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| Official Gene Symbol | Other Aliases |
|---|---|
| HDAC1 | RPD3L1 |
| Sequence Length (AA) | Molecular Weight (Da) |
|---|---|
| 482 | 55103 |
| Protein Name |
|---|
| Histone deacetylase 1 |
| Sources | |
|---|---|
|
UniProt PhosphoSitePlus ® GeneCards |
Human Protein Atlas |
| 10 | 20 | 30 | 40 | 50 |
| MAQTQGTRRK | VCYYYDGDVG | NYYYGQGHPM | KPHRIRMTHN | LLLNYGLYRK |
| 60 | 70 | 80 | 90 | 100 |
| MEIYRPHKAN | AEEMTKYHSD | DYIKFLRSIR | PDNMSEYSKQ | MQRFNVGEDC |
| 110 | 120 | 130 | 140 | 150 |
| PVFDGLFEFC | QLSTGGSVAS | AVKLNKQQTD | IAVNWAGGLH | HAKKSEASGF |
| 160 | 170 | 180 | 190 | 200 |
| CYVNDIVLAI | LELLKYHQRV | LYIDIDIHHG | DGVEEAFYTT | DRVMTVSFHK |
| 210 | 220 | 230 | 240 | 250 |
| YGEYFPGTGD | LRDIGAGKGK | YYAVNYPLRD | GIDDESYEAI | FKPVMSKVME |
| 260 | 270 | 280 | 290 | 300 |
| MFQPSAVVLQ | CGSDSLSGDR | LGCFNLTIKG | HAKCVEFVKS | FNLPMLMLGG |
| 310 | 320 | 330 | 340 | 350 |
| GGYTIRNVAR | CWTYETAVAL | DTEIPNELPY | NDYFEYFGPD | FKLHISPSNM |
| 360 | 370 | 380 | 390 | 400 |
| TNQNTNEYLE | KIKQRLFENL | RMLPHAPGVQ | MQAIPEDAIP | EESGDEDEDD |
| 410 | 420 | 430 | 440 | 450 |
| PDKRISICSS | DKRIACEEEF | SDSEEEGEGG | RKNSSNFKKA | KRVKTEDEKE |
| 460 | 470 | 480 | 482 | |
| KDPEEKKEVT | EEEKTKEEKP | EAKGVKEEVK | LA |
Data source: UniProt
Uniprot Database Entry PhosphoSitePlus ®
loading
Data source: Panorama
Data source: Panorama
Johns Hopkins University-I
Data source: Panorama
Data source: Panorama
Retrieving Data
Data source: Panorama
| Average intra-assay CV (within day CV) |
Average inter-assay CV (between day CV) |
Total CV |
n= | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High |
| y9 (1+) | 13.8 | 3.9 | 6.8 | 11.1 | 6.5 | 7.5 | 17.7 | 7.6 | 10.1 | 15 | 15 | 15 |
| y8 (1+) | 14.3 | 6.7 | 5.9 | 12.6 | 9.4 | 6.4 | 19.1 | 11.5 | 8.7 | 15 | 15 | 15 |
| y7 (1+) | 4.9 | 4.2 | 4.5 | 6.2 | 7.2 | 5.3 | 7.9 | 8.3 | 7 | 15 | 15 | 15 |
| sum | 5.3 | 4.2 | 4.5 | 5.9 | 7.2 | 5.3 | 7.9 | 8.3 | 7 | 15 | 15 | 15 |
Data source: Panorama
Data source: Panorama
Johns Hopkins University-I
Data source: Panorama
Data source: Panorama
Retrieving Data
Data source: Panorama
| Average intra-assay CV (within day CV) |
Average inter-assay CV (between day CV) |
Total CV |
n= | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High |
| y5 (1+) | 22 | 5 | 4.7 | 28 | 7.1 | 9.5 | 35.6 | 8.7 | 10.6 | 15 | 15 | 15 |
| y6 (1+) | 30.7 | 6.6 | 5.6 | 20.9 | 7 | 11.2 | 37.1 | 9.6 | 12.5 | 15 | 15 | 15 |
| y7 (1+) | 14.9 | 4.2 | 3.2 | 19.5 | 7 | 7.6 | 24.5 | 8.2 | 8.2 | 15 | 15 | 15 |
| sum | 16.3 | 2.9 | 2.5 | 14.5 | 6.1 | 8.3 | 21.8 | 6.8 | 8.7 | 15 | 15 | 15 |
")
.appendTo(all_in_one_graph)
.click(function (e) {
e.preventDefault();
all_in_one_plot.pan(offset);
});
}
addArrow("left", 55, 40, {left: -100});
addArrow("right", 25, 40, {left: 100});
addArrow("up", 40, 25, {top: -100});
addArrow("down", 40, 55, {top: 100});
// Disable the mouse wheel functionality for panning and zooming
$('#all_in_one_graph canvas.flot-overlay').unmousewheel();
$(all_in_one_graph).bind("plotclick", function (event, pos, item) {
// Splice Junctions
// http://www.uniprot.org/uniprot/P04626#section_features
if ((item != null) && (item.series.data[0][3] != null) && (item.series.data[0][3] == 'splice_junction')) {
var url = 'http://www.uniprot.org/uniprot/' + uniprot_id + '#section_features';
window.open(url, '_blank');
}
// Isoforms
if ((item != null) && (item.series.data[0][4] != null) && (item.series.data[0][4] == 'isoform')) {
var url = 'http://www.uniprot.org/uniprot/' + item.series.data[item.dataIndex][3];
window.open(url, '_blank');
}
// SNPs
if ((item != null) && (item.series.data[0][3] != null) && (item.series.data[0][3] == 'snp')) {
var url = 'http://www.uniprot.org/blast/?about=' + uniprot_id + '[' + item.datapoint[0] + ']';
window.open(url, '_blank');
}
// MRM Assays
if ((item != null) && (item.series.data[0][4] != null) && (item.series.data[0][4] == 'mrm_assay')) {
var this_peptide_sequence = item.series.data[item.dataIndex][3];
var this_protein_id = item.series.data[item.dataIndex][5];
var div_id = '.' + this_protein_id;
// Change our States (URL, title in title bar)
History.replaceState({state: 1}, "HDAC1, CPTAC-" + this_protein_id + " - CPTAC Assay Portal", "CPTAC-" + this_protein_id);
// Scroll to assays area
scrollToAnchor('assay_details_anchor');
$('.assay-details-wrapper').hide();
$('#preloader_loading_assay_details').fadeIn(500);
$('#preloader_loading_assay_details').hide();
$(div_id).fadeIn(300);
// Load Disqus commenting
//loadDisqus($('#comments_container_' + this_protein_id), this_peptide_sequence, 'http://assays.cancer.gov/CPTAC-2607/#!' + this_peptide_sequence);
}
});
///////////////////////////////////////////////////////////
// [BEGIN] Highlighted Peptide Sequence Links ///////////////
// Use sequence values from the 'genes_distinct' array
var mouseY;
var mouseX;
$(document).mousemove(function (e) {
mouseX = e.pageX;
mouseY = e.pageY;
});
var starts = JSON.parse('[{"peptide_sequence":"YGEYFPGTGDLR","manage":2607},{"peptide_sequence":"YYAVNYPLR","manage":1248}]');
var last_clicked = false;
$.each(starts, function (index, starts_data) {
// On click event for peptide sequence links in the gene sequence
var this_peptide_sequence = starts_data.peptide_sequence;
var this_protein_id = starts_data.manage;
var div_id = '.' + this_protein_id;
var clickable_class = 'seq-' + this_peptide_sequence;
$('.' + clickable_class).on('click', function () {
$("rect, line, .close").tooltip();
if (last_clicked != this_peptide_sequence) {
$('.detail-modal').attr('style', 'display: none');
last_clicked = false;
}
var div_height = $('.all-details-' + this_peptide_sequence).height();
var offset = (div_height > 25) ? 450 : 390;
$('.all-details-' + this_peptide_sequence).css({'top': mouseY - offset}).fadeIn('fast');
$('.detail-modal .close').on('click', function () {
$('.detail-modal').fadeOut('fast');
});
});
var detail_link_class = this_peptide_sequence + '-' + this_protein_id;
$('.protein-sequence').on('click', '.' + detail_link_class, function () {
// close the pop up
$('.detail-modal').fadeOut('fast');
// Change our States (URL, title in title bar)
History.replaceState({state: 1}, "HDAC1, CPTAC-" + this_protein_id + " - CPTAC Assay Portal", "CPTAC-" + this_protein_id);
// Scroll to assays area
scrollToAnchor('assay_details_anchor');
$('.assay-details-wrapper').hide();
$('#preloader_loading_assay_details').fadeIn(500);
$('#preloader_loading_assay_details').hide();
$(div_id).fadeIn(300);
// Load Disqus commenting
//loadDisqus($('#comments_container_' + this_protein_id), this_peptide_sequence, 'http://assays.cancer.gov/CPTAC-2607/#!' + this_peptide_sequence);
});
});
// $("rect, line, .peptide_highlight").tooltip({
// 'container': 'body',
// 'placement': 'top'
// });
// [END] Highlighted Peptide Sequence Links ///////////////
// Tooltips on hover of data points
var previousPoint = null;
$(all_in_one_graph).bind("plothover", function (event, pos, item) {
if (item) {
document.body.style.cursor = 'pointer';
if (previousPoint != item.dataIndex) {
previousPoint = item.dataIndex;
$("#tooltip").remove();
showTooltip(item.pageX, item.pageY, item.series.data[item.dataIndex][2]);
}
} else {
document.body.style.cursor = 'default';
$("#tooltip").remove();
previousPoint = null;
}
});
// Pop-out entire sequence
$('div.sequence').on('mouseenter', '.protein-sequence', function (event) {
$(this).attr('style', 'overflow: visible;');
$('table.sequence').addClass('sequence_table_shadow');
});
$('div.sequence').on('mouseleave', '.protein-sequence', function (event) {
$(this).attr('style', 'overflow: hidden;');
$('table.sequence').removeClass('sequence_table_shadow');
$('.detail-modal').attr('style', 'display: none');
});
// Tooltips
$('.span4 img, .chart-legend, .chart-legend-text').tooltip();
// Show the Assay details for the page id we're on
var details_div_id = $('#outer-wrapper .2607');
$(details_div_id).show();
//loadDisqus($('#comments_container_2607'), 'YGEYFPGTGDLR', 'http://assays.cancer.gov/CPTAC-2607/#!YGEYFPGTGDLR');
// History.js
(function (window, undefined) {
// Bind to StateChange Event
History.Adapter.bind(window, 'statechange', function () { // Note: We are using statechange instead of popstate
var State = History.getState(); // Note: We are using History.getState() instead of event.state
});
})(window);
$.ajax({
type: "GET"
, dataType: "html"
, url: "/assays/get_protein_map_svg"
, data: ({uniprot_ac_id: uniprot_id})
, success: function (svg_return) {
d3.select("#proteincartoon").html(svg_return);
}
});
$('#proteincartoon').click(function () {
var win = window.open('http://www.phosphosite.org/uniprotAccAction.do?id=' + uniprot_id, '_blank');
win.focus();
});
});
// FUNCTIONS ///////////////
function scrollToAnchor(aid) {
var aTag = $("a[name='" + aid + "']");
$('html,body').animate({scrollTop: aTag.offset().top}, 'slow');
}
function showTooltip(x, y, contents) {
$("Table data unavailable
'; // Display the preloaders $.each(genes, function (index, gene) { $('div.span12.' + gene.peptide_sequence + '_' + gene.laboratory_abbreviation + ' .loc_lloq_preloader_loading').show(); }); // Send the request via AJAX $.ajax({ url: "/assays/get_plots_table_data" , dataType: "json" , type: "post" , data: {genes: JSON.stringify(genes)} , success: function (data) { if (data) { $.each(data, function (index, single_gene_data) { /* * Build out the LOC/LOQ data table */ if (single_gene_data.lod_loq_comparison_data[0].length) { var crude = (single_gene_data.peptide_standard_purity_types_id == 3) ? true : false; var peptide_sequence = single_gene_data.lod_loq_comparison_data[0][0].peptide; var lod_loq_units = single_gene_data.lod_loq_comparison_data[0][0].lod_loq_units; var crude_style = (crude) ? 'class="crude-header"' : ''; var lod_loq_units_note = (crude) ? 'Response Curves Data Unavailable
'); }); } }); } } }); }
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