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/ The Kruppel-like factor KLF4 is a critical regulator of monocyte differentiation. The Kruppel-like factor KLF4 is a critical regulator of monocyte differentiation. The EMBO journal 2007 imex curation 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 mfeinberg@rics.bwh.harvard.edu,Mukesh.Jain2@case.edu 21-10-2015: Contacted by IntAct-Help. Only protein-protein interactions imex curation 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 I have checked EMBO and PMC sites - none of the references have numbers - but probably not a very relevant ref. anyway... mfeinberg@rics.bwh.harvard.edu,Mukesh.Jain2@case.edu Accepted 2015-OCT-02 AT 09:30 BST AT 09:30 BST by ORCHARD The EMBO journal 2007 Only protein-protein interactions imex curation imex curation The Kruppel-like factor KLF4 is a critical regulator of monocyte differentiation. The Kruppel-like factor KLF4 is a critical regulator of monocyte differentiation. The EMBO journal 2007 imex curation 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 mfeinberg@rics.bwh.harvard.edu,Mukesh.Jain2@case.edu 21-10-2015: Contacted by IntAct-Help. Only protein-protein interactions imex curation 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. I have checked EMBO and PMC sites - none of the references have numbers - but probably not a very relevant ref. anyway... mfeinberg@rics.bwh.harvard.edu,Mukesh.Jain2@case.edu Accepted 2015-OCT-02 AT 09:30 BST AT 09:30 BST by ORCHARD The EMBO journal 2007 Only protein-protein interactions imex curation imex curation The Kruppel-like factor KLF4 is a critical regulator of monocyte differentiation. The Kruppel-like factor KLF4 is a critical regulator of monocyte differentiation. The EMBO journal 2007 imex curation 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 mfeinberg@rics.bwh.harvard.edu,Mukesh.Jain2@case.edu 21-10-2015: Contacted by IntAct-Help. Only protein-protein interactions imex curation 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 Accepted 2015-OCT-02 AT 09:30 BST AT 09:30 BST by ORCHARD The EMBO journal 2007 Only protein-protein interactions imex curation imex curation cd14_proximal_promoter_probe dna deoxyribonucleic acid DNA deoxyribonucleic acid dna DNA deoxyribonucleic acid human Homo sapiens Human GGGGAG cd14_distal_promoter_probe dna deoxyribonucleic acid DNA deoxyribonucleic acid dna DNA deoxyribonucleic acid human Homo sapiens Human CCCACACCCACC klf4_human_gene Krueppel-like factor 4 KLF4 EZF GKLF gene gene human Homo sapiens Human 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 DIP protein O43474 original sequence version: 126 DIP protein O43474 original sequence version: 139 DIP protein O43474 original sequence version: 115 mint 3B6113A3EF333935 spi1_human Transcription factor PU.1 SPI1 31 kDa-transforming protein protein protein human Homo sapiens Human MLQACKMEGFPLVPPPSEDLVPYDTDLYQRQTHEYYPYLSSDGESHSDHYWDFHPHHVHSEFESFAENNFTELQSVQPPQLQQLYRHMELEQMHVLDTPMVPPHPSLGHQVSYLPRMCLQYPSLSPAQPSSDEEEGERQSPPLEVSDGEADGLEPGPGLLPGETGSKKKIRLYQFLLDLLRSGDMKDSIWWVDKDKGTFQFSSKHKEALAHRWGIQKGNRKKMTYQKMARALRNYGKTGEVKKVKKKLTYQFSGEVLGRGGLAERRHPPH DIP protein P17947 original sequence version: 88 9592DAA1D85053ED cd14_distal_promoter_probe-klf4-1 2 7 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 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 5 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 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 CC TT certain certain sequence position certain certain certain sequence position certain CCC TGT certain certain sequence position certain certain certain sequence position certain C T certain certain sequence position certain certain certain sequence position certain C T chemical synthesis Chemical synthesis (Chemical synthesis) direct interaction direct interaction 3D O43474 increases expression at RNA level of ENSG00000170458 O43474 increases expression at protein level of ENSG00000170458 cd14_proximal_promoter_probe-klf4-2 2 7 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 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 4 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 G1T,G3T mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain G T certain certain sequence position certain certain certain sequence position certain G T chemical synthesis Chemical synthesis (Chemical synthesis) direct interaction direct interaction 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 1 7 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 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 5 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 chemical synthesis Chemical synthesis (Chemical synthesis) physical association physical association 3D cd14_proximal_promoter_probe-klf4-1 1 7 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 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 4 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 chemical synthesis Chemical synthesis (Chemical synthesis) physical association physical association 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 3 8 unspecified role unspecified role bait bait 6 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 association association 5G