{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# CCLE Tissue Expression Clustergrammer Visualizations\n", "This notebook will use the [Clustergrammer-Widget](http://clustergrammer.readthedocs.io/clustergrammer_widget.html) to visualize the Cancer cell line Encyclopedia gene expression data ([Broad-Institute CCLE](https://software.broadinstitute.org/software/cprg/?q=node/11)). The CCLE project measured genetic data from over 1000 cancer cell lines. We'lll use Clustergrammer-Widget to visualize the data. We will start by importing required libraries and initializing the Clustergrammer [Network](http://clustergrammer.readthedocs.io/clustergrammer_py.html#clustergrammer-py-api) object: \n" ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "collapsed": true }, "outputs": [], "source": [ "from clustergrammer_widget import *\n", "import pandas as pd\n", "import numpy as np\n", "net = Network(clustergrammer_widget)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Reformatted CCLE data\n", "We are using a slightly reformatted version of the CCLE gene expression data with modified cell line meta-data (category) formatting. You can see below how cell-line categorical information (e.g. tissue) information is encoded as column tuples. The matrix has 18,874 rows (genes) and 1,037 columns (cell-lines)." ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "(18874, 1037)\n" ] }, { "data": { "text/html": [ "
\n", " | (cell line: LN18, tissue: central_nervous_system, histology: glioma, sub-histology: astrocytoma_Grade_IV, gender: M) | \n", "(cell line: 769P, tissue: kidney, histology: carcinoma, sub-histology: clear_cell_renal_cell_carcinoma, gender: F) | \n", "(cell line: 786O, tissue: kidney, histology: carcinoma, sub-histology: clear_cell_renal_cell_carcinoma, gender: M) | \n", "(cell line: CAOV3, tissue: ovary, histology: carcinoma, sub-histology: adenocarcinoma, gender: F) | \n", "(cell line: HEPG2, tissue: liver, histology: carcinoma, sub-histology: hepatocellular_carcinoma, gender: M) | \n", "(cell line: MOLT4, tissue: haematopoietic_and_lymphoid_tissue, histology: lymphoid_neoplasm, sub-histology: acute_lymphoblastic_T_cell_leukaemia, gender: M) | \n", "(cell line: NCIH524, tissue: lung, histology: carcinoma, sub-histology: small_cell_carcinoma, gender: M) | \n", "(cell line: NCIH209, tissue: lung, histology: carcinoma, sub-histology: small_cell_carcinoma, gender: M) | \n", "(cell line: MIAPACA2, tissue: pancreas, histology: carcinoma, sub-histology: ductal_carcinoma, gender: M) | \n", "(cell line: MCAS, tissue: ovary, histology: carcinoma, sub-histology: adenocarcinoma, gender: F) | \n", "... | \n", "(cell line: SLR21, tissue: kidney, histology: carcinoma, sub-histology: renal_cell_carcinoma, gender: NA) | \n", "(cell line: LNZ308, tissue: central_nervous_system, histology: glioma, sub-histology: astrocytoma_Grade_IV, gender: NA) | \n", "(cell line: LN340, tissue: central_nervous_system, histology: glioma, sub-histology: astrocytoma_Grade_IV, gender: NA) | \n", "(cell line: HCC827GR5, tissue: lung, histology: carcinoma, sub-histology: adenocarcinoma, gender: NA) | \n", "(cell line: SLR20, tissue: kidney, histology: carcinoma, sub-histology: renal_cell_carcinoma, gender: NA) | \n", "(cell line: HK2, tissue: kidney, histology: other, sub-histology: immortalized_epithelial, gender: NA) | \n", "(cell line: EW8, tissue: bone, histology: Ewings_sarcoma-peripheral_primitive_neuroectodermal_tumour, sub-histology: NS, gender: NA) | \n", "(cell line: UOK101, tissue: kidney, histology: carcinoma, sub-histology: clear_cell_renal_cell_carcinoma, gender: NA) | \n", "(cell line: JHESOAD1, tissue: oesophagus, histology: carcinoma, sub-histology: barrett_associated_adenocarcinoma, gender: NA) | \n", "(cell line: CH157MN, tissue: central_nervous_system, histology: meningioma, sub-histology: NS, gender: NA) | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
LOC100009676 | \n", "5.987545 | \n", "5.444892 | \n", "5.838828 | \n", "6.074743 | \n", "5.788600 | \n", "5.459675 | \n", "5.755560 | \n", "7.190493 | \n", "5.449818 | \n", "5.801820 | \n", "... | \n", "5.473156 | \n", "5.517208 | \n", "5.858379 | \n", "5.196033 | \n", "5.831437 | \n", "5.362021 | \n", "5.799747 | \n", "5.865606 | \n", "5.463812 | \n", "5.720593 | \n", "
AKT3 | \n", "6.230233 | \n", "7.544216 | \n", "7.328450 | \n", "4.270720 | \n", "4.478293 | \n", "6.212102 | \n", "7.562398 | \n", "8.642669 | \n", "5.556191 | \n", "6.808673 | \n", "... | \n", "6.375324 | \n", "6.119814 | \n", "6.561409 | \n", "4.521773 | \n", "6.830904 | \n", "7.031690 | \n", "4.881235 | \n", "6.914640 | \n", "5.313795 | \n", "5.757825 | \n", "
MED6 | \n", "9.363550 | \n", "8.715909 | \n", "8.410834 | \n", "9.845271 | \n", "9.761157 | \n", "10.532820 | \n", "10.393960 | \n", "9.478429 | \n", "9.112954 | \n", "9.815614 | \n", "... | \n", "8.849773 | \n", "8.767192 | \n", "8.521635 | \n", "8.224544 | \n", "9.325785 | \n", "8.362727 | \n", "8.990524 | \n", "8.958629 | \n", "9.748100 | \n", "9.758431 | \n", "
NR2E3 | \n", "3.803069 | \n", "4.173643 | \n", "3.776557 | \n", "3.934091 | \n", "3.822202 | \n", "3.949198 | \n", "3.807546 | \n", "3.930186 | \n", "4.161937 | \n", "4.028581 | \n", "... | \n", "3.717506 | \n", "3.977377 | \n", "3.659459 | \n", "3.933996 | \n", "4.515748 | \n", "4.434658 | \n", "4.127832 | \n", "3.942736 | \n", "4.062648 | \n", "4.074257 | \n", "
NAALAD2 | \n", "3.586430 | \n", "3.663081 | \n", "4.047007 | \n", "3.817250 | \n", "6.444302 | \n", "4.081071 | \n", "5.462774 | \n", "4.252446 | \n", "3.932451 | \n", "3.835827 | \n", "... | \n", "3.520843 | \n", "4.036661 | \n", "4.168351 | \n", "3.535915 | \n", "4.445632 | \n", "3.622032 | \n", "5.436580 | \n", "3.666404 | \n", "3.556565 | \n", "3.728828 | \n", "
5 rows × 1037 columns
\n", "\n", " | (Cluster: cluster-0, Majority-tissue: haematopoietic_and_lymphoid_tissue, Majority-histology: lymphoid_neoplasm, Majority-sub-histology: mycosis_fungoides-Sezary_syndrome, Majority-gender: M, number in clust: 2) | \n", "(Cluster: cluster-1, Majority-tissue: lung, Majority-histology: carcinoma, Majority-sub-histology: NS, Majority-gender: F, number in clust: 2) | \n", "(Cluster: cluster-2, Majority-tissue: upper_aerodigestive_tract, Majority-histology: carcinoma, Majority-sub-histology: squamous_cell_carcinoma, Majority-gender: M, number in clust: 47) | \n", "(Cluster: cluster-3, Majority-tissue: autonomic_ganglia, Majority-histology: neuroblastoma, Majority-sub-histology: NS, Majority-gender: M, number in clust: 11) | \n", "(Cluster: cluster-4, Majority-tissue: skin, Majority-histology: malignant_melanoma, Majority-sub-histology: NS, Majority-gender: M, number in clust: 50) | \n", "(Cluster: cluster-5, Majority-tissue: lung, Majority-histology: carcinoma, Majority-sub-histology: NS, Majority-gender: F, number in clust: 26) | \n", "(Cluster: cluster-6, Majority-tissue: haematopoietic_and_lymphoid_tissue, Majority-histology: lymphoid_neoplasm, Majority-sub-histology: diffuse_large_B_cell_lymphoma, Majority-gender: M, number in clust: 31) | \n", "(Cluster: cluster-7, Majority-tissue: large_intestine, Majority-histology: carcinoma, Majority-sub-histology: adenocarcinoma, Majority-gender: M, number in clust: 2) | \n", "(Cluster: cluster-8, Majority-tissue: lung, Majority-histology: carcinoma, Majority-sub-histology: NS, Majority-gender: M, number in clust: 15) | \n", "(Cluster: cluster-9, Majority-tissue: liver, Majority-histology: carcinoma, Majority-sub-histology: hepatocellular_carcinoma, Majority-gender: M, number in clust: 16) | \n", "... | \n", "(Cluster: cluster-90, Majority-tissue: stomach, Majority-histology: carcinoma, Majority-sub-histology: tubular_adenocarcinoma, Majority-gender: M, number in clust: 1) | \n", "(Cluster: cluster-91, Majority-tissue: breast, Majority-histology: carcinoma, Majority-sub-histology: NS, Majority-gender: F, number in clust: 1) | \n", "(Cluster: cluster-92, Majority-tissue: haematopoietic_and_lymphoid_tissue, Majority-histology: lymphoid_neoplasm, Majority-sub-histology: Hodgkin_lymphoma, Majority-gender: M, number in clust: 1) | \n", "(Cluster: cluster-93, Majority-tissue: central_nervous_system, Majority-histology: glioma, Majority-sub-histology: astrocytoma_Grade_IV, Majority-gender: M, number in clust: 17) | \n", "(Cluster: cluster-94, Majority-tissue: autonomic_ganglia, Majority-histology: neuroblastoma, Majority-sub-histology: NS, Majority-gender: F, number in clust: 2) | \n", "(Cluster: cluster-95, Majority-tissue: thyroid, Majority-histology: carcinoma, Majority-sub-histology: papillary_carcinoma, Majority-gender: F, number in clust: 1) | \n", "(Cluster: cluster-96, Majority-tissue: stomach, Majority-histology: carcinoma, Majority-sub-histology: adenocarcinoma, Majority-gender: M, number in clust: 1) | \n", "(Cluster: cluster-97, Majority-tissue: oesophagus, Majority-histology: carcinoma, Majority-sub-histology: squamous_cell_carcinoma, Majority-gender: F, number in clust: 1) | \n", "(Cluster: cluster-98, Majority-tissue: kidney, Majority-histology: carcinoma, Majority-sub-histology: clear_cell_renal_cell_carcinoma, Majority-gender: NA, number in clust: 2) | \n", "(Cluster: cluster-99, Majority-tissue: liver, Majority-histology: carcinoma, Majority-sub-histology: hepatocellular_carcinoma, Majority-gender: M, number in clust: 8) | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
LOC100009676 | \n", "5.665593 | \n", "5.284315 | \n", "5.673244 | \n", "5.363738 | \n", "6.057420 | \n", "5.840425 | \n", "5.841230 | \n", "5.685825 | \n", "5.680019 | \n", "5.610437 | \n", "... | \n", "6.599907 | \n", "5.425919 | \n", "6.363237 | \n", "5.773302 | \n", "4.631328 | \n", "5.855566 | \n", "6.583266 | \n", "5.077296 | \n", "5.626497 | \n", "5.672558 | \n", "
AKT3 | \n", "6.435427 | \n", "6.952967 | \n", "5.605452 | \n", "8.122674 | \n", "7.267956 | \n", "6.011819 | \n", "5.094038 | \n", "4.558152 | \n", "7.085084 | \n", "6.115605 | \n", "... | \n", "7.688763 | \n", "4.401639 | \n", "7.052142 | \n", "6.299563 | \n", "8.859103 | \n", "7.864197 | \n", "4.341758 | \n", "5.051193 | \n", "5.370956 | \n", "4.430994 | \n", "
MED6 | \n", "9.518722 | \n", "8.762060 | \n", "9.502653 | \n", "9.341522 | \n", "8.839631 | \n", "9.507497 | \n", "9.699576 | \n", "9.673724 | \n", "8.788507 | \n", "8.855337 | \n", "... | \n", "9.539184 | \n", "8.672265 | \n", "9.594567 | \n", "8.579562 | \n", "9.669472 | \n", "9.377676 | \n", "9.125494 | \n", "10.045597 | \n", "8.782129 | \n", "9.287517 | \n", "
NR2E3 | \n", "3.989407 | \n", "3.901817 | \n", "4.051622 | \n", "3.875381 | \n", "3.804977 | \n", "3.931573 | \n", "3.993905 | \n", "3.990742 | \n", "3.864638 | \n", "3.927532 | \n", "... | \n", "4.132590 | \n", "4.118239 | \n", "3.706916 | \n", "3.829621 | \n", "3.748747 | \n", "4.071493 | \n", "3.678901 | \n", "3.869146 | \n", "4.106636 | \n", "3.887731 | \n", "
NAALAD2 | \n", "4.389125 | \n", "4.678008 | \n", "3.844582 | \n", "7.318395 | \n", "4.123212 | \n", "4.142046 | \n", "3.873645 | \n", "3.872935 | \n", "3.751903 | \n", "4.138593 | \n", "... | \n", "3.763763 | \n", "3.873275 | \n", "3.599781 | \n", "3.703137 | \n", "6.849774 | \n", "3.681915 | \n", "3.948763 | \n", "3.678124 | \n", "3.535314 | \n", "6.393138 | \n", "
5 rows × 100 columns
\n", "