E3 ubiquitin ligase sub-families


""/>

Sequence information

>RGAP V7 Locus >Family >Domain position >Chromosome >5' end >3' end >Alternative spliced products >RGAP V7 Annotation >RAP-DB Locus >NCBI Blast >Literature information Check/Uncheck All

Plant orthologs

>Arabidopsis thaliana >Brachypodium distachyon >Zea mays >Cucumis sativus >Medicago truncatula >Mimulus guttatus >Populus trichocarpa >Ricinus communis >Vitis vinifera >Sorghum bicolor >Glycine max >Solanum lycopersicum >Triticum aestivum >Setaria italica >Hordeum vulgare Check/Uncheck All

Topology

>Transmembrane Domain (TM) >N-terminal Signal Peptide (SignalP) >Chloroplast Transit Peptide (ChloroP) >Predicted Subcellular Localization Check/Uncheck All

Mutants

>DJ-Ds >INDICA-Ds >AFFJP >CIRAD >GSNU >GSNU >OSTID >PFG_FSTs >RIFGP >RMD >SHIP >TRIM >UCD >UCD_FN Check/Uncheck All

Microarray

Affymetrix: >Anatomy >Anatomy_Simplified >Abiotic >Biotic
Agilent: >Anatomy >Hormone
Scale bar for single channel array: 7,13       Scale bar for two channel array: -1,0,1 -2,0,2 -3,0,3

RNASeq

RNASEq: >Anatomy >Abiotic
>Display Values >Display Heatmap


0 ) { $tree_length = array('AB13VPI' => '13.2' , 'Alfin-like' => '12.5' , 'AP2-EREBP' => '13.28', 'ARF' => '12.95', 'ARR-B' => '12.5', 'ARID' => '11.9', 'AUX' => '13.02', 'Coactivator' => '10.9','BBR_BPC' => '11.5', 'BES1' => '12', 'bHLH' => '13.26', 'BSD' => '12.4', 'bZIP' => '13.25' , 'C2C2-CO-like' => '12.8', 'C2C2-Dof' => '13', 'C2C2-GATA' => '13' , 'C2C2-YABBY' => '12.1' , 'C2H2' => '13.23' , 'C3H' => '13.2' , 'CAMTA' => '12' , 'CCAAT' => '13.1', 'CPP' => '12.5', 'CSD' => '11', 'DBP' => '12.1', 'E2F-DP' => '12.35', 'EIL' => '12.5' , 'FAR1' => '13.27', 'FHA' => '12.9', 'G2_like' => '13.1', 'GeBP' => '11.8', 'GRAS' => '13.18', 'GRF' => '12.6', 'HB' => '13.23', 'HRT' => '28.23', 'HSF' => '13', 'LFY' => '26.1', 'LIM' => '12', 'LOB' => '13.05', 'MADS' => '13.2', 'mTERF' => '13.05', 'MYB' => '13.25', 'MYB-related' => '13.23', 'NAC' => '13.26', 'OFP' => '13', 'Orphans' => '13.21', 'PBF-2-like' => '17.2', 'PLATZ' => '12.7', 'RWP-RK' => '12.65', 'S1Fa-like' => '17.3', 'SBP' => '12.9', 'Sigma70-like' => '11.5', 'SRS' => '12', 'TAZ' => '11', 'TCP' => '12.9', 'Tify' => '12.8', 'Trihelix' => '12.9', 'TUB' => '12.7', 'ULT' => '16.2', 'VOZ' => '16.2', 'WRKY' => '13.25', 'zf-HD' => '12.7', 'DDT' => '11.95', 'GNAT' => '13.1', 'HMG' => '12.4', 'Jumonji' => '12.7', 'LUG' => '12.1', 'PHD' => '13.15', 'pseudoarrb' => '11.3', 'Rcd1' => '11.7', 'SET' => '13.04', 'SNF2' => '13.07', 'SWIBAF60b' => '12.5', 'SW13' => '11.7', 'TRAF' => '13.22', 'IWS1' => '27.2', 'MBF1' => '17.2', 'MED6' => '12', 'MED7' => '12', 'RB' => '11.8', 'SOH1' => '17.5'); } elseif(strlen(strstr($agent,"Firefox")) > 0 ) { $tree_length = array('AB13VPI' => '13.2' , 'Alfin-like' => '12.5' , 'AP2-EREBP' => '13.27', 'ARF' => '12.99', 'ARR-B' => '12.7', 'ARID' => '12', 'AUX' => '13.04', 'Coactivator' => '11.5','BBR_BPC' => '12', 'BES1' => '12.5', 'bHLH' => '13.27', 'BSD' => '12.4', 'bZIP' => '13.2' , 'C2C2-CO-like' => '12.9', 'C2C2-Dof' => '13.1', 'C2C2-GATA' => '13' , 'C2C2-YABBY' => '12.7' , 'C2H2' => '13.25' , 'C3H' => '13.23' , 'CAMTA' => '12.5' , 'CCAAT' => '13.15', 'CPP' => '12.7', 'CSD' => '11.6', 'DBP' => '12.5', 'E2F-DP' => '12.55', 'EIL' => '12.5' , 'FAR1' => '13.25', 'FHA' => '12.9', 'G2_like' => '13.18', 'GeBP' => '12.2', 'GRAS' => '13.2', 'GRF' => '12.6', 'HB' => '13.23', 'HRT' => '27.3', 'HSF' => '13', 'LFY' => '27.1', 'LIM' => '12.5', 'LOB' => '13.12', 'MADS' => '13.2', 'mTERF' => '13.1', 'MYB' => '13.26', 'MYB-related' => '13.22', 'NAC' => '13.25', 'OFP' => '13.07', 'Orphans' => '13.2', 'PBF-2-like' => '17.5', 'PLATZ' => '12.9', 'RWP-RK' => '12.6', 'S1Fa-like' => '17.6', 'SBP' => '13.01', 'Sigma70-like' => '11.9', 'SRS' => '12.4', 'TAZ' => '11.5', 'TCP' => '13', 'Tify' => '12.9', 'Trihelix' => '13', 'TUB' => '12.8', 'ULT' => '17.1', 'VOZ' => '17.5', 'WRKY' => '13.25', 'zf-HD' => '12.82', 'DDT' => '12', 'GNAT' => '13.1', 'HMG' => '12.55', 'Jumonji' => '12.8', 'LUG' => '12.1', 'PHD' => '13.15', 'pseudoarrb' => '11.5', 'Rcd1' => '12.2', 'SET' => '13.1', 'SNF2' => '13.1', 'SWIBAF60b' => '12.65', 'SW13' => '11.7', 'TRAF' => '13.2', 'IWS1' => '27.2', 'MBF1' => '17.2', 'MED6' => '12', 'MED7' => '12', 'RB' => '12.2', 'SOH1' => '18.2'); } elseif(strlen(strstr($agent,"Trident")) > 0 ) { $tree_length = array('AB13VPI' => '13.2' , 'Alfin-like' => '12.5' , 'AP2-EREBP' => '13.27', 'ARF' => '12.99', 'ARR-B' => '12.7', 'ARID' => '12', 'AUX' => '13.04', 'Coactivator' => '11.5','BBR_BPC' => '12', 'BES1' => '12.5', 'bHLH' => '13.27', 'BSD' => '12.4', 'bZIP' => '13.2' , 'C2C2-CO-like' => '12.9', 'C2C2-Dof' => '13.1', 'C2C2-GATA' => '13' , 'C2C2-YABBY' => '12.7' , 'C2H2' => '13.25' , 'C3H' => '13.18' , 'CAMTA' => '12.5' , 'CCAAT' => '13.15', 'CPP' => '12.7', 'CSD' => '11.6', 'DBP' => '12.5', 'E2F-DP' => '12.55', 'EIL' => '12.5' , 'FAR1' => '13.25', 'FHA' => '12.8', 'G2_like' => '13.18', 'GeBP' => '12.2', 'GRAS' => '13.2', 'GRF' => '12.6', 'HB' => '13.23', 'HRT' => '27.3', 'HSF' => '13', 'LFY' => '27.1', 'LIM' => '12.5', 'LOB' => '13.12', 'MADS' => '13.2', 'mTERF' => '13.1', 'MYB' => '13.26', 'MYB-related' => '13.22', 'NAC' => '13.25', 'OFP' => '13.07', 'Orphans' => '13.2', 'PBF-2-like' => '17.5', 'PLATZ' => '12.9', 'RWP-RK' => '12.6', 'S1Fa-like' => '17.6', 'SBP' => '13.01', 'Sigma70-like' => '12.5', 'SRS' => '12.4', 'TAZ' => '11.5', 'TCP' => '13', 'Tify' => '12.9', 'Trihelix' => '13', 'TUB' => '12.8', 'ULT' => '17.1', 'VOZ' => '17.5', 'WRKY' => '13.25', 'zf-HD' => '12.82', 'DDT' => '12', 'GNAT' => '13.1', 'HMG' => '12.55', 'Jumonji' => '12.8', 'LUG' => '12.1', 'PHD' => '13.15', 'pseudoarrb' => '11', 'Rcd1' => '12.2', 'SET' => '13.1', 'SNF2' => '13.1', 'SWIBAF60b' => '12.6', 'SW13' => '11.7', 'TRAF' => '13.2', 'IWS1' => '27.2', 'MBF1' => '17.2', 'MED6' => '12.5', 'MED7' => '12.5', 'RB' => '12.2', 'SOH1' => '18.2'); } else { $tree_length = array('AB13VPI' => '13.2' , 'Alfin-like' => '12.5' , 'AP2-EREBP' => '13.27', 'ARF' => '12.99', 'ARR-B' => '12.7', 'ARID' => '12', 'AUX' => '13.04', 'Coactivator' => '11.5','BBR_BPC' => '12', 'BES1' => '12.5', 'bHLH' => '13.27', 'BSD' => '12.4', 'bZIP' => '13.2' , 'C2C2-CO-like' => '12.9', 'C2C2-Dof' => '13.1', 'C2C2-GATA' => '13' , 'C2C2-YABBY' => '12.7' , 'C2H2' => '13.25' , 'C3H' => '13.18' , 'CAMTA' => '12.5' , 'CCAAT' => '13.15', 'CPP' => '12.7', 'CSD' => '11.6', 'DBP' => '12.5', 'E2F-DP' => '12.55', 'EIL' => '12.5' , 'FAR1' => '13.25', 'FHA' => '12.8', 'G2_like' => '13.18', 'GeBP' => '12.2', 'GRAS' => '13.2', 'GRF' => '12.6', 'HB' => '13.23', 'HRT' => '27.3', 'HSF' => '13', 'LFY' => '27.1', 'LIM' => '12.5', 'LOB' => '13.12', 'MADS' => '13.2', 'mTERF' => '13.1', 'MYB' => '13.26', 'MYB-related' => '13.22', 'NAC' => '13.25', 'OFP' => '13.07', 'Orphans' => '13.2', 'PBF-2-like' => '17.5', 'PLATZ' => '12.9', 'RWP-RK' => '12.6', 'S1Fa-like' => '17.6', 'SBP' => '13.01', 'Sigma70-like' => '12.5', 'SRS' => '12.4', 'TAZ' => '11.5', 'TCP' => '13', 'Tify' => '12.9', 'Trihelix' => '13', 'TUB' => '12.8', 'ULT' => '17.1', 'VOZ' => '17.5', 'WRKY' => '13.25', 'zf-HD' => '12.82', 'DDT' => '12', 'GNAT' => '13.1', 'HMG' => '12.55', 'Jumonji' => '12.8', 'LUG' => '12.1', 'PHD' => '13.15', 'pseudoarrb' => '11', 'Rcd1' => '12.2', 'SET' => '13.1', 'SNF2' => '13.1', 'SWIBAF60b' => '12.6', 'SW13' => '11.7', 'TRAF' => '13.2', 'IWS1' => '27.2', 'MBF1' => '17.2', 'MED6' => '12.5', 'MED7' => '12.5', 'RB' => '12.2', 'SOH1' => '18.2'); }; $ordered_gene = $newtre.'.txt'; $data = file_get_contents("./ord/$ordered_gene"); $checked = implode(',',$_POST['check_list']); $database = implode(',',$_POST['check_list2']); $database_part = explode('*',$database); //this array contains list of all databases// $database2= explode(',',$database_part[0]); //this array contains display options ie, values and/or heatmap// $mode2=array($database_part[1],$database_part[2]); $mode2 = str_replace('values,', 'values', $mode2); //this variable contains two channel scale// $scale_multi = $_POST['radio']; //..................................................to get the button value. This value is to 1) make the tree figure 2)get the gene list from the file with same name $selected = explode(",", $checked); $fam=array_shift($selected); $values = implode(",", $selected); //this array contains all the checked items// $values2 = explode(",", $values); //this varaible contains number of checked items, for later table colums making// $len2 = count($values2); //this removes display mode if user didnt select any database and but selected display method// $database2 = array_filter($database2); $mode2 = array_filter($mode2); if (empty($database2)) { if (in_array('values',$mode2)) { unset($mode2); } } //this set the default display mode as values if user selected a database but not a display mode// if ($database2) { if (empty($mode2)) { $mode2[0]="values"; } } //if values are opted instead of heatmap, then add the intesnity values to the select * items// if (in_array("values", $mode2)) { if(in_array('tf_anatomy',$database2) || in_array('tf_anatomy_simplified',$database2) || in_array('tf_abiotic',$database2) || in_array('tf_biotic',$database2) || in_array('tf_hormone',$database2) || in_array('tf_anatomyrna',$database2) || in_array('tf_abioticrna',$database2) || in_array('tf_agilanatomy',$database2)) { $pool = array_merge($values2, $database2); $replace_1 = preg_replace('/\btf_anatomy\b/','`Affy anatomy_probe_ID`, `Callus_indica` , `Callus_Japonica` , `Coleoptile` , `Leaf_indica` , `Leaf_japonica` , `FLB tip` , `FLB` , `FLS` , `Radicle_indica` , `Root_indica` , `Root_japonica` , `Root tip_Indica` , `Root tip_Japonica` , `Plumule` , `Shoot_Indica` , `Shoot_Japonica` , `Stem` , `Collar` , `Lamina joint` , `Node` , `Internode` , `SAM_indica` , `SAM_Japonica` , `Panicle_indica` , `Panicle_japonica` , `Panicle branch` , `Flower` , `Stamen` , `Anther` , `Pollen` , `Ovary`, `Stigma` , `Stigma ovary`, `Palea lemma`, `Spikelet`, `Seed`, `Embryo_dry seed` , `Embryo_germinating seed`, `Embryosac`, `Endosperm`',$pool); $replace_2 = preg_replace('/\btf_anatomy_simplified\b/','`Callus` , `Leaf` , `Flag leaf` , `Root` , `Shoot` , `Stems` , `SAM` , `Panicles` , `Flowers` , `Whole anther` , `Pollens` , `Stigma_ovary` , `Seeds` , `Embryo` , `Endosperms` ',$pool); $replace_3 = preg_replace('/\btf_abiotic\b/','`Affy abiotic Probe_ID`, `Pb_100 uM`, `Cd_100 uM`, `Cr (VI)_100 uM`, `AsV_100 uM`, `Arsenate_1ppm`, `Root_+Fe+P`, `Root_+Fe-P`, `Root_-Fe+P`, `Shoot_+Fe+P`, `Shoot_+Fe-P`, `Shoot_-Fe+P`, `MeOH_1d`, `Root drought`, `Leaf dought`, `Slight drought_D1`, `Moderate drought_D2`, `Severe drought _D3`, `Panicle Drought`, `Seedling drought`, `Seedling salt`, `Bulk sensitive salt`, `Bulk tolerant salt`, `50mM NaCl`, `200mM NaCl (3hrs)`, `Seedling cold`, `Low temp. (12C)`, `Cold stress (4C)_2hr`, `Cold stress (4C)_6hr`, `Cold stress (4C)_12hr`, `Cold stress (4C)_24hr`, `Cold stress (4C)_48hr`, `High temp.(45C)`, `Seedling heat`, `Anaerobic_1hr`, `Anaerobic_3hr`, `Anaerobic_12hr`, `Anaerobic_24hr`, `Anaerobic_27hr`, `Anaerobic_30hr`, `Pi_6hr`, `Pi_24hr`, `Pi_48hr`, `Pi_72hr`, `K+-deficient_6hr`, `K+-deficient_3d`, `K+-deficient_5d`',$pool); $replace_4 = preg_replace('/\btf_biotic\b/','`Affy biotic Probe_ID`,`M. grisea_isolate FR13` ,`M. grisea_isolate BR29`,`M. grisea_isolate BR32`,`M. grisea_isolate CL367`, `M. oryzae _24hr`, `M. oryzae_Guy11 2dpi`,`RSV_KT95 418`, RSV_WuYun3,Xoo,`Xoo_IR24_3hr-24hr`,`Xoo_IRBB5_3hr -24hr`,`Xoo_IRBB7_3hr-24hr`,`Xoo_Nipponbare_2 hai`,`Xoo_Nipponbare_4 hai`,`Xoo_Nipponbare_8 hai`,`Xoo_Nipponbare_24 hai`,`Xoo_Nipponbare_96 hai`, `Brown planthopper`',$pool); $replace_5 = preg_replace('/\btf_agilanatomy\b/','`Agilent anatomy probe_ID`, `Leaf blade`, `Leaf sheath`, `Flag leaves`, `Whole stem`, `Root hair`, `Roots`, `Inflorescence`, `Anther tissue`, `Ovaries`, `Pistils`, `Palea`, `Lemma`, `Embryos`, `Seed endosperm`',$pool); $replace_6 = preg_replace('/\btf_hormone\b/','`Agilent hormone Probe_ID`, `Root ABA_15 min`, `Root ABA_30 min`, `Root ABA_1 hr`, `Root ABA_3 hr`, `Root ABA_6 hr`, `Shoot ABA_1 hr`, `Shoot ABA_3 hr`, `Shoot ABA_6 hr`, `Shoot ABA_12 hr`, `Root GA3_15 min`, `Root GA3_30 min`, `Root GA3_1 hr`, `Root GA3_3 hr`, `Root GA3_6 hr`, `Shoot GA3_1 hr`, `Shoot GA3_3 hr`, `Shoot GA3_6 hr`, `Shoot GA3_12 hr`, `Root IAA_15 min`, `Root IAA_30 min`, `Root IAA_1 hr`, `Root IAA_3 hr`, `Root IAA_6 hr`, `Shoot IAA_1 hr`, `Shoot IAA_3 hr`, `Shoot IAA_6 hr`, `Shoot IAA_12 hr`, `Root BL_15 min`, `Root BL_30 min`, `Root BL_1 hr`, `Root BL_3 hr`, `Root BL_6 hr`, `Shoot BL_1 hr`, `Shoot BL_3 hr`, `Shoot BL_6 hr`, `Shoot BL_12 hr`, `Root tZ_15 min`, `Root tZ_30 min`, `Root tZ_1 hr`, `Root tZ_3 hr`, `Root tZ_6 hr`, `Shoot tZ_1 hr`, `Shoot tZ_3 hr`, `Shoot tZ_6 hr`, `Shoot tZ_12 hr`, `Root JA_15 min`, `Root JA_30 min`, `Root JA_1 hr`, `Root JA_3 hr`, `Root JA_6 hr`, `Shoot JA_1 hr`, `Shoot JA_3 hr`, `Shoot JA_6 hr`, `Shoot JA_12 hr`',$pool); $replace_7 = preg_replace('/\btf_anatomyrna\b/','`Callus_1`, `Callus_2`, `Callus_3`, `Leaf_1`, `Leaf_2`, `Root_1`, `Root_2`, `Root_3`, `Shoot_1`, `Shoot_2`, `Shoot_3`, `SAM_1`, `SAM_2`, `SAM_3`, `Panicle_1`, `Panicle_2`, `Panicle_3` , `Pollen_5`, Pollen_6, Pollen_7, Embryo_1, Embryo_2, Endosperm_1, Endosperm_2, Seed_1, Seed_2, Seed_3',$pool); $replace_8 = preg_replace('/\btf_abioticrna\b/','`Root_1hr+Pi` , `Root_1hr-Pi` , `Root_6hr+Pi` , `Root_6hr-Pi`, `Root_24hr+Pi`, `Root_24hr-Pi`, `Root_3d+Pi`, `Root_3d-Pi`, `Root_7d+Pi`, `Root_7d-Pi`, `Root_21d+Pi`, `Root_21d-Pi`, `Root_21d+1hr+Pi`, `Root_21d+1hr-Pi`, `Root_21d+1hr_Pi_resupply`, `Root_21d+6hr+Pi`, `Root_21d+6hr-Pi`, `Root_21d+6hr_Pi_resupply`, `Root_21d+24 hr+Pi`, `Root_21d+24hr-Pi`, `Root_21d+24hr_Pi_resupply`, `Shoot_1hr+Pi`, `Shoot_1hr-Pi`, `Shoot_6hr+Pi`, `Shoot_6hr-Pi`, `Shoot_24hr+Pi`, `Shoot_24hr-Pi`, `Shoot_3d+Pi`, `Shoot_3d-Pi`, `Shoot_7d+Pi`, `Shoot_7d-Pi`, `Shoot_ 21d+Pi`, `Shoot_21d-Pi` , `Shoot_21d+1hr+Pi`, `Shoot_21d+1hr -Pi`, `Shoot_21d+1hr Pi_resupply`, `Shoot_21d + 6 hr +Pi`, `Shoot_21d + 6 hr-Pi`, `Shoot_21d+6hr_Pi_resupply`, `Shoot_21d+24hr+Pi`, `Shoot_21d+24hr-Pi`, `Shoot_21d+24hr_Pi_resupply`', $pool); $fetched=array_merge($replace_1, $replace_2, $replace_3, $replace_4,$replace_5, $replace_6, $replace_7, $replace_8); $fetched = array_unique($fetched); $fetched = array_filter($fetched); $fetched = array_diff($fetched, array('tf_anatomy', 'tf_anatomy_simplified','tf_abiotic','tf_biotic', 'tf_agilanatomy', 'tf_hormone','tf_anatomyrna','tf_abioticrna')); $fetched = implode(',', $fetched); } } else { $fetched = join(',',$values2); } $fetched="`RGAP 7 Model`, ".$fetched; //NOTE: $locus holds the value for fetched ordred locus list & $values2 holds the checkd items $locus = explode("\n", $data); $len = count($locus); $scale_single=713; //this finds the total number of colums, ir how many table heading to display and its namae// $titles=explode(",",$fetched); $length_head=count($titles); //mysql connection using pdo $dbc = "mysql:host=localhost;dbname=microarray"; $user = "root"; $pass = "microarray123"; $dbo = new PDO($dbc, $user, $pass); //checking if a heatmap option is selected $heat= "$database".",$mode"; $image_related_param = explode(",", $heat); $tffamily = $_SESSION["treetype"]; //############################################################# if (in_array("heatmap", $mode2)) { if (in_array("tf_anatomy", $database2)) { // echo here; $array_file = $newtre.".tf_anatomy.csv"; $array_file = trim($array_file); $filename = "/var/www/html/tf/fetched/$array_file"; if (file_exists($filename)) { $cmd = "php /var/www/html/tf/jpgraph/src/Examples/tf_anatomy.php $fam $len $array_file $tffamily "; system($cmd); } else { $data = fopen("/var/www/html/tf/fetched/$array_file", 'w'); for ($i=0;$i<=$len-2;$i++) { $id=$locus[$i]; $id=trim($id); $sql = "SELECT * FROM tf_anatomy WHERE `RGAP 7 Model`='$id'"; echo $sql; $qry = $dbo->prepare($sql); $qry->execute(); $row = $result->fetch(PDO::FETCH_ASSOC); unset($row['RGAP 7 Model']); unset($row['Affy anatomy_probe_ID']); unset($row['border']); fputcsv($data, $row); } chmod("/var/www/html/tf/fetched/$array_file",0777); $cmd = "php /var/www/html/tf/jpgraph/src/Examples/tf_anatomy.php $fam $len"; system($cmd); } } } //------------------------------------------------------------------------ if (in_array("heatmap", $mode2)) { if (in_array("tf_anatomy_simplified", $database2)) { $array_file = $newtre.".tf_anatomy_simplified.csv"; $array_file = trim($array_file); $filename = "/var/www/html/tf/fetched/$array_file"; if (file_exists($filename)) { $cmd = "php /var/www/html/tf/jpgraph/src/Examples/tf_anatomy_simplified.php $fam $len $array_file $tffamily "; system($cmd); } else { $data = fopen("/var/www/html/tf/fetched/$array_file", 'w'); for ($i=0;$i<=$len-2;$i++) { $id=$locus[$i]; $id=trim($id); $sql = "SELECT * FROM tf_anatomy_simplified WHERE `RGAP 7 Model`='$id'"; //echo sql; $qry = $dbo->prepare($sql); $qry->execute(); $row = $qry->fetch(PDO::FETCH_ASSOC); unset($row['RGAP 7 Model']); //unset($row['Anatomy Probe_ID']); fputcsv($data, $row); } chmod("/var/www/html/tf/fetched/$array_file",0777); $cmd = "php /var/www/html/tf/jpgraph/src/Examples/tf_anatomy_simplified.php $fam $len"; system($cmd); } } } //------------------------------------------------------------------------ if (in_array("heatmap", $mode2)) { if (in_array("tf_abiotic", $database2)) { $array_file = $newtre.".tf_abiotic.csv"; $array_file = trim($array_file); $filename = "/var/www/html/tf/fetched/$array_file"; if (file_exists($filename)) { $cmd = "php /var/www/html/tf/jpgraph/src/Examples/tf_abiotic.php $fam $len $array_file $tffamily $scale_multi"; system($cmd); } else { $data = fopen("/var/www/html/tf/fetched/$array_file", 'w'); for ($i=0;$i<=$len-2;$i++) { $id=$locus[$i]; $id=trim($id); $sql = "SELECT * FROM tf_abiotic WHERE `RGAP 7 Model`='$id'"; echo $sql; $qry = $dbo->prepare($sql); $qry->execute(); $row = $qry->fetch(PDO::FETCH_ASSOC); unset($row['RGAP 7 Model']); //unset($row['Abiotic Probe_ID']); fputcsv($data, $row); } chmod("/var/www/html/tf/fetched/$array_file",0777); $cmd = "php /var/www/html/tf/jpgraph/src/Examples/tf_abiotic.php $fam $len"; system($cmd); } } } //------------------------------------------------------------------------ if (in_array("heatmap", $mode2)) { if (in_array("tf_biotic", $database2)) { $array_file = $newtre.".tf_biotic.csv"; $array_file = trim($array_file); $filename = "/var/www/html/tf/fetched/$array_file"; if (file_exists($filename)) { $cmd = "php /var/www/html/tf/jpgraph/src/Examples/tf_biotic.php $fam $len $array_file $tffamily $scale_multi"; system($cmd); } else { $data = fopen("/var/www/html/tf/fetched/$array_file", 'w'); for ($i=0;$i<=$len-2;$i++) { $id=$locus[$i]; $id=trim($id); $sql = "SELECT * FROM tf_biotic WHERE `RGAP 7 Model`='$id'"; $qry = $dbo->prepare($sql); $qry->execute(); $row = $qry->fetch(PDO::FETCH_ASSOC); unset($row['RGAP 7 Model']); //unset($row['Biotic Probe_id']); fputcsv($data, $row); } chmod("/var/www/html/tf/fetched/$array_file",0777); $cmd = "php /var/www/html/tf/jpgraph/src/Examples/tf_biotic.php $fam $len"; system($cmd); } } } //------------------------------------------------------------------------ if (in_array("heatmap", $mode2)) { if (in_array("tf_hormone", $database2)) { $array_file = $newtre.".tf_hormone.csv"; $array_file = trim($array_file); $filename = "/var/www/html/tf/fetched/$array_file"; if (file_exists($filename)) { $cmd = "php /var/www/html/tf/jpgraph/src/Examples/tf_hormone.php $fam $len $array_file $tffamily $scale_multi"; system($cmd); } else { $data = fopen("/var/www/html/tf/fetched/$array_file", 'w'); for ($i=0;$i<=$len-2;$i++) { $id=$locus[$i]; $id=trim($id); $sql = "SELECT * FROM tf_hormone WHERE `RGAP 7 Model`='$id'"; $qry = $dbo->prepare($sql); $qry->execute(); $row = $qry->fetch(PDO::FETCH_ASSOC); unset($row['RGAP 7 Model']); //unset($row['Hormone Probe_id']); fputcsv($data, $row); } chmod("/var/www/html/tf/fetched/$array_file",0777); $cmd = "php /var/www/html/tf/jpgraph/src/Examples/tf_hormone.php $fam $len"; system($cmd); } } } //------------------------------------------------------------------------ //------------------------------------------------------------------------ if (in_array("heatmap", $mode2)) { if (in_array("tf_anatomyrna", $database2)) { $array_file = $newtre.".tf_anatomyrna.csv"; $array_file = trim($array_file); $filename = "/var/www/html/tf/fetched/$array_file"; if (file_exists($filename)) { $cmd = "php /var/www/html/tf/jpgraph/src/Examples/tf_anatomyrna.php $fam $len $array_file $tffamily $scale_multi"; system($cmd); } else { $data = fopen("/var/www/html/tf/fetched/$array_file", 'w'); for ($i=0;$i<=$len-2;$i++) { $id=$locus[$i]; $id=trim($id); $sql = "SELECT * FROM tf_anatomyrna WHERE `RGAP 7 Model`='$id'"; $qry = $dbo->prepare($sql); $qry->execute(); $row = $qry->fetch(PDO::FETCH_ASSOC); unset($row['RGAP 7 Model']); //unset($row['Anatomy Probe_ID']); fputcsv($data, $row); } chmod("/var/www/html/tf/fetched/$array_file",0777); $cmd = "php /var/www/html/tf/jpgraph/src/Examples/tf_anatomyrna.php $fam $len"; system($cmd); } } } //------------------------------------------------------------------------ if (in_array("heatmap", $mode2)) { if (in_array("tf_abioticrna", $database2)) { $array_file = $newtre.".tf_abioticrna.csv"; $array_file = trim($array_file); $filename = "/var/www/html/tf/fetched/$array_file"; if (file_exists($filename)) { $cmd = "php /var/www/html/tf/jpgraph/src/Examples/tf_abioticrna.php $fam $len $array_file $tffamily $scale_multi"; system($cmd); } else { $data = fopen("/var/www/html/tf/fetched/$array_file", 'w'); for ($i=0;$i<=$len-2;$i++) { $id=$locus[$i]; $id=trim($id); $sql = "SELECT * FROM tf_abioticrna WHERE `RGAP 7 Model`='$id'"; $qry = $dbo->prepare($sql); $qry->execute(); $row = $qry->fetch(PDO::FETCH_ASSOC); unset($row['RGAP 7 Model']); //unset($row['Anatomy Probe_ID']); fputcsv($data, $row); } chmod("/var/www/html/tf/fetched/$array_file",0777); $cmd = "php /var/www/html/tf/jpgraph/src/Examples/tf_anatomyrna.php $fam $len"; system($cmd); } } } //------------------------------------------------------------------------ if (in_array("heatmap", $mode2)) { if (in_array("tf_agilanatomy", $database2)) { $array_file = $newtre.".tf_agilanatomy.csv"; $array_file = trim($array_file); $filename = "/var/www/html/tf/fetched/$array_file"; if (file_exists($filename)) { $cmd = "php /var/www/html/tf/jpgraph/src/Examples/tf_agilanatomy.php $fam $len $array_file $tffamily $scale_multi"; system($cmd); } else { $data = fopen("/var/www/html/tf/fetched/$array_file", 'w'); for ($i=0;$i<=$len-2;$i++) { $id=$locus[$i]; $id=trim($id); $sql = "SELECT * FROM tf_agilanatomy WHERE `RGAP 7 Model`='$id'"; $qry = $dbo->prepare($sql); $qry->execute(); $row = $qry->fetch(PDO::FETCH_ASSOC); unset($row['RGAP 7 Model']); //unset($row['Anatomy Probe_ID']); fputcsv($data, $row); } chmod("/var/www/html/tf/fetched/$array_file",0777); $cmd = "php /var/www/html/tf/jpgraph/src/Examples/tf_agilanatomy.php $fam $len"; system($cmd); } } } //####################################################################### //display tree image $fam = $_SESSION["treetype"]; $tffam = $_SESSION["treetype"].'.png'; $tffamily = $_SESSION["treetype"]; echo ""; echo ""; echo ""; echo '"; //TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT } $anatomy = $tffamily.".tf_anatomy.png"; $anatomy_simplified = $tffamily.".tf_anatomy_simplified.png"; $abiotic = $tffamily.".tf_abiotic.png"; $biotic = $tffamily.".tf_biotic.png"; $hormone = $tffamily.".tf_hormone.png"; $anatomyrna = $tffamily.".tf_anatomyrna.png"; $abioticrna = $tffamily.".tf_abioticrna.png"; $agilanatomy = $tffamily.".tf_agilanatomy.png"; //print_r ($database2); //display heatmap if corresponding option is selected if (in_array("heatmap", $mode2)) { if (in_array("tf_anatomy", $database2)) { echo '"; echo "
"; //[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ $multi = $tree_length [$tffamily]; $height = $len*$multi; if($height === 0) { $height = 30; } //[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ $total_checked_items = array_merge($values2, $database2); $total_checked_items = array_filter($total_checked_items); $str2='.png'; if($total_checked_items) { if($tffam === $str2) { //$tffam='AGC_other.png'; //echo "
"; //echo ""; unset($titles); echo "
"; echo "
"; echo "
"; exit("Please select a tf Subfamily"); } } if ($tffamily) { //echo "
"; //echo "
"; //echo "
"; echo ""; echo "
'; } //this nis to remove unwanted table broken structure of RGAP 7 Model $str='`RGAP 7 Model`, '; if ($fetched === $str) { $fetched = NULL; } //to call NCBI blast inside table// $str1='http://blast.ncbi.nlm.nih.gov/Blast.cgi?QUERY='; $str2='&db=protein&DATABASE=nr&BLAST_PROGRAMS=blastp&EXPECT=1e-5&MAX_NUM_SEQ=1000&SHORT_QUERY_ADJUST=TRUE&WORD_SIZE=3&COMPOSITION_BASED_STATISTICS=2&I_THRESH=0\.005&'; $str3='CDD_SEARCH=true&SELECTED_PROG_TYPE=blastp&SAVED_SEARCH=true&SHOW_OVERVIEW=true&SHOW_LINKOUT=true&NEW_VIEW=false&OLD_BLAST=true&PAGE_TYPE=BlastSearch&FORMAT_TYPE=HTML&PROGRAM=blastp&CLIENT=web&SERVICE=plain&PAGE=Proteins&CMD=request'; if($fetched) { echo ""; echo ""; echo ""; for ($i=0;$i<=$length_head-1;$i++) { $head=$titles[$i]; $head = str_replace('`', '', $head); echo ""; } echo ""; //print_r ($fethed); //display table next to tree image if any value is checked for ($i=0;$i<=$len-2;$i++) { $id=$locus[$i]; $id=trim($id); $sql = "SELECT $fetched FROM tf WHERE `RGAP 7 Locus`='$id'"; //echo $sql; $qry = $dbo->prepare($sql); $qry->execute(); $row = $qry->fetch(PDO::FETCH_ASSOC); $val = array_values($row); $len3 = count($val); echo ""; for ($j=0;$j<=$len3-1;$j++) { $x=$val[$j]; trim($x); $x = str_replace('"', '', $x); if (preg_match('/^LOC/', $x)) { echo ""; } elseif (preg_match('/^AT[0-9]G/', $x)) { if (preg_match('/^AT[0-9]G[0-9][0-9][0-9][0-9][0-9]\.[0-9]$/', $x)) { echo ""; } else { $tags = explode(';', $x); foreach($tags as $tag) { $arr[] = "$tag"; } $xy = implode(",",$arr); echo ""; $arr = array(); } } elseif (preg_match('/^PF[0-9][0-9]/', $x)) { $y= explode(" (",$x); echo ""; } elseif (preg_match('/GRMZ/', $x)) { echo ""; } elseif (preg_match('/^RAP/', $x)) { echo ""; } elseif (preg_match('/^M[A-Z][A-Z][A-Z][A-Z][A-Z][A-Z][A-Z][A-Z][A-Z][A-Z][A-Z][A-Z][A-Z][A-Z][A-Z][A-Z][A-Z][A-Z][A-Z][A-Z][A-Z][A-Z][A-Z][A-Z][A-Z][A-Z].............+/', $x)) { $blast=$str1.$x.$str2.$str3; echo ""; } else { echo ""; } } echo ""; } echo "
$head
" . "". $x .'' . "" . "". $x .'' . "".$xy."" . "". $y[0] .'' . "" . "". $x .'' . "" . "". $x .'' . "" . "". 'NCBI BLAST' .'' . " $x  
"; //for download provision of the selected database values by clciking link if(in_array('tf_anatomy',$database2)) { if(in_array('values',$mode2) || in_array('heatmap',$mode2)) { echo "DOWNLOAD ANATOMY"; echo "
"; } } if(in_array('tf_anatomy_simplified',$database2)) { if(in_array('values',$mode2) || in_array('heatmap',$mode2)) { echo "DOWNLOAD ANATOMY SIMPLIFIED"; echo "
"; } } if(in_array('tf_abiotic',$database2)) { if(in_array('values',$mode2) || in_array('heatmap',$mode2)) { echo "DOWNLOAD ABIOTIC"; echo "
"; } } if(in_array('tf_biotic',$database2)) { if(in_array('values',$mode2) || in_array('heatmap',$mode2)) { echo "DOWNLOAD BIOTIC"; echo "
"; } } if(in_array('tf_hormone',$database2)) { if(in_array('values',$mode2) || in_array('heatmap',$mode2)) { echo "DOWNLOAD HORMONE"; echo "
"; } } if(in_array('tf_anatomyrna',$database2)) { if(in_array('values',$mode2) || in_array('heatmap',$mode2)) { echo "DOWNLOAD ANATOMY RNASeq"; echo "
"; } } if(in_array('tf_abioticrna',$database2)) { if(in_array('values',$mode2) || in_array('heatmap',$mode2)) { echo "DOWNLOAD ABIOTIC RNASeq"; echo "
"; } } if(in_array('tf_agilanatomy',$database2)) { if(in_array('values',$mode2) || in_array('heatmap',$mode2)) { echo "DOWNLOAD AGILENT ANATOMY"; echo "
"; } } echo "
'; echo '

'; echo ""; echo ""; echo '

'; } if (in_array("tf_anatomy_simplified", $database2)) { echo '

'; echo '

'; echo ""; echo ""; echo '

'; } if (in_array("tf_abiotic", $database2)) { echo '

'; echo '

'; echo ""; $scale = $scale_multi."abio.png"; echo ""; echo '

'; } if (in_array("tf_biotic", $database2)) { echo '

'; echo '

'; echo ""; $scale = $scale_multi."bio.png"; echo ""; echo '

'; } if (in_array("tf_hormone", $database2)) { echo '

'; echo '

'; echo ""; $scale = $scale_multi."hor.png"; echo ""; echo '

'; } if (in_array("tf_anatomyrna", $database2)) { echo '

'; echo '

'; echo ""; echo ""; echo '

'; } if (in_array("tf_abioticrna", $database2)) { echo '

'; echo '

'; echo ""; echo ""; echo '

'; } if (in_array("tf_agilanatomy", $database2)) { echo '

'; echo '

'; echo ""; echo ""; echo '

'; } } echo "

"; echo ""; echo ""; ?>