Curation Information

Publication
Global transcriptional control by glucose and carbon regulator CcpA in Clostridium difficile.;Antunes A, Camiade E, Monot M, Courtois E, Barbut F, Sernova NV, Rodionov DA, Martin-Verstraete I, Dupuy B;Nucleic acids research 2012 Nov; 40(21):10701-18 [22989714]
TF
CcpA [Q18AR8, view regulon]
Reported TF sp.
Clostridium difficile JIR8094
Reported site sp.
Clostridium difficile JIR8094
Created by
Dinara Sagitova
Curation notes
-
External databases
NCBI GEO (GSE35152) http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE35152.

Experimental Process

DNA microarray analysis of the wild-type and ccpA mutant strains identified gene differentially expressed in the presence of glucose. Microarray results were confirmed by performing qRT-PCR with RNA of 15 representative genes. ChIP-on-chip experiments identified the direct target sites of CcpA in vivo. CcpA consensus sequence in the ChIP-chip peaks with enrichment factor > 5 was identified by MEME. The identified CcpA motif was then used to search for for similar CcpA binding sites for all genes identified by the ChIP-on-Chip experiment. EMSAs with 15 DNA fragments containing a putative CcpA binding sites validated the targets identified in by ChIP-chip experiments. Furthermore, the binding was abolished in DNA fragments in which the CcpA binding sites were deleted.

ChIP assay conditions
The chromatin immunoprecipitations (ChIP) were performed using three independent cultures for each strain. The C. difficile JIR8094 and its isogenic ccpA mutant (negative control) strains were grown in TYG medium until an optic density (OD)600 of 0.6. The cells were treated with formaldehyde (final concentration: 1%) and incubated for 10 min at 37°C. Cross-linking was quenched by addition of glycine (final concentration: 400 mM). Cells were then collected by centrifugation, washed twice with Tris-buffered saline (20 mM Tris–HCl pH 7.5, 150 mM NaCl) and stored at −80°C.
ChIP notes
Pellets were resuspended in 10 ml of buffer A [50 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES)–KOH pH 7.5, 150 mM NaCl, 1 mM ethylenediaminetetraacetic acid (EDTA), 1% Triton X-100, 0.1% sodium dodecyl sulphate (SDS), 0.1% sodium deoxycholate and Complete antiprotease] and sonicated in a water bath sonicator (Bioruptor, Diagenode) to shear DNA to an average size of 400–600 bp. After centrifugation, the supernatant was incubated for 3 h at 4°C in the presence of 40 µl of Dynabeads® Pan mouse IgG (Life Technologies™) on a rotating wheel. Dynabeads were then removed (non-specific immunoprecipitation), and supernatant was incubated at 4°C overnight with polyclonal anti-CcpA antibodies (1/500 dilution). The mixture was then incubated with 50 µl of Dynabeads® Pan mouse IgG (Life Technologies™) for 90 min at 4°C and washed twice with buffer A, once with buffer A plus 500 mM NaCl, once with buffer B (10 mM Tris–HCl pH 8.0, 1 mM EDTA, 0.1% Nonidet-P40,0.5% sodium deoxycholate) and once with 10 mM Tris–HCl pH 7.5, 1 mM EDTA. Antibodies bound to the magnetic beads were then eluted for 20 min at 65°C with 100 µl of elution buffer (50 mM Tris–HCl pH 7.5, 10 mM EDTA, 1% SDS). Samples were then treated with proteinase K (50 µg) for 2 h at 56°C and 6 h at 65°C in a 0.5× elution buffer. Immunoprecipitated DNA samples were finally purified using the QIAquick polymerase chain reaction (PCR) purification kit (QIAGEN). DNA obtained from immunoprecipitation was then labelled with Cy5 or Cy3 using the Bioprime plus array CGH indirect genomic labelling system (Invitrogen) as recommended by the manufacturer. Labelled DNA hybridization to microarrays and array scanning were done according to Saujet et al. The complete experimental data set were deposited in the GEO database with the accession number GSE34971.

Transcription Factor Binding Sites


AGTAAAACGGTTTCCT
AAGAAAACGTTATTAC
GAGAAAATGTTTACAG
AGGAAAACGTTATGCT
TCAAAAAGATTTTCAT
AAGAAAACGTTAAGCA
AGGAAAACGTATTATA
GAGAAAAGGATTTCTA
AGAAAAACGTTAACTT
ATGATAACATTTTCTT
GGGAAAACGATACCAA
GAGAAAAAGACATCAT
AGGAAATGGTATTTGT
AAGAAAACCTTATCTA
GAGAAAAGGTTTCCAA
GAAAAAATGTTTTTTT
TGTAAAAAGTTTAGTT
AGGAAATAGTTAACTT
TAGAAAACGTTTTAAA
AAGAAAGCGTTTTGAA
AAGATAACGATTGCTT
AAGAAAACGATTTTGT
TAGAAAAGGTTATCAT
TTGAAAACGTTTAGTG
AGGAAATAGATAAGTT
GAGAAAAGGTTTTGTT
TATAAAACGTTTTCTT
AAATAAAGGTTTTCTT
TAGAAAATGTTTGCAG
GAGAAAAAATTATAAA
AAGAAAAAGTTTTCAT
AAGAAATCGTTTCTTT
GGGAAAACATTTTCTT
AAGATAAAATTTTTTT
CAGAAAAGGTTTGCAA
GAGAAAAGGTATGCAA
TTGAAAAAGATTACTA
TGGAAATAGTTTTCTT
AGGATAACGTTATCAT
GAGAAAAAATATACAA
ATGTAAACGTTATCTT
AAGAAAAAAATAGGTT
GGGAAAACGTTAACAA
TAGATAAGGTTTTCTT
ATGAAAAAGTTTTCTT
AGGAGAACATTATCAA
TAGATTTGGTTTAAAT
GAGTTAACGTTTTCAA
GAGAAAATGTTTACAA
CTGATAACGTTTTCTA
AAGAAAAGGCTTTCTA
AAGAAAACATTTTCAT
AGTAAAACGGTTTCCT
AAGAAAACGTTATTAC
GAGAAAATGTTTACAG
AGGAAAACGTTATGCT
TCAAAAAGATTTTCAT
AAGAAAACGTTAAGCA
AGGAAAACGTATTATA
GAGAAAAGGATTTCTA
AGAAAAACGTTAACTT
ATGATAACATTTTCTT
GGGAAAACGATACCAA
GAGAAAAAGACATCAT
AGGAAATGGTATTTGT
AAGAAAACCTTATCTA
GAGAAAAGGTTTCCAA
GAAAAAATGTTTTTTT
TGTAAAAAGTTTAGTT
AGGAAATAGTTAACTT
TAGAAAACGTTTTAAA
AAGAAAGCGTTTTGAA
AAGATAACGATTGCTT
AAGAAAACGATTTTGT
TAGAAAAGGTTATCAT
TTGAAAACGTTTAGTG
AGGAAATAGATAAGTT
GAGAAAAGGTTTTGTT
TATAAAACGTTTTCTT
AAATAAAGGTTTTCTT
TAGAAAATGTTTGCAG
GAGAAAAAATTATAAA
AAGAAAAAGTTTTCAT
AAGAAATCGTTTCTTT
GGGAAAACATTTTCTT
AAGATAAAATTTTTTT
CAGAAAAGGTTTGCAA
GAGAAAAGGTATGCAA
TTGAAAAAGATTACTA
TGGAAATAGTTTTCTT
AGGATAACGTTATCAT
GAGAAAAAATATACAA
ATGTAAACGTTATCTT
AAGAAAAAAATAGGTT
GGGAAAACGTTAACAA
TAGATAAGGTTTTCTT
ATGAAAAAGTTTTCTT
AGGAGAACATTATCAA
TAGATTTGGTTTAAAT
GAGTTAACGTTTTCAA
GAGAAAATGTTTACAA
CTGATAACGTTTTCTA
AAGAAAAGGCTTTCTA
AAGAAAACATTTTCAT

Gene Regulation

Regulated genes for each binding site are displayed below. Gene regulation diagrams show binding sites, positively-regulated genes, negatively-regulated genes, both positively and negatively regulated genes, genes with unspecified type of regulation. For each indvidual site, experimental techniques used to determine the site are also given.

Site sequence Regulated genes Gene diagram Experimental techniques TF function TF type
AGTAAAACGGTTTCCT rbsR, rbsK, rbsB, rbsA, rbsC
... ... rbsR rbsK rbsB rbsA rbsC
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor not specified
AAGAAAACGTTATTAC CD630_02791
... ... CD630_02791
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
GAGAAAATGTTTACAG CD630_02010,
... ... CD630_02010 CD630_02000
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
AGGAAAACGTTATGCT hadA, ldhA, hadI, hadB, hadC, acdB, etfB1, etfA1
... ... hadA ldhA hadI hadB hadC acdB etfB1 etfA1
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor not specified
TCAAAAAGATTTTCAT CD630_04670, CD630_04680, CD630_04690
... ... CD630_04670 CD630_04680 CD630_04690
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
AAGAAAACGTTAAGCA CD630_04940,
... ... CD630_04940 CD630_04960 CD630_04970 CD630_04980 CD630_04981 CD630_04990 CD630_04991 CD630_05000 CD630_05010 CD630_05020 CD630_05030 CD630_05040 CD630_05060
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
AGGAAAACGTATTATA CD630_05300, CD630_05290, CD630_05280,
... ... CD630_05300 CD630_05290 CD630_05280 CD630_05310
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
GAGAAAAGGATTTCTA CD630_05760
... ... CD630_05760
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
AGAAAAACGTTAACTT gapN,
... ... gapN CD630_05790
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
ATGATAACATTTTCTT CD630_06790,
... ... CD630_06790 CD630_06800 CD630_06810 CD630_06820 CD630_06830
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
GGGAAAACGATACCAA glpK1, CD630_07420,
... ... glpK1 CD630_07420 CD630_07400
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
GAGAAAAAGACATCAT CD630_07790, CD630_07800
... ... CD630_07790 CD630_07800
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
AGGAAATGGTATTTGT acnB, icd
... ... acnB icd
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor not specified
AAGAAAACCTTATCTA oppC,
... ... oppC oppA oppD oppF
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor not specified
GAGAAAAGGTTTCCAA CD630_11160,
... ... CD630_11160 CD630_11150 CD630_11140 CD630_11130 CD630_11120 CD630_11110 CD630_11100 CD630_11090 CD630_11080 CD630_11071 CD630_11070 CD630_11061 topB CD630_11050 CD630_11042 CD630_11041
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
GAAAAAATGTTTTTTT rnfC,
... ... rnfC rnfD rnfG rnfE rnfA rnfB
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TGTAAAAAGTTTAGTT spo0A
... ... spo0A
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor not specified
AGGAAATAGTTAACTT CD630_13210,
... ... CD630_13210 dapG tepA ftsK CD630_13250 rimO pgsA
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TAGAAAACGTTTTAAA CD630_13360,
... ... CD630_13360 CD630_13370 CD630_13380
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
AAGAAAGCGTTTTGAA CD630_13850,
... ... CD630_13850 CD630_13840 CD630_13830 CD630_13860 CD630_13870
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
AAGATAACGATTGCTT feoA,
... ... feoA feoA feoB1 CD630_14800
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
AAGAAAACGATTTTGT CD630_15360,
... ... CD630_15360 sseA aspB
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TAGAAAAGGTTATCAT CD630_15860,
... ... CD630_15860 CD630_15870 CD630_15880 CD630_15890
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TTGAAAACGTTTAGTG thiD,
... ... thiD thiM thiE CD630_16020
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
AGGAAATAGATAAGTT gcvPB,
... ... gcvPB gcvTPA
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
GAGAAAAGGTTTTGTT CD630_17680,
... ... CD630_17680 CD630_17671
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
TATAAAACGTTTTCTT CD630_18930,
... ... CD630_18930 CD630_18940
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
AAATAAAGGTTTTCTT spoVS
... ... spoVS
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TAGAAAATGTTTGCAG CD630_21110,
... ... CD630_21110 CD630_21100
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
GAGAAAAAATTATAAA CD630_21730,
... ... CD630_21730 CD630_21720
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
AAGAAAAAGTTTTCAT nanE,
... ... nanE nanA CD630_22390 CD630_22380
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
AAGAAATCGTTTCTTT CD630_22800,
... ... CD630_22800 CD630_22790 araD CD630_22770
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
GGGAAAACATTTTCTT CD630_23270,
... ... CD630_23270 CD630_23260 CD630_23250 CD630_23240 CD630_23230 tkt tkt'
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor not specified
AAGATAAAATTTTTTT CD630_23440,
... ... CD630_23440 cat1 sucD CD630_23450
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
CAGAAAAGGTTTGCAA CD630_23470,
... ... CD630_23470 CD630_23460
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
GAGAAAAGGTATGCAA CD630_24290,
... ... CD630_24290 CD630_24280 CD630_24270
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TTGAAAAAGATTACTA ung,
... ... ung CD630_24800
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TGGAAATAGTTTTCTT cstA
... ... cstA
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
AGGATAACGTTATCAT CD630_26250,
... ... CD630_26250 CD630_26240 CD630_26230 sepF CD630_26210 CD630_26200 CD630_26190
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
GAGAAAAAATATACAA CD630_26260
... ... CD630_26260
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
ATGTAAACGTTATCTT scoB,
... ... scoB bdhA CD630_26800
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
AAGAAAAAAATAGGTT CD630_26930
... ... CD630_26930
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
GGGAAAACGTTAACAA brnQ
... ... brnQ
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
TAGATAAGGTTTTCTT CD630_28790,
... ... CD630_28790 fhuD fhuB fhuG fhuC CD630_28740
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
ATGAAAAAGTTTTCTT celA,
... ... celA celB celF celG celC
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
AGGAGAACATTATCAA cggR,
... ... cggR gapA
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TAGATTTGGTTTAAAT dpaL,
... ... dpaL CD630_31830 CD630_31820 CD630_31810
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
GAGTTAACGTTTTCAA CD630_32180,
... ... CD630_32180 CD630_32170
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
GAGAAAATGTTTACAA prdA,
... ... prdA CD630_32430 prdB prdD prdE CD630_32380 prdF CD630_32360
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
CTGATAACGTTTTCTA CD630_34060,
... ... CD630_34060 CD630_34070
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
AAGAAAAGGCTTTCTA rlmH,
... ... rlmH licB licA
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified
AAGAAAACATTTTCAT CD630_36640
... ... CD630_36640
Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - not specified not specified