junjun-zhang

# 1.create_nodes_for_dag.1.sh
curl -XPUT 'localhost:9200/.d.dag.data.a/A/a1.1' -H 'Content-Type: application/json' -d'
{
  "type": "A",
  "id": "a1",
  "p_id": [ ],
  "a_id": [ ],
  "data": { }
}
'

junjun-zhang

Demo use cases

Use case 1
Find commonly mutated genes with high impact mutations between Ovary cancer and Prostate cancer;
how many of these common genes are in the Cancer Gene Census? Save this gene set and share it with
a colleague.

Use case 2
A colleague identified 458 ‘interesting’ mutations and shared the list with you: https://icgc.org/Z37.
You may wonder what are the genes affected by these mutations and whether these genes over-represented

junjun-zhang

TP53, PIK3CA, APC, VHL, KRAS, ARID1A, PBRM1, NAV3, EGFR, NF1, PIK3R1,
CDKN2A, SETD2, ATM, GATA3, RB1, NOTCH1, FBXW7, MTOR, CTNNB1, DNMT3A,
ATRX, LRRK2, MAP3K1, FLT3, MALAT1, BRCA2, TSHZ3, KEAP1, CDH1, ARHGAP35,
EP300, CTCF, POLQ, ATR, NSD1, NFE2L2, TAF1, SETBP1, STAG2, NCOR1, EPHA3,
ERBB4, USP9X, BAP1, KDM6A, KDM5C, TLR4, BRCA1, PDGFRA, NPM1, TSHZ2,
PIK3CG, HGF, RUNX1, ARID5B, TET2, EPHB6, NRAS, IDH1, BRAF, FGFR2,
PPP2R1A, CDK12, SMC1A, MECOM, TBX3, MAP2K4, EPPK1, KIT, SMAD4, ASXL1,
SF3B1, AR, LIFR, SMC3, TGFBR2, SIN3A, RPL22, WT1, FGFR3, PTPN11, ACVR1B,
STK11, AKT1, PRX, CHEK2, SMAD2, AXIN2, RAD21, AJUBA, U2AF1, FOXA1, IDH2,
NFE2L3, EIF4A2, PHF6, TBL1XR1, EZH2, CRIPAK, SOX9, CDKN1B, CBFB, MAPK8IP1,

junjun-zhang

curl -XGET "http://192.170.232.56:8200/gdc_v12/participant-centric/_search?pretty=1" -d '
{
   "aggs":{
      "project":{
         "terms":{
            "field":"admin.disease_code",
            "size":1000
         },
         "aggs":{
            "file_size":{