_enriched
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
Osmotic stress	Transcripts that showed significantly altered expression with 500 mM salt (NaCl) vs 100 mM salt when food was present	DESeq(version 1.10.1), FDR < 0.05.	WBPaper00050726:OsmoticStress_regulated_Food
	Transcripts that showed significantly increased 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_upregulated
	Transcripts that showed significantly increased 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_upregulated
	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 that showed significantly increased 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_upregulated
	Transcripts that showed significantly increased 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_upregulated
	Transcripts that showed significantly decreased expression in atfs-1(cmh15) (null allele) animals comparing to in N2 animals at L4 larva stage.	edgeR, fold change > 2, FDR < 0.05	WBPaper00060909:atfs-1(cmh15)_downregulated
	Transcripts that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_downregulated_daf-16(mu86);glp-1(e2141)
	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 decreased expression in lipl-4 overexpression transgenic lines comparing to wild type control animals.	DESeq2 fold change > 2, FDR < 0.05.	WBPaper00064156:lipl-4(overexpress)_downregulated
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 10 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_12h
	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: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 2 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_12h
	Transcripts that showed significantly increased expression in aak-1(tm1944);aak-2(ok524) animals comparing to in N2.	DEseq 1.18.0, adjusted p-value < 0.05.	WBPaper00056471:aak-1(tm1944);aak-2(ok524)_upregulated
	Transcripts that showed significantly increased expression in nhr-114(gk849) comparing to wild type animals at L4 larva.	DESeq2 1.26.0, fold change > 2, FDR < 0.05.	WBPaper00064539:nhr-114(gk849)_upregulated
	Transcripts that showed significantly increased expression in alg-1(gk214), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-1(gk214)_upregulated
	Genes that showed significantly increased expression in daf-2(e1370);hel-1(gk148684) comparing to in hel-1(gk148684)	To identify DEGs, Students t test and the log2 median ratio test were performed to compute t values and median ratios for all the annotated genes. The adjusted P values from each test were computed using an empirical distribution of the null hypothesis, which was obtained from random permutations of the samples. Finally, the adjusted P values from the individual tests were combined to compute the overall P values using Stouffers method , and genes with overall P < 0.05 and fold change > 1.5 were selected as DEGs.	WBPaper00047131:daf-2(e1370)_upregulated_hel-1(gk148684)-background
	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
	Transcripts that showed significantly increased expression in animal with pgph-2 overepxreesion [pgph-2p-pgph-2; myo-2p-mcherry] in glucose excess condition.	Genes with anadjusted P-value <= 0.05 found by DESeq2 were assigned as differentially expressed.	WBPaper00065926:pgph-2(overepxreesion)_upregulated_glucose
	Transcripts that showed significantly increased expression in cco-1(RNAi) comparing to in vector control animals.	The limma package47 was used for differential expression. Genes with a Benjamini-Hochberg adjusted P-value <0.05 and an absolute log fold change of 2 were considered differentially expressed.	WBPaper00053402:cco-1(RNAi)_upregulated
	Transcripts that showed significantly increased expression after exposure to 75uM paraquat(PQ) from L1 to day 2 adult stage in skn-1(lax188) animals	fold change > 2	WBPaper00058711:paraquat_upregulated
25C vs. 20C	Transcripts that showed significantly increased expression in 1-day post L4 adult hermaphrodite N2 grown at 25C, comparing to in N2 animals grown at 20C.	CuffDiff, fold change > 2.	WBPaper00065096:25C_vs_20C_upregulated
	Transcripts that showed significantly increased expression in 10-days post L4 adult hermaphrodite N2 grown at 20C, comparing to in 1-day post L4 adult hermaphrodite N2 animals grown at 20C.	CuffDiff, fold change > 2.	WBPaper00065096:Day10_vs_Day1_upregulated
	Transcripts that showed significantly increased expression in wdr-5(ok1417);skn-1(lax188) comparing to in skn-1(lax188) at day 2 adult stage.	fold change > 2	WBPaper00058711:wdr-5(ok1417)_upregulated
	Transcripts that showed significantly decreased expression in 10-days post L4 adult hermaphrodite npr-8(ok1439) animals grown at 20C, comparing to in N2 animals.	CuffDiff, fold change > 2.	WBPaper00065096:npr-8(ok1439)_downregulated_Day10_20C

9 Expression Patterns

• Primary Identifier: Expr1031068
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1151890
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1200002
• Pattern: Data from the TransgeneOme project

• Primary Identifier: Expr3416
• Subcellular Localization: Immunostaining revealed that HAM-1 localizes to the cell periphery and is distributed asymmetrically in some embryonic cells, including the HSN/PHB neuroblast.

• Primary Identifier: Expr2030600
• 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: Expr1024520
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr12679
• Reporter Gene: Expression in the nucleus assessed also with embryonic subcellular fractionation.
• Subcellular Localization: HAM-1 is primarily a nuclear localized protein.

• Primary Identifier: Expr1604
• Pattern: HAM-1 is first expressed at the onset of gastrulation, approximately 100 minutes after cleavage of the zygote. At this time, HAM-1 often localizes to the periphery of cells in crescent shaped patterns that are restricted to one side of dividing cells. HAM-1 expression persists until the 1.5 fold stage of embryonic development, approximately 430 minutes after cleavage of the zygote. No HAM-1 expression can be detected later during embryonic or larval hermaphrodite development. HAM-1 protein is expressed in many mitotic and postmitotic cells. To determine whether HAM-1 is expressed in the lineage that produces the HSN and PHB neurons, embryos were stained at 260-300 minutes after cleavage of the zygote. HAM-1 is restricted to the posterior half of the HSN/PHB neuroblast. After division of the HSN/PHB neuroblast, HAM-1 ring staining can occasionally be seen in cells that, by position, could be the HSN/PHB precursor. This staining, however, is usually not detectable suggesting that HAM-1 is degraded rapidly after division of the HSN/PHB neuroblast.
• Subcellular Localization: HAM-1 expressed in cells at metaphase. Chromosomes are condensed and HAM-1 is distributed to one side of the cell. HAM-1 expressed in cells at telophase. Two nuclear envelopes have reformed and HAM-1 is distributed to the side of the cell that will be inherited with the posterior nucleus. HAM-1 staining also appears as rings that surround cells. HAM-1 often localizes to the periphery of cells in crescent shaped patterns that are restricted to one side of dividing cells.

• Primary Identifier: Expr2012364
• 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).

24 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00001820
• Start: 12542183
• End: 12545737
• Strand: 1

24 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 3555

1 Sequence Ontology Term

• Name: gene

8 Strains

• WBStrain00027070
• WBStrain00029404
• WBStrain00029437
• WBStrain00029492
• WBStrain00029490
• WBStrain00029499
• WBStrain00029500
• WBStrain00029505

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrIV_12536641..12542182
• Length (nt): 5542
• Chromosome Location: IV: 12536641-12542182
• Organism: Caenorhabditis elegans