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ddx21
Commit 6f3c7a03 authored by Venkat Malladi's avatar Venkat Malladi
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Add in analysis for spikein normalized data.

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README.md
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......@@ -27,6 +27,9 @@ PARP-1 interacting snoRNA and DDX21
## Analysis of RNA-seq
- spike_in_correlation.py: Script to look at Spike-in counts to correlation
- spike_in_correlation.sh: Script to analyze spike-ins
- RNA-seq.Rmd: RNA-seq of data analysis regardless of spike-ins
## General Analysis
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RNA-seq_spikein.Rmd 0 → 100644
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figures/DDX21_regulated_genes.cdt 0 → 100644
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"GID" "YORF" "NAME" "LUCKD" "DDX21KD" "WT" "MUT"
"6575" "ENSG00000148303.12" "RPL7A" 0 -1 -0.259291629899229 -0.449506630852822
"10470" "ENSG00000184949.11" "FAM227A" 0 -1 -0.256510773847042 -0.283375490758114
"373" "ENSG00000033327.8" "GAB2" 0 -1 -0.239354847680858 -0.560144654856979
"11660" "ENSG00000204628.7" "GNB2L1" 0 -1 -0.246815671182654 -0.572680416856648
"12493" "ENSG00000234857.2" "HNRNPUL2-BSCL2" 0 -1 -0.178004667273657 -0.160229776096772
"2024" "ENSG00000102317.13" "RBM3" 0 -1 -0.211193891137497 -0.590586756495283
"11977" "ENSG00000215030.4" "RPL13P12" 0 -1 -0.20685825263711 -0.341402192505837
"9513" "ENSG00000175061.13" "C17orf76-AS1" 0 -1 -0.329497605226728 -0.266769167961129
"12660" "ENSG00000241370.1" "RPP21" 0 -1 -0.32390386292658 -0.195820643510665
"13378" "ENSG00000265681.2" "RPL17" 0 -1 -0.321321315917947 -0.0681730650201384
"5575" "ENSG00000138175.8" "ARL3" 0 -1 -0.292833258659547 0.00402248791976751
"10210" "ENSG00000182628.8" "SKA2" 0 -1 -0.296782782410002 -0.614289760133776
"6726" "ENSG00000150540.9" "HNMT" 0 -1 -0.308854208925129 -0.269274497394847
"6702" "ENSG00000149806.6" "FAU" 0 -1 -0.303362046093514 -0.259572955021615
"11617" "ENSG00000204387.8" "C6orf48" 0 -1 -0.302564025712188 -0.230638405521634
"12589" "ENSG00000237883.1" "DGUOK-AS1" 0 -1 -0.355647780891432 -0.371456206230603
"12359" "ENSG00000230989.2" "HSBP1" 0 -1 -0.37042811757272 -0.475704424134617
"12731" "ENSG00000243678.7" "NME1-NME2" 0 -1 -0.365078803091647 -0.325081366484849
"13286" "ENSG00000261485.1" "PAN3-AS1" 0 -0.958749062606917 -0.393404539403541 -1
"4577" "ENSG00000130255.8" "RPL36" 0 -1 -0.420254497097943 -0.36805256119101
"10856" "ENSG00000188483.6" "IER5L" 0 -1 -0.396998465220999 -0.735883249907464
"10069" "ENSG00000181019.8" "NQO1" 0 -1 0.702246043804737 0.198263566163276
"2930" "ENSG00000111341.5" "MGP" 0 -1 0.075051473736394 -0.665905748214854
"7326" "ENSG00000158427.10" "TMSB15B" 0 -1 -0.0388351634481664 -0.319828397870383
"8256" "ENSG00000165732.8" "DDX21" 0 -1 -0.0612472237433242 -0.0322143784991788
"3610" "ENSG00000118181.6" "RPS25" 0 -1 -0.442736428130959 -0.00437386232622415
"12301" "ENSG00000229117.4" "RPL41" 0 -1 -0.438193803703272 -0.05103739584508
"4183" "ENSG00000125356.6" "NDUFA1" 0 -1 -0.457022249174771 -0.440331604432744
"7385" "ENSG00000159199.9" "ATP5G1" 0 -1 -0.467628416573922 -0.537289769429211
"6303" "ENSG00000144935.10" "TRPC1" 0 -0.946185459993292 -0.527526432642783 -1
"8917" "ENSG00000170091.6" "NSG2" 0 -0.942311136078745 -0.505382647495403 -1
"9590" "ENSG00000175768.8" "TOMM5" 0 -1 -0.539887572938722 -0.476311267933874
"5473" "ENSG00000137563.7" "GGH" 0 -1 -0.525947656702851 -0.482734753801642
"12946" "ENSG00000251928.1" "RNU6-585P" 0 -1 -0.519218284051912 -0.613134214673837
"1689" "ENSG00000100142.10" "POLR2F" 0 -1 -0.487627696420955 -0.290721803356872
"7182" "ENSG00000156482.6" "RPL30" 0 -1 -0.484677068221715 -0.438063056438316
"12489" "ENSG00000234741.3" "GAS5" 0 -1 -0.483432615922367 -0.262784574086306
"2563" "ENSG00000107223.8" "EDF1" 0 -1 -0.495359772187569 -0.60534137629071
"9589" "ENSG00000175764.10" "TTLL11" 0 -1 -0.503604371065877 -0.354138381805198
"10174" "ENSG00000182240.11" "BACE2" 0 -1 -0.506376781112603 -0.960120699618985
"10957" "ENSG00000189403.10" "HMGB1" 0 -1 -0.571087477535587 -0.526002102651654
"11952" "ENSG00000214595.7" "EML6" 0 -1 -0.567210844129215 -0.499783242280499
"10383" "ENSG00000184194.5" "GPR173" 0 -1 -0.578897803270124 -0.708692810265114
"1339" "ENSG00000087245.8" "MMP2" 0 -1 -0.589179914997358 0.658329932332413
"6089" "ENSG00000143222.7" "UFC1" 0 -1 -0.584578560020082 -0.43482430906772
"7882" "ENSG00000163644.10" "PPM1K" 0 -1 -0.586066257157298 -0.943404281974684
"4160" "ENSG00000124813.16" "RUNX2" 0 -0.942062123305916 -0.599400807055966 -1
"3377" "ENSG00000115758.8" "ODC1" 0 -0.974887643481951 -0.609289186726763 -1
"11606" "ENSG00000204316.8" "MRPL38" 0 -1 -0.601020540887356 -0.451969125552638
"12357" "ENSG00000230873.4" "STMND1" 0 -1 -0.609021778149115 -0.475548021318145
"3920" "ENSG00000122026.6" "RPL21" 0 -0.991828550600218 -0.617281303035962 -1
"10871" "ENSG00000188612.7" "SUMO2" 0 -1 -0.61911873328624 -0.545532799769525
"9225" "ENSG00000172428.6" "MYEOV2" 0 -1 -0.82524903969743 -0.497935572661993
"2034" "ENSG00000102543.10" "CDADC1" 0 -1 -0.766329452584357 0.0517729658707944
"11303" "ENSG00000198034.6" "RPS4X" 0 -1 -0.733246531821575 -0.906774728553396
"11289" "ENSG00000197958.8" "RPL12" 0 -1 -0.699903349006058 -0.975199043997027
"2338" "ENSG00000105329.5" "TGFB1" 0 -1 -0.697058167326636 -0.803809322744816
"10731" "ENSG00000187109.9" "NAP1L1" 0 -1 -0.697851309558922 -0.931129738072123
"13502" "ENSG00000269858.1" "EGLN2" 0 -1 -0.676345336463788 -0.543540081749014
"5436" "ENSG00000137267.5" "TUBB2A" 0 -1 -0.68167983628864 -0.522987187204123
"7841" "ENSG00000163479.9" "SSR2" 0 -1 -0.684285515098785 -0.367057886007922
"8370" "ENSG00000166441.8" "RPL27A" 0 -1 -0.635062720624566 -0.848853066427527
"4245" "ENSG00000125835.13" "SNRPB" 0 -1 -0.633759791490139 -0.845257062866378
"6653" "ENSG00000149260.10" "CAPN5" 0 -1 -0.633627467891963 -0.567557163075033
"7772" "ENSG00000163041.5" "H3F3A" 0 -1 -0.642452217688981 -0.853918662632115
"7862" "ENSG00000163584.13" "RPL22L1" 0 -1 -0.639582897673436 -0.799340749898383
"6973" "ENSG00000153574.8" "RPIA" 0 -1 -0.667498886320712 -0.793493511046235
"3634" "ENSG00000118515.7" "SGK1" 0 -1 -0.657521287809424 -0.791648246237144
"5737" "ENSG00000139579.8" "NABP2" 0 -1 -0.648917278129512 -0.573552165061392
"251" "ENSG00000013583.4" "HEBP1" 0 0.591073727672592 0.47531479873542 1
"6883" "ENSG00000152409.8" "JMY" 0 1 0.41341022244312 0.545572578809404
"4072" "ENSG00000124098.9" "FAM210B" 0 1 0.445027391385085 0.366894844293312
"12671" "ENSG00000241781.2" "AL161626.1" 0 1 0.440499292816783 0.858725306002536
"6110" "ENSG00000143367.11" "TUFT1" 0 1 0.456568782908754 0.549690868979347
"12692" "ENSG00000242299.1" "RP11-234A1.1" 0 1 0.466761662514677 0.509501467232065
"4689" "ENSG00000131069.15" "ACSS2" 0 0.901535815117477 0.475396904913733 1
"7573" "ENSG00000161202.13" "DVL3" 0 0.95635062679373 0.466507805802869 1
"9542" "ENSG00000175265.13" "GOLGA8A" 0 1 0.522205455885712 0.506343180653645
"4844" "ENSG00000132561.9" "MATN2" 0 1 0.495315235608566 0.0739617650233378
"12055" "ENSG00000220842.5" "RP11-572P18.1" 0 1 0.508612694369989 0.0297101345510955
"13094" "ENSG00000257084.1" "U47924.27" 0 1 0.506313233083149 0.451550383331052
"1720" "ENSG00000100276.9" "RASL10A" 0 1 0.56612216218496 0.738404052261622
"585" "ENSG00000057294.9" "PKP2" 0 1 0.572009540465615 0.297243493726589
"1462" "ENSG00000090581.5" "GNPTG" 0 1 0.573455896057002 0.722435540667495
"6066" "ENSG00000143061.13" "IGSF3" 0 1 0.542755063249404 0.635347635714383
"6331" "ENSG00000145348.12" "TBCK" 0 1 0.546214724915017 0.797498941364701
"7404" "ENSG00000159348.8" "CYB5R1" 0 1 0.554920124322913 0.75885831924491
"8188" "ENSG00000165288.10" "BRWD3" 0 1 0.559920332751134 0.435188732587294
"921" "ENSG00000072274.8" "TFRC" 0 1 0.675252938963592 0.783395355254841
"1096" "ENSG00000078114.14" "NEBL" 0 1 0.649378960211372 0.867935570369383
"12176" "ENSG00000225791.2" "TRAM2-AS1" 0 1 0.644213223679953 0.731071903819352
"6357" "ENSG00000145685.9" "LHFPL2" 0 1 0.637188852452039 0.703828909721836
"11224" "ENSG00000197563.5" "PIGN" 0 1 0.631661820520365 0.904497272701011
"9275" "ENSG00000172869.10" "DMXL1" 0 0.944838189382231 0.60411240666733 1
"4263" "ENSG00000125952.14" "MAX" 0 1 0.597417850789008 0.690864504646611
"7168" "ENSG00000156273.11" "BACH1" 0 1 0.622135789520344 0.697017935366309
"6642" "ENSG00000149177.8" "PTPRJ" 0 1 0.616735185428519 0.705112826115606
"11176" "ENSG00000197265.4" "GTF2E2" 0 1 0.615314921996045 0.89161530739901
"3708" "ENSG00000119574.8" "ZBTB45" 0 1 0.715610523345718 0.222061506202278
"118" "ENSG00000006831.9" "ADIPOR2" 0 1 0.74071479675078 0.834789826525939
"1954" "ENSG00000101639.14" "CEP192" 0 1 0.728095800585357 0.969218261558476
"5869" "ENSG00000140905.5" "GCSH" 0 1 0.733764136897481 0.26433116101688
"3057" "ENSG00000112414.10" "GPR126" 0 0.926649233108986 0.790117863227818 1
"6254" "ENSG00000144455.9" "SUMF1" 0 1 0.813957898386459 0.739629528750039
"6365" "ENSG00000145736.10" "GTF2H2" 0 1 0.780407116267696 0.807047660498584
"4701" "ENSG00000131171.8" "SH3BGRL" 0 1 -0.838995008612552 -0.343922528330215
"12547" "ENSG00000236824.1" "BCYRN1" 0 0.730981858140711 -0.353095135742429 -1
"4075" "ENSG00000124126.9" "PREX1" 0 1 -0.446668445616761 0.0244508293888281
"9336" "ENSG00000173391.4" "OLR1" 0 1 -0.469588846495123 0.198763622567183
"9437" "ENSG00000174307.5" "PHLDA3" 0 1 -0.45843290638089 -0.190505463820357
"9766" "ENSG00000177606.5" "JUN" 0 1 -0.11451285797351 -0.0457354291035481
"1964" "ENSG00000101825.7" "MXRA5" 0 1 -0.0549250691348075 0.0916066230917265
"4148" "ENSG00000124762.9" "CDKN1A" 0 1 -0.0486070893147965 -0.122787494853853
"6777" "ENSG00000151240.11" "DIP2C" 0 1 0.348128418047094 0.318603640507497
"2747" "ENSG00000109099.9" "PMP22" 0 1 0.280169235294298 0.986716267717722
"6714" "ENSG00000150093.14" "ITGB1" 0 1 0.30492351589521 0.639295211711425
"7780" "ENSG00000163083.5" "INHBB" 0 1 0.0638345729609293 0.38984919936399
"4362" "ENSG00000127415.8" "IDUA" 0 1 0.197321504752081 0.302555404350811
"10406" "ENSG00000184363.5" "PKP3" 0 1 0.201538414259564 0.609634615646393
figures/DDX21_regulated_genes.jtv 0 → 100644
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<DocumentConfig><UrlExtractor/><ArrayUrlExtractor/><Views><View type="Dendrogram" dock="1"><ColorExtractor contrast="1.4" logtransform="0"><ColorSet up="#FEF437" down="#2CFCF5"/></ColorExtractor><ArrayDrawer/><GlobalXMap current="Fill"><FixedMap type="Fixed" scale="44.0"/><FillMap type="Fill"/><NullMap type="Null"/></GlobalXMap><GlobalYMap current="Fill"><FixedMap type="Fixed" scale="7.0"/><FillMap type="Fill"/><NullMap type="Null"/></GlobalYMap><ZoomXMap current="Fill"><FixedMap type="Fixed"/><FillMap type="Fill"/><NullMap type="Null"/></ZoomXMap><ZoomYMap current="Fill"><FixedMap type="Fixed"/><FillMap type="Fill"/><NullMap type="Null"/></ZoomYMap><TextView><TextView><GeneSummary/></TextView><TextView><GeneSummary/></TextView><TextView><GeneSummary/></TextView></TextView><ArrayNameView><ArraySummary included="0"/></ArrayNameView><AtrSummary/><GtrSummary/></View></Views></DocumentConfig>
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tables/kd_down_genes_spikein.csv 0 → 100644
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tables/wt_down_genes_spikein.csv 0 → 100644
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