IntAct European Bioinformatics Institute IntAct intact http://www.ebi.ac.uk/ http://www.ebi.ac.uk/intact/query/${ac} EBI-[0-9]+|IA:[0-9]+ INTerAction database (IntAct) provides an open source database and toolkit for the storage, presentation and analysis of molecular interactions. http://www.ebi.ac.uk/intact European Bioinformatics Institute; Wellcome Trust Genome Campus; Hinxton, Cambridge; CB10 1SD; United Kingdom http://www.ebi.ac.uk/intact/ http://www.ebi.ac.uk/ feinberg-2007-1 in vitro In vitro emsa electrophoretic mobility shift assay Gel retardation assay band shift band shift Gel retardation assay emsa autoradiography autoradiography Feinberg MW., Wara AK., Cao Z., Lebedeva MA., Rosenbauer F., Iwasaki H., Hirai H., Katz JP., Haspel RL., Gray S., Akashi K., Segre J., Kaestner KH., Tenen DG., Jain MK. IBD - Inflammatory bowel disease EMSA methods section states "mobility shift analyses were performed as described (46)" - however it is not known which reference "46" refers to, as none of the references have numbers. Probe sequences were taken or deduced from figure 3C. mfeinberg@rics.bwh.harvard.edu,Mukesh.Jain2@case.edu The EMBO journal 2007 Only protein-protein interactions imex curation imex curation feinberg-2007-2 in vitro In vitro emsa supershift electrophoretic mobility supershift assay emsa supershift autoradiography autoradiography Feinberg MW., Wara AK., Cao Z., Lebedeva MA., Rosenbauer F., Iwasaki H., Hirai H., Katz JP., Haspel RL., Gray S., Akashi K., Segre J., Kaestner KH., Tenen DG., Jain MK. IBD - Inflammatory bowel disease EMSA methods section states "mobility shift analyses were performed as described (46)" - however it is not known which reference "46" refers to, as none of the references have numbers. Probe sequences were taken or deduced from figure 3B mfeinberg@rics.bwh.harvard.edu,Mukesh.Jain2@case.edu The EMBO journal 2007 Only protein-protein interactions imex curation imex curation feinberg-2007-3 human Homo sapiens Human ch-ip chromatin immunoprecipitation assay ch-ip primer specific pcr primer specific pcr Feinberg MW., Wara AK., Cao Z., Lebedeva MA., Rosenbauer F., Iwasaki H., Hirai H., Katz JP., Haspel RL., Gray S., Akashi K., Segre J., Kaestner KH., Tenen DG., Jain MK. IBD - Inflammatory bowel disease The cell line used for this experiment is not stated, however primers given in the supplement are human in origin. mfeinberg@rics.bwh.harvard.edu,Mukesh.Jain2@case.edu The EMBO journal 2007 Only protein-protein interactions imex curation imex curation klf4_human Krueppel-like factor 4 KLF4 EZF GKLF Epithelial zinc finger protein EZF Gut-enriched krueppel-like factor protein protein human Homo sapiens Human MRQPPGESDMAVSDALLPSFSTFASGPAGREKTLRQAGAPNNRWREELSHMKRLPPVLPGRPYDLAAATVATDLESGGAGAACGGSNLAPLPRRETEEFNDLLDLDFILSNSLTHPPESVAATVSSSASASSSSSPSSSGPASAPSTCSFTYPIRAGNDPGVAPGGTGGGLLYGRESAPPPTAPFNLADINDVSPSGGFVAELLRPELDPVYIPPQQPQPPGGGLMGKFVLKASLSAPGSEYGSPSVISVSKGSPDGSHPVVVAPYNGGPPRTCPKIKQEAVSSCTHLGAGPPLSNGHRPAAHDFPLGRQLPSRTTPTLGLEEVLSSRDCHPALPLPPGFHPHPGPNYPSFLPDQMQPQVPPLHYQGQSRGFVARAGEPCVCWPHFGTHGMMLTPPSSPLELMPPGSCMPEEPKPKRGRRSWPRKRTATHTCDYAGCGKTYTKSSHLKAHLRTHTGEKPYHCDWDGCGWKFARSDELTRHYRKHTGHRPFQCQKCDRAFSRSDHLALHMKRHF mint cd14_distal_promoter_probe dna deoxyribonucleic acid DNA deoxyribonucleic acid dna DNA deoxyribonucleic acid human Homo sapiens Human CCCACACCCACC cd14_proximal_promoter_probe dna deoxyribonucleic acid DNA deoxyribonucleic acid dna DNA deoxyribonucleic acid human Homo sapiens Human GGGGAG spi1_human Transcription factor PU.1 SPI1 31 kDa-transforming protein protein protein human Homo sapiens Human MLQACKMEGFPLVPPPSEDLVPYDTDLYQRQTHEYYPYLSSDGESHSDHYWDFHPHHVHSEFESFAENNFTELQSVQPPQLQQLYRHMELEQMHVLDTPMVPPHPSLGHQVSYLPRMCLQYPSLSPAQPSSDEEEGERQSPPLEVSDGEADGLEPGPGLLPGETGSKKKIRLYQFLLDLLRSGDMKDSIWWVDKDKGTFQFSSKHKEALAHRWGIQKGNRKKMTYQKMARALRNYGKTGEVKKVKKKLTYQFSGEVLGRGGLAERRHPPH klf4_human_gene Krueppel-like factor 4 KLF4 EZF GKLF gene gene human Homo sapiens Human cd14_distal_promoter_probe-klf4-1 1858012 N/A 1858015 unspecified role unspecified role prey prey region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 1858016 unspecified role unspecified role bait bait region 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false C2T,C3T,C5T,C7T,C8G,C9T,C11T mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false chemical synthesis Chemical synthesis (Chemical synthesis) direct interaction direct interaction false false false 3D O43474 increases expression at RNA level of ENSG00000170458 O43474 increases expression at protein level of ENSG00000170458 cd14_proximal_promoter_probe-klf4-2 1858012 N/A 1858015 unspecified role unspecified role prey prey region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 1858017 unspecified role unspecified role bait bait region 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false G1T,G3T mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false chemical synthesis Chemical synthesis (Chemical synthesis) direct interaction direct interaction false false false 3Di The sequence given for the -82 to -92 probe in figure 3C is only 6 nucleotides long, and is thus a partial sequence only. An unambiguous location for this sequence (GAGGGG) cannot be found in the CD14 promoter. cd14_distal_promoter_probe-klf4-3 1858013 N/A 1858015 unspecified role unspecified role prey prey region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 1858016 unspecified role unspecified role bait bait region 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false chemical synthesis Chemical synthesis (Chemical synthesis) physical association physical association false false false 3D cd14_proximal_promoter_probe-klf4-1 1858013 N/A 1858015 unspecified role unspecified role prey prey region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 1858017 unspecified role unspecified role bait bait region 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false chemical synthesis Chemical synthesis (Chemical synthesis) physical association physical association false false false 3Di The sequence given for the -82 to -92 probe in figure 3C is only 6 nucleotides long, and is thus a partial sequence only. An unambiguous location for this sequence (GAGGGG or GGGGAG) cannot be found in the CD14 promoter. spi1-klf4-1 1858014 N/A 1858018 unspecified role unspecified role bait bait N/A 1858019 unspecified role unspecified role prey prey promoter_region sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false association association false false false 5G