WormMine: Gene WBGene00002136

• WormBase Gene ID: WBGene00002136
• Gene Name: inx-14
• Sequence Name: F07A5.1
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable gap junction hemi-channel activity. Acts upstream of or within with a positive effect on germ cell proliferation. Acts upstream of or within with a negative effect on oocyte maturation. Located in gap junction. Expressed in several structures, including GABAergic neurons; germ cell; germ line; non-striated muscle; and somatic gonad precursor.
• Biotype: SO:0001217
• Genetic Position: I :1.94615 ±0.007328
• Length (nt): 1927

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00002136

Genomics

3 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F07A5.1a.1	F07A5.1a.1	1547	I: 7350309-7352217
Transcript:F07A5.1a.2	F07A5.1a.2	1483	I: 7350309-7352092
Transcript:F07A5.1b.1	F07A5.1b.1	1568	I: 7350312-7352235

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F07A5.1a	F07A5.1a	1299	I: 7350474-7350511
CDS:F07A5.1b	F07A5.1b	1305	I: 7350474-7350511

25 RNAi Result

• WBRNAi00085629
• WBRNAi00025012
• WBRNAi00003327
• WBRNAi00025013
• WBRNAi00030590
• WBRNAi00065248
• WBRNAi00001922
• WBRNAi00025014
• WBRNAi00043847
• WBRNAi00087925
• WBRNAi00087923
• WBRNAi00083396
• WBRNAi00083420
• WBRNAi00083465
• WBRNAi00083469
• WBRNAi00083463
• WBRNAi00083466
• WBRNAi00083468
• WBRNAi00086481
• WBRNAi00083411
• WBRNAi00023694
• WBRNAi00023182
• WBRNAi00023400
• WBRNAi00083379
• WBRNAi00023982

18 Allele

• gk962858
• gk962706
• gk963902
• tm2864
• gk757334
• gk710939
• gk808906
• gk739378
• ok3267
• gk114807
• ag17
• gk114808
• gk114809
• gk114805
• gk114806
• gk1667
• gk960004
• tm2593

1 Chromosome

• WormBase ID: I
• Organism: Caenorhabditis elegans
• Length (nt): 15072434

1 Chromosome Location

• Feature . Primary Identifier: WBGene00002136
• Start: 7350309
• End: 7352235
• 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

146 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Genes with expression altered >= 3-fold in dpy-10(e128) mutants.	Data across the wild type series was analyzed using the Significance analysis of Microarrays (SAM) algorithm (to calculate the False Discovery Rate (FDR)).	WBPaper00035873:dpy-10_regulated
	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
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
	Genes that were downregulated in lin-15B(n744).	For each gene in each microarray hybridization experiment, the ratio of RNA levels from the two samples was transformed into a log2 value and the mean log2 ratio was calculated. The log2 ratios were normalized by print-tip Loess normalization (Dudoit and Yang, 2002). All genes with a false discovery rate of <= 5% (q <= 0.05) (Storey and Tibshirani, 2003) and a mean fold-change ratio of >= 1.5 were selected for further analysis.	WBPaper00038168:lin-15B(n744)_downregulated
	Genes with expression level regulated by genotype (N2 vs CB4856) and age at L3 larva and Late reproduction stage (96 hours at 24 centigrade).	For model 2, authors used 100 permutations to estimate the FDR threshold. Per permutation, genotypes and ages were independently randomly distributed, keeping the among-gene structure intact. Then for each spot (23,232) on the array, model 2 was tested. The obtained P-values were used to estimate a threshold for each of the explanatory factors. Authors also used a genome-wide threshold of -log10 P-value = 2, which resembles an FDR of 0.072 and 0.060 for marker and the interaction age-marker for the developing worms and FDR of 0.050 and 0.065 for marker and age-marker for the aging worms. For the physiological age effect, authors used a log10 P-value = 8 in developing worms (0.012 FDR) and -log10 P-value = 6 (0.032 FDR).	WBPaper00040858:eQTL_age_regulated_developing
	Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_fem-3(q20)
	Transcripts that showed significantly increased expression in day 3 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_upregulated_fem-3(q20)
Bacteria diet: Sphingomonas aquatilis Yellow. Fed for 30 generations.	Transcripts that showed significantly decreased expression after fed by bacteria Sphingomonas aquatilis (Yellow) for 30 generations comparing to animals fed by E. coli OP50.	DESeq2 fold change > 2, p-value < 0.01.	WBPaper00061007:S.aquatilis_downregulated
	Maternal class (M): genes that are called present in at least one of the three PC6 replicates.	A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing.	[cgc5767]:expression_class_M
	Strictly maternal class (SM): genes that are the subset of maternal genes that are not also classified as embryonic.	A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing.	[cgc5767]:expression_class_SM
	Transcripts that showed significantly increased expression in animals exposed to 400uM tamoxifen from L1 to L4 larva stage.	DEseq2, fold change > 2	WBPaper00064505:tamoxifen_upregulated
	Significantly differentially expressed genes as determined by microarray analysis of wild-type and cde-1 mutant germlines.	RNAs that changed at least 2-fold with a probability of p < 0.05 were considered differentially regulated between wildtype and cde-1.	WBPaper00035269:cde-1_regulated
	Genes down regulated by mir-243(n4759).	RNAs that changed at least 2-fold with a probability of p > 0.05 in three biological replicates were considered differentially regulated between wild-type and mir-243.	WBPaper00036130:mir-243_down_regulated
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
Temprature shift to 28C for 24 hours.	Transcripts that showed significantly decreased expression after animals were exposed to 28C temperature for 24 hours.	Differentially expressed genes wereidentified using DESeq (v.1.18.0) by normalizing readsbased on the negative binomial distribution method andcomparing each HS timepoint to the 0-h control.	WBPaper00061341:28C_24h_downregulated
	Transcripts that showed significantly decreased expression in tetraploid N2 comparing to diploid N2 animals at L4 larva stage.	DESeq2 R package (1.20.0), fold change > 2, and FDR < 0.05.	WBPaper00066110:tetraploid_vs_diploid_downregulated
Temprature shift to 28C for 48 hours.	Transcripts that showed significantly decreased expression after animals were exposed to 28C temperature for 48 hours.	Differentially expressed genes wereidentified using DESeq (v.1.18.0) by normalizing readsbased on the negative binomial distribution method andcomparing each HS timepoint to the 0-h control.	WBPaper00061341:28C_48h_downregulated
	Transcripts that showed significantly increased expression in mbl-1(syb4318), referred to as mbl-1short(ex7-), comparing to in N2 at L4 larva stage.	DESeq2, Fold change > 2 and FDR < 0.05	WBPaper00066410:mbl-1(syb4318)_upregulated
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 0hr 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:germline-precursors_blastula-embryo_expressed
	Transcripts that showed significantly decreased expression in hpl-2(tm1489) comparing to in N2 animals.	DESeq2, adjusted p-value < 0.05, log2 fold change > 2 or < -2.	WBPaper00054493:hpl-2(tm1489)_downregulated
	Transcripts that showed significantly increased expression in ilc-17.1(syb5296) comparing to in N2 animals at L4 larva stage.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00066594:ilc-17.1(syb5296)_upregulated
	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
	Transcripts detected in germline isolated from day-1 adult hermaphrodite animals.	All three experiments have CPM >= 1.	WBPaper00067147:germline_expressed
	Proteins that showed significantly increased expression in CB4856 animals growing in 15mg per mL doxycycline from L1 to L4 larva stage.	edgeR (version 3.24.3), fold change > 2, FDR < 0.05.	WBPaper00062456:doxycycline_upregulated_CB4856_protein
Bacteria: B.thuringiensis	Transcripts in elt-2(RNAi) animals that were significantly differentially expressed at least for one time point and one pathogenic strain Bt247 and Bt679 compared to the non pathogenic strain Bt407.	Cuffdiff	WBPaper00060358:B.thuringiensis_pathogen_regulated_elt-2(RNAi)
Bacteria: B.thuringiensis	Transcripts in N2 animals that were significantly differentially expressed at least for one time point and one pathogenic strain Bt247 and Bt679 compared to the non pathogenic strain Bt407.	Cuffdiff	WBPaper00060358:B.thuringiensis_pathogen_regulated_N2
	Genes that were not enriched in either spermatogenic fem-3(q96gf) nor oogenic fog-2(q71) gonads, according to RNAseq analysis.	To identify differentially expressed transcripts, authors used R/Bioconductor package DESeq.	WBPaper00045521:Gender_Neutral
	Transcripts that showed significantly decreased expression in nhl-2(ok818) comparing to in N2 at 25C.	EdgeR, FDR < 0.05, fold change < 0.5.	WBPaper00055971:nhl-2(ok818)_25C_upregulated

10 Expression Patterns

• Primary Identifier: Expr1031252
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr8682
• Remark: Picture: Fig 3.
• Pattern: Expression in the alimentary canal: Weak or rare expression in pm5, pm6, pm7. Expression in the nervous system: DDn, VDn. Expression in the reproductive system: In adult stage, expressed in vulval muscle, uterine muscle.

• Primary Identifier: Expr10637
• Pattern: INX-14 immunostaining of wild-type gonads confirmed the previously reported expression pattern. INX-14 localizes to discrete puncta at the sheath/oocyte interface in the proximal gonad and the germ cell/sheath interface in the distal gonad.

• Primary Identifier: Expr10638
• Pattern: INX-14 and INX-22 are expressed in the germline and colocalize at plaque-like structures, suggesting that they are components of sheath-oocyte gap junctions. Interestingly, we also observed INX-14 and INX-22 throughout the germline, beginning in the L2 stage.

• Primary Identifier: Expr11346
• Pattern: inx-14 is expressed in body wall musculature.

• Primary Identifier: Expr11975
• Pattern: Expression of INX-8, -9, -14, -21 and -22 overlapped closely throughout the gonad in wild-type adult hermaphrodites. In distal arms clusters of fine puncta were associated with each germ cell, as previously reported for INX-14 and INX-22 expression (Govindan et al. 2009). INX-14, -21 and -22 colocalized to puncta associated with long processes that extended from the DTC proximally, especially those running between germ cells and intercalating among them. At the distal limit of sheath cell coverage of germ cells, longer formations sometimes appeared associated with the apparent edge of the sheath cells. At the loop region of the gonad arm, individual puncta appeared in larger, higher-density aggregates. In the proximal arm puncta size was more variable, with many appearing to be considerably larger than the fine puncta seen in the distal arm. Although all innexins appeared to colocalize, INX-21 differed from the other innexins in that its expression level was relatively higher in the distal gonad compared to the proximal gonad. In contrast, the expression levels of INX-8, INX-9, INX-14, INX-22 appeared higher in the proximal gonad. Male gonads were examined and found to express INX-8, -9, -14, -21 and -22 as well. Presumptive gap junctions forming between both male distal tip cells and germ cells were detected with antibodies specific to INX-8/9, INX-14, INX-21, and INX-22. All 5 innexins are also expressed in the regions occupied by differentiated spermatocytes and sperm, with evidence of puncta formation. Examination of earlier developmental stages showed that all five innexins are expressed in the primordial gonad, consisting of somatic gonadal precursors Z1 and Z4 and the primordial germ cells Z2 and Z3. In a few serendipitous cases expression of INX-22 was detected prior to hatching, in pretzel-stage embryos. Early larval expression patterns differ from adults in that distinct, well-defined puncta potentially corresponding to gap junctions are less clearly discernible. In L2-L4 larval stages, germ cell innexins appear to be continually expressed, and somatic innexins are expressed predominantly in the DTC. In late L2 and early L3 stages, as the gonad arm lengthens, the migrating DTC seems to trail a process behind it that maintains contact with the germ cell compartment. The DTC appears to form gap junctions with germ cells at both long external processes and processes that intercalate between germ cells. At this time a second, more proximal focus of somatic innexin expression was sometimes detected. Though this second focus might represent extensions from the DTC, expression of inx-9::gfp suggested that other somatic cells besides the DTC might be involved. By the late L3 stage, the DTC no longer appears to be in contact with all of the germ cells. To better understand the contacts between germ cells and the DTC, we examined early L4-stage animals by TEM. We observed several processes trailing behind the DTC cell body on the outer edge of the germ line, as well as extensions that dig deeply between germ cells. The immunofluorescence results suggest that gap junctions form between the DTC and germ cells at both the outer and inner DTC arms.

• Primary Identifier: Expr1021999
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2012788
• 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: Expr2031027
• 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: Expr1147823
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

16 GO Annotation

8 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00002136
• Start: 7350309
• End: 7352235
• Strand: -1

16 Ontology Annotations

2 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly increased expression in animals with germline-specific inx-14(RNAi) comparing to in aniamls fed with control vector, both exposed to PA14 infection.	DESeq2. Differentially-expressed genes (DEG) were identified based on two criteria: FDR (False discovery rateusing Benjamini-Hochberg adjusted p-values) < 0.01 and absolute value of log2(Fold Change) > 1.	WBPaper00066146:germline-inx-14(RNAi)_upregulated_PA14
	Transcripts that showed significantly decreased expression in animals with germline-specific inx-14(RNAi) comparing to in aniamls fed with control vector, both exposed to PA14 infection.	DESeq2. Differentially-expressed genes (DEG) were identified based on two criteria: FDR (False discovery rateusing Benjamini-Hochberg adjusted p-values) < 0.01 and absolute value of log2(Fold Change) > 1.	WBPaper00066146:germline-inx-14(RNAi)_downregulated_PA14

1 Sequence

• Length: 1927

1 Sequence Ontology Term

• Name: gene

2 Strains

• WBStrain00037402
• WBStrain00000263

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrI_7352236..7352414
• Length (nt): 179
• Chromosome Location: I: 7352236-7352414
• Organism: Caenorhabditis elegans