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["Supplementary Table 5. Concordance of cCRM activity and expression pattern of adjacent genes."]
[]
["insufficient information to call"]
["no insert-specific GFP expression"]
["expression explained by proximal gene or genes"]
["expression potentially or partially explained by proximal gene or genes"]
["expression not present in proximal gene or genes"]
[]
["ID","location","gene1","gene1 exp","gene2","gene2 exp","validation call","validation finding"]
["CG7759_33","intergenic","CG30023","trunk mesoderm, clypeolabrum [BDGP]","CG7759","trunk mesoderm [doi:10.1242/dev.036426]","++","Robust mesodermal GFP @ st.11, largely but not completely meso-specific."]
["ChIPCRM3152","intergenic","CG14548","includes mesoderm, gut, and neurogenic ectoderm; BDGP","CG8337","includes mesoderm and neurogenic ectoderm; Pubmed id   10072784","++","Incredibly strong, widespread expression in mesoderm and ectoderm (but not quite ubiquitous) from st. 10 on."]
["ChIPCRM2497","intragenic (exonic noncoding)","CR31273","within the bxd noncoding RNA in BX-C; \"Strikingly, bxd ncRNAs are expressed in different germ layers (Figure 1C), suggesting that expression of individual bxd ncRNAs may be driven by different tissue-specific regulatory elements.\" [doi:10.1016/j.cell.2006.10.039]",null,null,"++","Robust, specific exp. in mesoderm from st. 10/11 on.  Late visible in heart & SM. Very few CD2-."]
["ChIPCRM2299","intronic","CG31317","stumps has strong tracheal pit and head mesoderm exp; BDGP",null,null,"+","Bright GFP in tracheal pits from st. 11, with strong head exp. in CD2+ cells, segmental clusters of ??CM??, some ventral CD2- (prob. neuroblasts)"]
["ChIPCRM2256","intronic","CG8651","trx has this expression pattern at stage 7-8 in BDGP in situs",null,null,"++","Strong exp. from st. 9/10 on in AbdA pattern plus head. Both CD2+ and CD2- in A1-8, CD2- in head domain."]
["ChIPCRM2078","intronic","CG6715","region is just upstream of KP78a/b dicistronic RNA gene, KP78b has strong mesoderm specific exp and perhaps weak ubiquitous; Estrada in situ","CG17228","KP78a/b and region fall within huge pros intron, pros exp is specific in nervous system; BDGP","++","Strong ubiquitous exp. from st. 8 on."]
["ChIPCRM2898","intragenic (intronic + UTR)","CG31163","segmental and head nervous system exp; BDGP",null,null,"-","Weak segmental & stronger head exp. from st. 11, all CD2-; looks like all CNS late."]
["CBP2862","intergenic","CG7004","strong VM, SM and VM expanded in Ras, FC; Estrada et al PLoS Gen ","CG32344","somatic and visceral meso plus gut; BDGP","++","Robust, specific mesodermal exp. from st. 11; late exp. in CNS, gut, & a subset of muscles."]
["ChIPCRM2847","intronic","CG18402","bizarrely, there doesn't seem to be an exp pattern for InR",null,null,"++","Robust GFP expression from ~st. 10 on. Largely mesodermal but amnioserosa also gets very bright."]
["ChIPCRM3407","intergenic","CG11315","head mesoderm and fat body; BDGP","CG1322","mesoderm, fat body, CNS (zfh1); BDGP","+","Many GFP+ cells in SM & VM from st.11 (or late 10). Some CD2- cells in head area and scattered ventral."]
["ChIPCRM5523","intronic","CG8965","mesoderm and CNS cells, look quite good; BDGP",null,null,"+","Scattered CD2+ & CD2- cells @ st. 11-12."]
["CBP5467","intronic","CG13425","all FCs, v. strong, pan-meso early; Estrada et al. PLoS Gen",null,null,"+","GFP @ st. 11 in a subset of CD2+ cells (FCs?) & a much larger group of neuronal precursors. Very late exp. in nerve cord & some muscles."]
["ChIPCRM5556","intergenic","CG13989","no embryonic expression (FlyBase)","CG34380","CNS; ecto; VM; endo; small subset of SM FCs [Estrada]","-","Strong & specific exp. in migrating endoderm from late st.11.  CD2- (or SUPER-weak CD2+?)"]
["ChIPCRM3043","intronic","CG5405","endoderm, VM, SM, ventral midline; BDGP",null,null,"+","GFP exp. from st. 11 in a variety of cell types, some CD2+, some CD2-. Definitely some neuroblasts, CD2+ structure in head, FCs?, VM?"]
["ChIPCRM2947+2948","intergenic","CG4677","FCMs (lmd!); looks like expression is visible but not called in or surrounding the hindgut [BDGP]","CG13833","BDGP: \"no staining\"","+","Strong exp. in CD2+ cells of, it looks like, hindgut primordium(?) @ st.11 + a few additional trunk CD2+ cells (weak)."]
["ChIPCRM5405","intergenic","CG3407","ubiquitous; BDGP","CG16738","slp1: trunk mesoderm, ectoderm, epidermis, misc (BDGP); element covers most of slp1-5-2 element with documented mesoderm and ectoderm exp (REDfly)","++","Very bright, widespread, and largely specific exp. in mesoderm at st.11 (SM and CM) with some ventral ectoderm as well."]
["ChIPCRM5432","intronic","CG3048","head & trunk mesoderm primordium around germ band extension, and nervous system at st. 11",null,null,"++","Abundant bright exp. from st. 9 on, both CD2+ and CD2-."]
["ChIPCRM2610","intragenic (intron+UTR+Nterm)","CG7223","htl has FC, cardiac progenitor exp",null,null,"+","Weak exp. in a few dorsal FCs & cardiac progenitors per hs from st. 11; late heart exp. gets very strong."]
["DHS_FC_33","intronic","CG5295","gnathal lobe exp ~st.10 and something visible in the tail ~st. 12; BDGP",null,null,"-","Super-bright head & tail exp. from ~st. 10 (head) or st. 12 (tail), looks to be all CD2-."]
["ChIPCRM3429","intronic","CG1447","posterior midgut, somatic muscle, ventral nerve cord; BDGP",null,null,"+","Few but very bright GFP+ cells at st.11, mostly VM but 1 or 2 per hs in SM and a few CD2- cells/hs ventrally."]
["ChIPCRM5900","intergenic","CG6464","VM, epidermis, tracheal system, VNC; BDGP","CG4922","endoderm, trunk mesoderm, epidermis, tracheal system; BDGP","+","Robust VM-specific expression from st. 11. A few scattered additional CD2- cells, and some bright cells late."]
["CBP5083","intronic","CG10197","FCs, head meso, CNS; NO HEMOCYTES; BDGP",null,null,"+","Early and late hemocyte exp. from st. 11 on, plus ~1-2 segmentally repeated CD2+ cells. More head exp. & some VNC cells late."]
["CBP1410",{"$nulls":5},"-","No GFP reliably detected @ st. 11-12 (maybe a few oddly positioned CD2- cells)"]
["rgr_a_6","intronic","CG8643","FCM exp, some anterior exp but doesn't look coincident with GFP [Estrada]",null,null,"-","Some CD2- cells in the head @ st.11; scattered bright CD2- cells late, probably neurons."]
["ChIPCRM3814",{"$nulls":5},"-","No GFP detected @ st. 11-12."]
["ChIPCRM5806",{"$nulls":5},"-","No detectable GFP @ st. 11-12; a few bright lateral cells / hs very late."]
["ChIPCRM1831","intergenic","CG44227","no embryonic expression (FlyBase)","CG9786","hb has brain, nervous system exp [BDGP]; FC exp [Busser list]","+","GFP comes on during st. 11, primarily in CNS but with some VM & one or a few FCs / hs."]
["ChIPCRM3343","intergenic","CG2014","no embryonic expression (FlyBase)","CG1897","Dr has FC, nervous system exp [BDGP, Busser]",0,"Super-weak exp. (and/or terrible staining) from st. 10/11 in MOSTLY CD2-; maybe a few CD2+ cells / hs but the staining is so poor it's impossible to say for sure."]
["DHS_FC_23",{"$nulls":5},"-","No GFP detected @ st. 11-12."]
["ChIPCRM752","intragenic (intron+coding)","CG10108","phyl has FC, nervous system exp [BDGP, Busser]",null,null,"+","Exp. from st. 11/12 in segmentally repeated cells, some CD2+ but mostly CD2-, + much brighter CD2- cluster in head region."]
["ChIPCRM5406",{"$nulls":5},"-","No consistently detected GFP @ st. 11-12."]
["ChIPCRM3427",{"$nulls":5},"-","No GFP detected @ st. 11-12."]
["ChIPCRM2162","intronic","CG6234","Can't find expression info.",null,null,"-","Ample GFP @ st. 11, but little or none mesodermal.  Late expression in a subset of neurons? muscles???"]
["jumu_a_8","intronic","CG4029","nerve cord [BDGP] + FCs [Estrada]",null,null,"+","Looks like a subset of FCs w/ CD2 coexp. @ st. 11 & some neurons"]
["CG33316_15",{"$nulls":5},"-","No GFP detected at. st.11-12. One non-meso cell per hemisegment VERY late."]
["ChIPCRM6146","intronic","CG3938","CycE is expressed in trunk mesoderm, neuroblasts, head (probably dividing cells) [BDGP] Not sure about the weird mid-trunk structure.",null,null,"+","Super-weak exp. in a few CD2+ cells / hs + stronger in head & some weird (weakly CD2+?) mid-trunk structure @ st. 11.  Not much visible late."]
["ChIPCRM6885",{"$nulls":5},"-","No GFP detected @ st. 11-12."]
["slou_Up_14",{"$nulls":5},"-","No GFP detected @ st. 11-12; only very common possible tendon cell exp. late."]
["CBP2861","intronic","CG7004","strong VM, SM and VM expanded in Ras, FC[Estrada et al PLoS Gen] No mention of hemocytes or amnioserosa, can't find images.",null,null,"+","Bright GFP from st. 10/11 in amnioserosa & hemocytes."]
["ChIPCRM770",{"$nulls":5},"-","No GFP detected @ st. 11-12. A few weak cells laterally and in the head, very late."]
["rst_8",{"$nulls":5},"-","No GFP detected."]
["eg_36",{"$nulls":5},"-","A few GFP+ CD2- cells in the head region @ st. 11. Very common head+lateral late, all CD2-."]
["ChIPCRM5561","intronic","CG34380","CNS; ecto; VM; endo; small subset of SM FCs [Estrada]",null,null,"+","Bright GFP from st. 11 in some nervous system & caudal VM."]
["ChIPCRM5439",{"$nulls":5},"-","No detectable GFP @ st. 11-12."]
["mid_30","intergenic","CG6634","segmental repeats in epidermis [BDGP]","CG14020","Can't find expression info.","-","No GFP detected @ st. 11-12. Comes on ~st. 13 in ectodermal stripes, very bright late."]
["ChIPCRM4222","intragenic (intron+alt.promoter+exon)","CG32066","faint ubiquitous, trunk mesoderm, ventral neurons [BDGP]",null,null,"+","Scattered strong GFP+ cells, MOSTLY CD2- but a few CD2+, from st. 10/11."]
["ChIPCRM3899",{"$nulls":5},"-","No detectable GFP @ st. 11-12."]
["ChIPCRM4235",{"$nulls":5},"-","No GFP detected @ st. 11-12; some CD2- in head area late + ~2 CD2+ nuclei / hs in body wall muscles."]
["slou_Up_30","intergenic","CR44033","no embryonic expression (FlyBase)","CG6534","slou has nerve cord expression possibly consistent with this weak staining [doi: 10.1101/gad.4.12a.2098]","-","Some CD2- cells in the head @ st. 11; others in ventral abdomen late."]
["slou_b_4",{"$nulls":5},"-","No GFP detected @ st. 11-12; only very common possible tendon cell exp. late."]
["ChIPCRM5101",{"$nulls":5},"-","No GFP detected."]
["CG10275_32",{"$nulls":5},"-","A few GFP+ CD2- cells in the head region @ st. 11. Very common head+lateral late, all CD2-."]
["ChIPCRM4514","intronic","CG9598","hindgut, foregut, segmentally repeated epidermis, midgut [BDGP]",null,null,"-","No detectable GFP @ st. 11-12; late exp. in hindgut, foregut?, a few bright lateral cells / hs."]
["rgr_a_7","intronic","CG8643","possible late hindgut exp (out of focus) [Estrada]",null,null,"-","No GFP detected @ st.11-12; VERY late hindgut (CD2+) expression."]
["CBP5827","intronic (but upstream of Kr in giant intron)","CG9380",null,"CG3340","FC exp; late muscle exp is probably Kr expression in VL3, VO4, LT2(&4?), LL1","+","A few isolated GFP+ CD2+ cells / hs (FCs?) @ st. 11-12, with more later. Clear GFP in a subset of mature myofibers @ st. 16."]
["abd-A_3","intragenic (within lncRNA)","CR43261","This transcript is first seen at about stage 6 [11] in the epidermis, but from stage 14 onward (germband shortening), the RNA is detected only in the developing central nervous system (CNS). [doi:10.1371/journal.pgen.1002720]",null,null,"-","GFP begins @ late  st.11 / early 12 in some neuroblasts & the primordium of a hindgut structure. Robust late exp. in brain, VNC, & brightest at the junction of midgut & hindgut. All CD2-."]
["ChIPCRM6372",{"$nulls":5},"-","No GFP detected @ st. 11-12. Some CD2- mid-head and a few lateral segmentally repeated cells (possibly CD2+) VERY late (not until after st.14)."]
["DHS_FCM_1",{"$nulls":5},"-","No detectable GFP @ st. 11-12; late CD2- in head region."]
["ChIPCRM5397","intergenic","CG3407","ubiquitous; BDGP","CG16738","slp1: trunk mesoderm, ectoderm, epidermis, misc (BDGP)","+","GFP in a few FCs / hs @ st. 11 plus more cells in head, mostly CD2-?"]
["ChIPCRM4236",{"$nulls":5},"-","No GFP reliably detected @ st. 11-12 (maybe 1 or 2 cells in st. 12 head?); only very common possible tendon cell exp. late."]
["ChIPCRM1739","intergenic (divergent promoters, overlaps both transcripts)","CG1104","faint ubiquitous, epidermis, salivary gland (staining is weak, could be unannotated mesodermal exp) [BDGP]","CG1943","ubiquitous, brain [BDGP]","+","Scattered weak GFP+ mesodermal cells (inc. VM) at st.11-12, plus brighter CD2- in head."]
["DHS_FC_15","intragenic (intron+coding)","CG13425","all FCs, v. strong, pan-meso early; Estrada et al. PLoS Gen",null,null,"-","GFP comes on ~st. 12 in some bright CD2- clusters in the head & a few CD2- cells in the abdomen."]
["ChIPCRM6845","intragenic (intron+coding)","CG2845","ubiquitous, trunk & head mesoderm, endoderm, nervous system [BDGP]",null,null,"-","GFP in 2 populations of CD2- cells @ st. 11-12: one in head and one in abdomen. Late exp. in brain lobes, lateral clusters (oenocytes?), & some mysterious gut structure."]
["slou_Dn_9",{"$nulls":5},"-","No GFP detected"]
["CG15319_down_1",{"$nulls":5},"-","No GFP detected @ st. 11-12; only very common possible tendon cell exp. late."]
["mud_a",{"$nulls":5},"-","No GFP detected @ st.11-12; some bright cells late, CD2-."]
["cib_Up_4","intronic","CG4944","complicated exp pattern includes somatic muscles [BDGP]",null,null,"-","A couple muscles late; nothing (?) early. RESTAIN"]
["nau_a_4","intronic","CG10250","subset of FCs & myofibers [BDGP]",null,null,"-","No detectable GFP @ st. 11-12; later exp (from st.13/14) in a subset of FCs & myofibers."]
["slou_Up_2","intragenic (overlaps promoter and ncRNA)","CR43372","no embryonic exp","CG6534","Slou expressed in a couple of ventral muscle FCs [PMID:\n    7556942]","+","One/few CD2+ cells in ventral meso. st.11-12."]
["Ubx_18",{"$nulls":5},"-","No detectable GFP @ st. 11-12."]
["CG15319_down_12",{"$nulls":5},"-","No GFP detected @ st. 11-12."]
["ChIPCRM5819","intronic","CG4722","ubiquitous early, trunk mesoderm (scattered cells), pericardial cells, nervous system [BDGP]",null,null,"+","GFP @ st. 11 in a subset of CD2+ cells (FCs?), VM, neuronal precursors, maybe CM?"]
["ChIPCRM4351","intragenic (intron+UTR)","CG32096","rols is exp in endoderm & muscle primordium including VM [BDGP]",null,null,"+","GFP from fairly late st. 12 in VM."]
["Sur_39","intragenic (overlaps promoter and UTR)","CG44153","little or no exp in embryo [FlyBase, BDGP]","CG5772","dorsal vessel [BDGP]","-","No GFP reliably detected @ st.11-12 (possibly VERY faint in head; CD2-); few cells (1 muscle???) late."]
["ChIPCRM5792","intronic","CG3779","blastoderm stripes, head mesoderm, nervous system; trunk meso exp not visible in BDGP in situs, but numb mutants have muscle phenotypes",null,null,"++","Robust mesodermal exp. (+ nonmesodermal) from st. 9 on."]
["ChIPCRM2613","intronic","CG7223","htl is early pan-mesodermal",null,null,"++","Robust and specific mesodermal exp. from st. 10 on + scattered CD2-. Weak nervous system & strong heart and hindgut late."]
["ChIPCRM2000","intronic","CG4029","jumu has ectoderm, nervous system, FC exp, very strong CNS late",null,null,"+","GFP from ~st. 10 mostly in CD2- cells but also much weaker exp. in CD2+. Very strong CNS and oenocytes late."]
["hth_3","intronic (contains small coding exon)","CG17117","hth has trunk and visceral mesoderm exp around relevant times (as well as much else not captured in this construct)",null,null,"++","Abundant mesodermally restricted GFP @ st. 11."]
["mud_c_d",{"$nulls":5},"-","No GFP detected @ st.11-12; few non-meso cells, faint, late."]
["numb_34",{"$nulls":5},"-","No GFP detected"]
["ChIPCRM6902","intronic","CG3653","kirre (duf) has VM primordium expression","CG3936","N has hindgut primordium exp","+","Strong exp. from st. 11 in hindgut primordium & a subset of VM circular muscle founders."]
["ChIPCRM4505",{"$nulls":5},"-","No GFP detected @ st. 11-12."]
["slou_Up_1",{"$nulls":5},"-","No GFP detected @ st.11-12; some bright cells late, CD2-."]
["ChIPCRM3430","intronic","CG1447","Ptx1 has muscle subset, segmentally repeated few cells at relevant stage",null,null,"+","Late GFP in a subset of muscles; from st. 11 exp. is in a few CD2+ (VM?) cells / hs."]
["CG15319_down_7","intragenic (3' UTR)","CG15319","bizarrely, there doesn't seem to be an exp pattern for nej",null,null,"-","GFP @ st. 11-2 limited to a few CD2- cells in head."]
["Mef2_29",{"$nulls":5},"-","No GFP detected @ st. 11-12; few bright cells very late."]
["noc_6",{"$nulls":5},"-","No GFP detected"]
["slou_Dn_4",{"$nulls":5},"-","No GFP detected @ st. 11-12; some lateral & posterior cells late."]
["CBP4280","intergenic (overlaps ncRNA)","CG3871","Six4 has lots of brain exp","CR43705","no exp in embryo","-","GFP barely visible in a couple of CD2- cells in head @ st. 11."]
["CG13830_19",{"$nulls":5},"-","No GFP detected"]
["pnut_13","intergenic","CG8705","no good expression info","CG14760","no good expression info","+","Abundant GFP from st.11 on. Some in CD2+, some not. ??Somatic gonad precursor???"]
["ChIPCRM6084","intergenic (overlaps a tRNA gene)","CG4491","noc has segmentally repeated trunk meso exp much like this cCRM","CG33648","no good expression info","+","GFP in a subset of CD2+ cells (FCs?) from st. 10/11 on, brightest in a head segment CD2+ cluster."]
["ChIPCRM5617","intronic","CG10377","ubiquitous",null,"nearby genes nop5 and x16 have some overlap with this pattern","+","GFP from ~st. 11 in CD2+ & CD2-, brightest in CD2- cells in head region. FC clusters???"]
["ChIPCRM5857","intronic","CG31721","Trim9 is expressed only in nervous system primordium, and nearby genes are all unexpressed in embryo",null,null,"+","Strong somatic mesoderm exp. from st. 10/11 w/ some CD2- exp. in head region."]
["ChIPCRM2929","intronic","CG31151","FC gene",null,null,"+","GFP exp. restricted to a few anterior cells, some CD2+ & some CD2-, from st. 11. One or a few cells / hs later."]
["sns_6",{"$nulls":5},"-","No GFP detected"]
["G-oalpha47A_5","intronic","CG2204","VM & heart, nerve cord later",null,null,"-","No GFP detected @ st.11-12; Amnioserosa (CD2-) late."]
["slou_Up_5","intergenic","CR44033","no exp in embryo","CG6534",null,"-","No coexp. at st.11, one thoracic CD2+ cell (FC?) later."]
["ChIPCRM6679","intronic","CG6172","vnd has no amnioserosa exp, although it does come on in migrating endoderm later","CG13366","cCRM is in a long transcript of this gene, but there's no good exp data for it","-","Strong, specific exp. in amnioserosa (internal as well as external) from st. 11."]
["ChIPCRM4231","intergenic","CG42831","no exp in embryo","CG7958","ubiquitous, brain, & some segmentally repeated nervous system exp","-","GFP comes on during st. 12 in ~1 CD2- cell / hs + a few CD2- head cells."]
["TyrR_33",{"$nulls":5},"-","No GFP detected at st.11-12; few cells (neurons?) very late."]
["slou_Dn_1",{"$nulls":5},"-","No GFP detected @ st. 11-12; 2 CD2- cells per hemisegment late."]
["CG2875_7",{"$nulls":5},"-","No GFP detected"]
["mew_35","intronic","CG1771","complex exp pattern includes faint ubiquitous, head ectoderm late",null,null,"-","No GFP detected in CD2+ cells; one cell per hs just VL to mesoderm; bright CD2- cells in late head."]
["nau_Dn_2",{"$nulls":5},"-","A few CD2- cells late in st. 12, with more very late."]