DEGenome – Differential expression across the genome¶
DEGenome transforms differential gene expression (DGE) data to Ideogram JSON.
Written in Python, the DEGenome pipeline takes in genome annotations and DGE matrices, and outputs Ideogram.js JSON annotation files.
You can then upload Ideogram JSON to the cloud, and explore it in an interactive genome visualization at https://eweitz.github.io/ideogram/differential-expression.
For a walk-through example, see the DEGenome tutorial on Terra.
Reduce GTF¶
Each organism processed by DEGenome will need a reduced GTF, i.e. a “gen_pos.tsv” file.
The gtf_to_gen_pos.py CLI module converts a GTF genome annotation file from GENCODE, Ensembl, or NCBI into a smaller, simpler, and more metadata-rich TSV gene position (“gen_pos”) file. The purpose is to speed up, simplify, and enrich downstream pipelines that require only data on genes, and not e.g. transcripts or exons.
Transform DGE matrix¶
Each differential gene expression (DGE) matrix needs to be transformed to Ideogram JSON.
The dge_to_ideogram.py CLI module converts a DGE matrix file containing gene expression summary statistics into an Ideogram.js annotations JSON file. The resulting JSON file is used for exploratory data analysis as demonstrated at:
https://eweitz.github.io/ideogram/differential-expression
DGE matrix format¶
The DGE matrix has several groups of columns, with headers ordered like so:
metadata: “REFSEQ”,”SYMBOL”,”GENENAME”,”ENSEMBL”,”ENTREZID”,”STRING_id”,”GOSLIM_IDS”
replicates: <sample_prefix>-<group>-<replicate_number>, e.g. “Mmus-C57-6T-TMS-FLT-Rep1”
stats: “All.mean”,”All.stdev”,”F.p.value”
stats_by_group: Group.<stat>_(<group>), e.g. “Group.Mean_(Space Flight)”
stats_by_comparison: <stat>_(<group1>)v(<group2>), e.g. “Log2fc_(Ground Control)v(Space Flight)”
Example DGE matrix¶
An example DGE matrix is GLDS-21_array_differential_expression.csv from GLDS-21, produced by NASA GeneLab. Below is an excerpt.
# Download example DGE matrix
curl -L https://genelab-data.ndc.nasa.gov/genelab/static/media/dataset/GLDS-21_array_differential_expression.csv?version=1 > GLDS-21_array_differential_expression.csv
# Print first 10 lines of example DGE matrix
head GLDS-21_array_differential_expression.csv
"REFSEQ","SYMBOL","GENENAME","ENSEMBL","ENTREZID","STRING_id","GOSLIM_IDS","Mmus-C57-6J-GST-M19-CTRL-Rep1","Mmus-C57-6J-GST-M1-CTRL-Rep2","Mmus-C57-6J-GST-M21-CTRL-Rep3","Mmus-C57-6J-GST-M22-CTRL-Rep4","Mmus-C57-6J-GST-M2-CTRL-Rep5","Mmus-C57-6J-GST-M14-HLU-RL-Rep1","Mmus-C57-6J-GST-M15-HLU-RL-Rep2","Mmus-C57-6J-GST-M16-HLU-RL-Rep3","Mmus-C57-6J-GST-M18-HLU-RL-Rep4","Mmus-C57-6J-GST-M33-HLU-RL-Rep5","Mmus-C57-6J-GST-M11-HLU-Rep1","Mmus-C57-6J-GST-M25-HLU-Rep2","Mmus-C57-6J-GST-M30-HLU-Rep3","Mmus-C57-6J-GST-M8-HLU-Rep4","Mmus-C57-6J-GST-M9-HLU-Rep5","Mmus-C57-6J-GST-M1-GC-Rep1","Mmus-C57-6J-GST-M2-GC-Rep2","Mmus-C57-6J-GST-M3-GC-Rep3","Mmus-C57-6J-GST-M4-GC-Rep4","Mmus-C57-6J-GST-M10-FLT-Rep1","Mmus-C57-6J-GST-M11-FLT-Rep2","Mmus-C57-6J-GST-M8-FLT-Rep3","Mmus-C57-6J-GST-M9-FLT-Rep4","All.mean","All.stdev","F.p.value","Group.Mean_(Vivarium Control)","Group.Mean_(Hindlimb Suspension and Reloading)","Group.Mean_(Hindlimb Suspension)","Group.Mean_(Ground Control)","Group.Mean_(Space Flight)","Group.Stdev_(Vivarium Control)","Group.Stdev_(Hindlimb Suspension and Reloading)","Group.Stdev_(Hindlimb Suspension)","Group.Stdev_(Ground Control)","Group.Stdev_(Space Flight)","Log2fc_(Ground Control)v(Hindlimb Suspension and Reloading)","Log2fc_(Ground Control)v(Hindlimb Suspension)","Log2fc_(Ground Control)v(Space Flight)","Log2fc_(Ground Control)v(Vivarium Control)","Log2fc_(Hindlimb Suspension and Reloading)v(Hindlimb Suspension)","Log2fc_(Hindlimb Suspension and Reloading)v(Space Flight)","Log2fc_(Hindlimb Suspension and Reloading)v(Vivarium Control)","Log2fc_(Hindlimb Suspension)v(Space Flight)","Log2fc_(Hindlimb Suspension)v(Vivarium Control)","Log2fc_(Space Flight)v(Vivarium Control)","Log2fc_(Hindlimb Suspension and Reloading)v(Ground Control)","Log2fc_(Hindlimb Suspension)v(Ground Control)","Log2fc_(Space Flight)v(Ground Control)","Log2fc_(Vivarium Control)v(Ground Control)","Log2fc_(Hindlimb Suspension)v(Hindlimb Suspension and Reloading)","Log2fc_(Space Flight)v(Hindlimb Suspension and Reloading)","Log2fc_(Vivarium Control)v(Hindlimb Suspension and Reloading)","Log2fc_(Space Flight)v(Hindlimb Suspension)","Log2fc_(Vivarium Control)v(Hindlimb Suspension)","Log2fc_(Vivarium Control)v(Space Flight)","P.value_(Ground Control)v(Hindlimb Suspension and Reloading)","P.value_(Ground Control)v(Hindlimb Suspension)","P.value_(Ground Control)v(Space Flight)","P.value_(Ground Control)v(Vivarium Control)","P.value_(Hindlimb Suspension and Reloading)v(Hindlimb Suspension)","P.value_(Hindlimb Suspension and Reloading)v(Space Flight)","P.value_(Hindlimb Suspension and Reloading)v(Vivarium Control)","P.value_(Hindlimb Suspension)v(Space Flight)","P.value_(Hindlimb Suspension)v(Vivarium Control)","P.value_(Space Flight)v(Vivarium Control)","P.value_(Hindlimb Suspension and Reloading)v(Ground Control)","P.value_(Hindlimb Suspension)v(Ground Control)","P.value_(Space Flight)v(Ground Control)","P.value_(Vivarium Control)v(Ground Control)","P.value_(Hindlimb Suspension)v(Hindlimb Suspension and Reloading)","P.value_(Space Flight)v(Hindlimb Suspension and Reloading)","P.value_(Vivarium Control)v(Hindlimb Suspension and Reloading)","P.value_(Space Flight)v(Hindlimb Suspension)","P.value_(Vivarium Control)v(Hindlimb Suspension)","P.value_(Vivarium Control)v(Space Flight)","Adj.p.value_(Ground Control)v(Hindlimb Suspension and Reloading)","Adj.p.value_(Ground Control)v(Hindlimb Suspension)","Adj.p.value_(Ground Control)v(Space Flight)","Adj.p.value_(Ground Control)v(Vivarium Control)","Adj.p.value_(Hindlimb Suspension and Reloading)v(Hindlimb Suspension)","Adj.p.value_(Hindlimb Suspension and Reloading)v(Space Flight)","Adj.p.value_(Hindlimb Suspension and Reloading)v(Vivarium Control)","Adj.p.value_(Hindlimb Suspension)v(Space Flight)","Adj.p.value_(Hindlimb Suspension)v(Vivarium Control)","Adj.p.value_(Space Flight)v(Vivarium Control)","Adj.p.value_(Hindlimb Suspension and Reloading)v(Ground Control)","Adj.p.value_(Hindlimb Suspension)v(Ground Control)","Adj.p.value_(Space Flight)v(Ground Control)","Adj.p.value_(Vivarium Control)v(Ground Control)","Adj.p.value_(Hindlimb Suspension)v(Hindlimb Suspension and Reloading)","Adj.p.value_(Space Flight)v(Hindlimb Suspension and Reloading)","Adj.p.value_(Vivarium Control)v(Hindlimb Suspension and Reloading)","Adj.p.value_(Space Flight)v(Hindlimb Suspension)","Adj.p.value_(Vivarium Control)v(Hindlimb Suspension)","Adj.p.value_(Vivarium Control)v(Space Flight)"
"NM_013477","Atp6v0d1","ATPase, H+ transporting, lysosomal V0 subunit D1","ENSMUSG00000013160","11972",NA,"GO:0003824, GO:0005215, GO:0006810, GO:0006811, GO:0006812, GO:0008324, GO:0015078, GO:0016787, GO:0022857, GO:0008152, GO:0051179",7.7257820950506,7.84313596519635,7.92196078756618,7.97589186470181,7.61839761490813,8.03409884224697,7.99157996281313,7.8050344911136,8.0891594337366,7.97378740316215,7.15547234247511,7.91405159713476,7.72493982766783,7.55328424180865,7.54464701803143,8.35918865982752,8.24377032548604,8.34427162732955,8.34482075283258,8.36167982612162,8.25621683710273,8.41104483446799,8.32697396108158,7.97909523095056,0.0282776063242181,2.03287461813406e-06,8.32301284136892,7.57847900542356,7.97873202661449,8.33897886469348,7.81703366548461,4.16150642068446,3.38919884443641,3.56819743715293,4.16948943234674,3.49588373168559,0.744533835945366,0.344280814754432,-0.0159660233245571,0.505979175884309,-0.400253021190934,-0.760499859269923,-0.238554660061057,-0.360246838078989,0.161698361129877,0.521945199208866,-0.744533835945366,-0.344280814754432,0.0159660233245571,-0.505979175884309,0.400253021190934,0.760499859269923,0.238554660061057,0.360246838078989,-0.161698361129877,-0.521945199208866,1.39848603457645e-06,0.00596001736520029,0.894438821528775,0.000194730292332154,0.00111028552834159,1.02256465728364e-06,0.0355777788013318,0.00429005146391487,0.143025685222599,0.000138451040149514,1.39848603457645e-06,0.00596001736520029,0.894438821528775,0.000194730292332154,0.00111028552834159,1.02256465728364e-06,0.0355777788013318,0.00429005146391487,0.143025685222599,0.000138451040149514,2.59951479789537e-05,0.0225242443781023,0.999966010284893,0.00194425788356654,0.161370011235908,1.54169429439341e-05,0.242275153466606,0.014447246095515,0.999991739420172,0.00107282753805176,2.59951479789537e-05,0.0225242443781023,0.999966010284893,0.00194425788356654,0.161370011235908,1.54169429439341e-05,0.242275153466606,0.014447246095515,0.999991739420172,0.00107282753805176
"NM_001042484","Golga7","golgi autoantigen, golgin subfamily a, 7","ENSMUSG00000015341","57437",NA,"GO:0003824, GO:0005622, GO:0005737, GO:0005794, GO:0006464, GO:0006497, GO:0006605, GO:0006810, GO:0006886, GO:0008104, GO:0008152, GO:0009058, GO:0009987, GO:0015031, GO:0016043, GO:0016192, GO:0016740, GO:0016746, GO:0019538, GO:0032991, GO:0043226, GO:0043234, GO:0044238, GO:0044464, GO:0051179, GO:0071840",8.73243428421421,8.47265380141892,8.77071071861314,8.60891537447205,8.64612515594437,8.69056769224593,8.71110585060474,8.71393475048357,8.57994830337183,8.74384607040437,6.59566688844254,8.87991401739975,8.76274698871946,8.14604762785509,8.44873826358109,9.30634876836969,9.0650235670456,9.06884271394723,9.13873131245664,9.1350482687313,8.94483822547572,9.0563425770422,9.13555784621569,8.71104735074153,0.171885650625696,0.0138047337182277,9.14473659045479,8.16662275719959,8.68788053342209,9.06794672936623,8.64616786693254,4.57236829522739,3.65222472633901,3.88533829062578,4.53397336468311,3.8666838190671,0.978113833255202,0.4568560570327,0.076789861088562,0.498568723522252,-0.521257776222502,-0.90132397216664,-0.47954510973295,-0.380066195944138,0.041712666489552,0.42177886243369,-0.978113833255202,-0.4568560570327,-0.076789861088562,-0.498568723522252,0.521257776222502,0.90132397216664,0.47954510973295,0.380066195944138,-0.041712666489552,-0.42177886243369,0.00200100545517407,0.115036499678786,0.795869217192227,0.087149792786443,0.0597381365920112,0.00384094662787054,0.0813673994934013,0.185920886566873,0.875094197085245,0.143985974839089,0.00200100545517407,0.115036499678786,0.795869217192227,0.087149792786443,0.0597381365920112,0.00384094662787054,0.0813673994934013,0.185920886566873,0.875094197085245,0.143985974839089,0.00482584318462189,0.203831844165131,0.999966010284893,0.166776989941987,0.224211271219303,0.00738576847431212,0.256816952952497,0.272531452798223,0.999991739420172,0.223143312948443,0.00482584318462189,0.203831844165131,0.999966010284893,0.166776989941987,0.224211271219303,0.00738576847431212,0.256816952952497,0.272531452798223,0.999991739420172,0.223143312948443
"NM_133900","Psph","phosphoserine phosphatase","ENSMUSG00000029446","100678",NA,"GO:0003824, GO:0005488, GO:0005622, GO:0005737, GO:0006520, GO:0006796, GO:0006807, GO:0008152, GO:0008652, GO:0009058, GO:0009987, GO:0016787, GO:0016788, GO:0016791, GO:0044238, GO:0044464",4.86066785235675,4.85395026121031,4.93327403838069,5.05004369537868,4.7478500715842,4.74734097563494,4.98755847675237,4.96372179595896,5.02245488465075,4.97964714916791,4.35250955980416,4.94529632704556,5.0583490019893,4.89441712517217,5.12267612594413,6.14762517119975,5.86480970295413,5.76077647345354,5.7865402625027,5.91181373094812,5.82793376063711,5.8906715699905,5.79254533009815,5.23923797142673,0.0333456325100968,2.44663857184323e-09,5.88993790252753,4.87464962799106,4.94014465643299,5.85574109791847,4.88915718378212,2.94496895126376,2.18000958693642,2.2092998540933,2.92787054895923,2.18649756312365,1.01528827453647,0.949793246094543,0.0341968046090591,1.0007807187454,-0.0654950284419229,-0.981091469927406,-0.0145075557910612,-0.915596441485484,0.0509874726508617,0.966583914136345,-1.01528827453647,-0.949793246094543,-0.0341968046090591,-1.0007807187454,0.0654950284419229,0.981091469927406,0.0145075557910612,0.915596441485484,-0.0509874726508617,-0.966583914136345,3.97212622804918e-08,1.17764923990239e-07,0.793663492112051,5.03669409514894e-08,0.57653717865235,6.97262675567756e-08,0.901206460598853,2.10892623811735e-07,0.663283970863826,8.88039225813255e-08,3.97212622804918e-08,1.17764923990239e-07,0.793663492112051,5.03669409514894e-08,0.57653717865235,6.97262675567756e-08,0.901206460598853,2.10892623811735e-07,0.663283970863826,8.88039225813255e-08,3.26955400012536e-06,1.93683470368805e-05,0.999966010284893,1.45682740139007e-05,0.675695647154048,2.64214966379829e-06,0.932002660868356,1.27635014505965e-05,0.999991739420172,8.17323336511723e-06,3.26955400012536e-06,1.93683470368805e-05,0.999966010284893,1.45682740139007e-05,0.675695647154048,2.64214966379829e-06,0.932002660868356,1.27635014505965e-05,0.999991739420172,8.17323336511723e-06
"NM_021789","Trappc4","trafficking protein particle complex 4","ENSMUSG00000032112","60409",NA,"GO:0000166, GO:0003824, GO:0003924, GO:0005083, GO:0005085, GO:0005488, GO:0005622, GO:0006139, GO:0006796, GO:0006807, GO:0006810, GO:0008152, GO:0009056, GO:0009987, GO:0016192, GO:0016462, GO:0016787, GO:0030234, GO:0032991, GO:0043234, GO:0044238, GO:0044464, GO:0050789, GO:0050790, GO:0051179, GO:0065007, GO:0065009",6.86453094082816,6.95638709228716,6.93785154771474,6.9486345783565,6.59222784139469,6.75181927301955,6.89771530818833,6.54459667307327,6.74110826988262,6.87764590359797,6.35985747965413,6.62911491193238,6.7813538001846,6.41208543663296,6.93134932536261,7.59330837488809,7.65662035729898,7.20010997801657,7.37658626457963,7.20608578453671,7.05929575253853,7.75862969747448,7.42656569165268,6.97841218622154,0.0446230750445414,1.09489678297805e-05,7.45665624369582,6.62275219075334,6.76257708555235,7.3626442315506,6.85992640011625,3.72832812184791,2.96178481933202,3.02431641327549,3.6813221157753,3.06785235026107,0.833904052942482,0.694079158143471,0.0940120121452193,0.596729843579569,-0.139824894799011,-0.739892040797263,-0.237174209362913,-0.600067145998252,-0.0973493145639024,0.502717831434349,-0.833904052942482,-0.694079158143471,-0.0940120121452193,-0.596729843579569,0.139824894799011,0.739892040797263,0.237174209362913,0.600067145998252,0.0973493145639024,-0.502717831434349,7.06987423791989e-06,7.22064960303289e-05,0.53574491300652,0.000377643571619844,0.306947532554226,3.34122366049216e-05,0.0900576656311043,0.000356767187298876,0.474096451733305,0.00186000474881377,7.06987423791989e-06,7.22064960303289e-05,0.53574491300652,0.000377643571619844,0.306947532554226,3.34122366049216e-05,0.0900576656311043,0.000356767187298876,0.474096451733305,0.00186000474881377,7.47369983594678e-05,0.00095453100859969,0.999966010284893,0.00309114057196795,0.437566420039904,0.000181873086719885,0.259558775180826,0.00215554435623863,0.999991739420172,0.00758784845670623,7.47369983594678e-05,0.00095453100859969,0.999966010284893,0.00309114057196795,0.437566420039904,0.000181873086719885,0.259558775180826,0.00215554435623863,0.999991739420172,0.00758784845670623
"NM_010073","Dpm2","dolichol-phosphate (beta-D) mannosyltransferase 2","ENSMUSG00000026810","13481",NA,"GO:0003824, GO:0005622, GO:0005737, GO:0005783, GO:0005975, GO:0006464, GO:0006486, GO:0006497, GO:0006629, GO:0006644, GO:0006796, GO:0008152, GO:0009058, GO:0009987, GO:0016020, GO:0016740, GO:0016757, GO:0019538, GO:0030234, GO:0032991, GO:0042175, GO:0043226, GO:0043234, GO:0044238, GO:0044464, GO:0050789, GO:0050790, GO:0065007, GO:0065009",7.43251664828479,7.40034107493916,7.68505466921833,7.43623308853643,7.42341754145451,7.58558160457673,7.54197807107685,7.34245916718447,7.38456050585125,7.43572541017978,7.32550553659207,7.25206502700328,7.4396924490844,7.42549306000687,7.3578712328388,7.44140937172973,7.47235113367852,7.48503517065137,7.61458652583076,7.5035124858343,7.40665782584212,7.41309865421363,7.5093035753219,7.44845434043174,0.0134569002185024,0.413441717187866,7.5033455504726,7.36012546110508,7.45806095177382,7.45814313530299,7.47551260448665,3.7516727752363,3.29154817079159,3.33534625370061,3.72907156765149,3.34315087005773,0.143220089367512,0.0452845986987809,0.0452024151696087,0.0278329459859492,-0.0979354906687311,-0.0980176741979033,-0.115387143381563,-8.21835291722195e-05,-0.0174516527128317,-0.0173694691836594,-0.143220089367512,-0.0452845986987809,-0.0452024151696087,-0.0278329459859492,0.0979354906687311,0.0980176741979033,0.115387143381563,8.21835291722195e-05,0.0174516527128317,0.0173694691836594,0.0795862601252623,0.566682535664377,0.587285574201185,0.72408870344509,0.195923579135489,0.221361484841036,0.130423254288774,0.999167117868982,0.814242894433413,0.825487438078494,0.0795862601252623,0.566682535664377,0.587285574201185,0.72408870344509,0.195923579135489,0.221361484841036,0.130423254288774,0.999167117868982,0.814242894433413,0.825487438078494,0.100975314634834,0.662747136224388,0.999966010284893,0.788018812254457,0.334708241546515,0.250801717808537,0.286082379884573,0.999401902967564,0.999991739420172,0.867396904818759,0.100975314634834,0.662747136224388,0.999966010284893,0.788018812254457,0.334708241546515,0.250801717808537,0.286082379884573,0.999401902967564,0.999991739420172,0.867396904818759
"NM_011186","Psmb5","proteasome (prosome, macropain) subunit, beta type 5","ENSMUSG00000022193","19173",NA,"NA",10.4173824798625,10.4990702482183,10.6447732811381,10.5501469157437,10.5209031983952,10.3922555227939,10.5743274224454,10.2677063976684,10.4528265665837,10.4135204585091,8.12120679239209,10.519152233801,10.3692944750937,10.2372609439318,10.3485335430108,10.9254503733778,10.7862150372581,10.9361517053036,10.8895814813605,10.7514505837285,10.6842716500414,10.7715724998152,10.8084923910256,10.473110704413,0.201455965728848,0.03421279980501,10.884349649325,9.91908959764588,10.4201272736001,10.7539467811527,10.5264552246716,5.4421748246625,4.43595172304944,4.66002258359387,5.37697339057634,4.70757388889469,0.965260051679119,0.4642223757249,0.130402868172322,0.357894424653436,-0.501037675954219,-0.834857183506797,-0.607365627025683,-0.333819507552578,-0.106327951071464,0.227491556481114,-0.965260051679119,-0.4642223757249,-0.130402868172322,-0.357894424653436,0.501037675954219,0.834857183506797,0.607365627025683,0.333819507552578,0.106327951071464,-0.227491556481114,0.00416810674033423,0.137752767902032,0.685240373129938,0.24757282067751,0.0918020935349357,0.0112663932782583,0.044038508671896,0.279841086835283,0.711663297084332,0.458134464886741,0.00416810674033423,0.137752767902032,0.685240373129938,0.24757282067751,0.0918020935349357,0.0112663932782583,0.044038508671896,0.279841086835283,0.711663297084332,0.458134464886741,0.0086239019886695,0.231400006065372,0.999966010284893,0.355501880362283,0.242941577592378,0.018006488380896,0.242275153466606,0.374431127293228,0.999991739420172,0.548712916582601,0.0086239019886695,0.231400006065372,0.999966010284893,0.355501880362283,0.242941577592378,0.018006488380896,0.242275153466606,0.374431127293228,0.999991739420172,0.548712916582601
"NM_026819","Dhrs1","dehydrogenase/reductase (SDR family) member 1","ENSMUSG00000002332","52585",NA,"NA",7.30878427447465,7.23694159902284,7.23694159902284,7.28344547527175,7.32374234290042,7.14275255493379,7.29836625622201,7.1341174174193,7.21385434233633,7.23357835674116,7.29669408158391,7.2240345696726,7.25660031214864,7.23682095017222,7.28008608624929,7.04936184168956,7.08817567357559,7.24600272972142,7.27843743700347,7.06348665776695,7.22123755103474,7.39107448460253,7.06626770228387,7.22220888242826,0.0130512091683326,0.53492915172593,7.16549442049751,7.25884719996533,7.20453378553052,7.18551659892202,7.2779710581385,3.58274721024875,3.2462551554813,3.22196545812803,3.59275829946101,3.25480760485475,-0.0933527794678204,-0.0390393650330072,-0.0200221784245134,-0.112476637640987,0.0543134144348132,0.073330601043307,-0.0191238581731668,0.0190171866084938,-0.0734372726079799,-0.0924544592164738,0.0933527794678204,0.0390393650330072,0.0200221784245134,0.112476637640987,-0.0543134144348132,-0.073330601043307,0.0191238581731668,-0.0190171866084938,0.0734372726079799,0.0924544592164738,0.236408941714921,0.615665466089051,0.806603619829904,0.156710218133885,0.460397329345376,0.349298763292063,0.793784416787628,0.806379598057849,0.320776572413807,0.240802556281558,0.236408941714921,0.615665466089051,0.806603619829904,0.156710218133885,0.460397329345376,0.349298763292063,0.793784416787628,0.806379598057849,0.320776572413807,0.240802556281558,0.268780465251027,0.705303716832715,0.999966010284893,0.255449257795469,0.575440334319316,0.381928693144931,0.85339510038542,0.852401719270693,0.999991739420172,0.331541632745606,0.268780465251027,0.705303716832715,0.999966010284893,0.255449257795469,0.575440334319316,0.381928693144931,0.85339510038542,0.852401719270693,0.999991739420172,0.331541632745606
"NM_008910","Ppm1a","protein phosphatase 1A, magnesium dependent, alpha isoform","ENSMUSG00000021096","19042",NA,"GO:0000165, GO:0003824, GO:0004721, GO:0004857, GO:0005488, GO:0005515, GO:0006464, GO:0006468, GO:0007154, GO:0007165, GO:0008152, GO:0009987, GO:0016787, GO:0016788, GO:0016791, GO:0019207, GO:0019210, GO:0019538, GO:0030234, GO:0035556, GO:0044238, GO:0050790, GO:0065007, GO:0065009",10.2370668098058,10.146998463959,10.1686637334362,10.2064002643757,10.2287575926057,10.1331254886193,10.1577175591567,10.0327745993425,10.1903309700602,10.0707354085838,6.89873257226107,10.1326324940361,10.2025848380022,9.82831040481749,10.322918704684,10.539373290756,10.3399052916396,10.52107130054,10.714328811621,10.5204195281321,10.5363738400327,10.3228666740627,10.3988212136359,10.123952602355,0.406108489256907,0.136793545080982,10.5286696736392,9.47703580276017,10.1169368051525,10.4446203139658,10.1975773728365,5.26433483681958,4.23825925603421,4.52443168407811,5.22231015698292,4.56049524229522,1.05163387087898,0.411732868486649,0.0840493596733012,0.331092300802672,-0.639901002392332,-0.967584511205679,-0.720541570076309,-0.327683508813347,-0.080640567683977,0.24704294112937,-1.05163387087898,-0.411732868486649,-0.0840493596733012,-0.331092300802672,0.639901002392332,0.967584511205679,0.720541570076309,0.327683508813347,0.080640567683977,-0.24704294112937,0.022454534419192,0.346217138358068,0.853789690555001,0.447092774810973,0.126999608250982,0.034098121512033,0.0879608778055581,0.451721412899901,0.84330412901312,0.569359037898152,0.022454534419192,0.346217138358068,0.853789690555001,0.447092774810973,0.126999608250982,0.034098121512033,0.0879608778055581,0.451721412899901,0.84330412901312,0.569359037898152,0.0336712546422125,0.459867406281112,0.999966010284893,0.552377586526329,0.271564801970034,0.0469976267359592,0.257897212486433,0.544350518328936,0.999991739420172,0.651916172657653,0.0336712546422125,0.459867406281112,0.999966010284893,0.552377586526329,0.271564801970034,0.0469976267359592,0.257897212486433,0.544350518328936,0.999991739420172,0.651916172657653
"NM_025498","Psenen","presenilin enhancer gamma secretase subunit","ENSMUSG00000036835","66340",NA,"GO:0005886, GO:0016020, GO:0032991, GO:0043234, GO:0044464",9.75392835561914,9.74987430120933,9.93583953479859,9.93382155866816,9.76327439364241,9.74000573921616,9.91120717844081,9.63793061755572,9.68663642313116,9.81913412138686,7.29199382929261,9.96188296867934,9.62645287651746,9.71584419494504,9.78372625711475,10.2277886712033,10.1655910243692,10.2070187039487,10.2241072860301,10.2229225135366,10.2752745910896,10.25162938515,10.1381634065352,9.8271325187861,0.243458411980911,0.050888166544347,10.2061264213878,9.27598002530984,9.75898281594614,10.2219974740779,9.82734762878752,5.10306321069391,4.1483443789046,4.36434979354158,5.11099873703893,4.39492346729805,0.930146396077985,0.447143605441685,-0.0158710526900254,0.378778792600302,-0.4830027906363,-0.946017448768011,-0.551367603477683,-0.46301465813171,-0.0683648128413825,0.394649845290328,-0.930146396077985,-0.447143605441685,0.0158710526900254,-0.378778792600302,0.4830027906363,0.946017448768011,0.551367603477683,0.46301465813171,0.0683648128413825,-0.394649845290328,0.0103563336793443,0.190808706430109,0.964138436816396,0.265085844794998,0.136312714305422,0.00929132341712647,0.0914886662440544,0.17615408535817,0.828664828172563,0.246165852258643,0.0103563336793443,0.190808706430109,0.964138436816396,0.265085844794998,0.136312714305422,0.00929132341712647,0.0914886662440544,0.17615408535817,0.828664828172563,0.246165852258643,0.0177347699820349,0.296343962138762,0.999966010284893,0.373265656415496,0.279697105281305,0.0153136551415469,0.260859803196553,0.261385971418061,0.999991739420172,0.337414037862577,0.0177347699820349,0.296343962138762,0.999966010284893,0.373265656415496,0.279697105281305,0.0153136551415469,0.260859803196553,0.261385971418061,0.999991739420172,0.337414037862577
Tutorial¶
For a walk-through example of using DEGenome to convert a differential gene expression matrix to Ideogram JSON, see the “DEGenome tutorial” Jupyter Notebook on Terra.