markziemann / dee2_gene_signatures Goto Github PK

• confused at the start -- documentation required
• more intensive - whole day workshops to start with
• More coding and data crunching to see the outcome of the project

Hi @aaronsk7 these are the remaining contrasts for diabetes.

Studies that fit criteria

GSE97655: alpha vs beta cells

GSE98485: control (siCTL) vs SRp55 (siSR#2)

GSE106148: non-diabetic control versus type 1 diabetes (T1D)

GSE108413: control vs cytokine treatment

GSE109140: gene expression changes in HepG2 cells in response to hyperglycemia and valproic acid

GSE111876:CD3+ T cells of nondiabetic individuals vs type 1 diabetes

GSE114051:Comparison of WT and GLIS3-/- cells at various stages of human pancreatic differentiation???

GSE116369: BCL11A control vs BCL11A knockdown

GSE102371: no replicates but vital information on diabetes, islets of Langerrhans preparations in normo-glycemic individuals, long duration type 1 diabetes, short duration type 1 diabetes

GSE117469:pericytes and endothelial cells differentiated from iPS cells cultured in controlled, diabetic or diabetic media supplemented (pDAPT) (the primary cells were excluded)

GSE120904: Gene expression profiles of human tissue-resident IE-CTLs (both in vitro and ex vivo), before and after simulation with IL-15 and IL-21 (individually and in combination)

GSE50386: Pancreatic islets from 6 donors and separate populations of alpha, beta, and exocrine cells used in RNA-Seq analysis

GSE106177: Human primary cardiac mesenchymal cells (CMSC) from 7 diabetic (D) and 7 non-diabetic (ND) donors were analyzed after few rounds of ex vivo expansion

Studies that don't fit criteria

GSE97647: no replicates

GSE99068: Sorted NK cells from obese and lean peripheral blood mononuclear cells (PBMC) in IL6Ra+ and IL6Ra-, (the mouse samples were excluded)

GSE101207: Human Pancreatic islet from non-diabetic donor versus Type II diabetic donor (the mouse samples were excluded)

GSE102498: based on coronary artery disease

GSE106520: focuses on intracranial aneurysms

GSE109265: no replicates???

GSE110935: has mouse samples???

GSE44639: different instruments used???

GSE120299: not enough replicates for the treatment group

GSE116559: only has control groups and no groups to compare with

Contrasts

SRP103811:alpha cells versus beta cells from three East-Asian non-diabetic subjects:alpha;SRX2733099,SRX2733104,SRX2733110,SRX2733111,SRX2733112,SRX2733113,SRX2733115,SRX2733117,SRX2733119,SRX2733123,SRX2733126,SRX2733128,SRX2733130,SRX2733132,SRX2733133,SRX2733135,SRX2733140,SRX2733141,SRX2733143,SRX2733146,SRX2733147,SRX2733149,SRX2733150,SRX2733151,SRX2733153,SRX2733156,SRX2733157,SRX2733158,SRX2733159,SRX2733160,SRX2733161,SRX2733162,SRX2733163,SRX2733164,SRX2733170,SRX2733177,SRX2733180,SRX2733183,SRX2733184,SRX2733187,SRX2733189,SRX2733190,SRX2733191,SRX2733192,SRX2733205,SRX2733206,SRX2733210,SRX2733211,SRX2733212,SRX2733212,SRX2733213,SRX2733213,SRX2733215,SRX2733215,SRX2733216,SRX2733216,SRX2733217,SRX2733217,SRX2733218,SRX2733218,SRX2733221,SRX2733221,SRX2733222,SRX2733222,SRX2733223,SRX2733223,SRX2733224,SRX2733224,SRX2733225,SRX2733225,SRX2733228,SRX2733228,SRX2733229,SRX2733229,SRX2733231,SRX2733231,SRX2733232,SRX2733232,SRX2733233,SRX2733233,SRX2733234,SRX2733234,SRX2733235,SRX2733235,SRX2733237,SRX2733237,SRX2733238,SRX2733238,SRX2733243,SRX2733243,SRX2733247,SRX2733247,SRX2733248,SRX2733248,SRX2733249,SRX2733249,SRX2733250,SRX2733250,SRX2733251,SRX2733251,SRX2733252,SRX2733252,SRX2733253,SRX2733253,SRX2733255,SRX2733255,SRX2733256,SRX2733256,SRX2733257,SRX2733257,SRX2733258,SRX2733258,SRX2733259,SRX2733259,SRX2733260,SRX2733260,SRX2733261,SRX2733261,SRX2733262,SRX2733262,SRX2733263,SRX2733263,SRX2733264,SRX2733264,SRX2733265,SRX2733265,SRX2733266,SRX2733266,SRX2733268,SRX2733268,SRX2733269,SRX2733269,SRX2733270,SRX2733270,SRX2733271,SRX2733271,SRX2733272,SRX2733272,SRX2733273,SRX2733273,SRX2733274,SRX2733274,SRX2733275,SRX2733275,SRX2733276,SRX2733276,SRX2733277,SRX2733277,SRX2733278,SRX2733278,SRX2733279,SRX2733279,SRX2733280,SRX2733280,SRX2733281,SRX2733281,SRX2733282,SRX2733282,SRX2733283,SRX2733283,SRX2733285,SRX2733285,SRX2733286,SRX2733286,SRX2733287,SRX2733287,SRX2733289,SRX2733289,SRX2733290,SRX2733290,SRX2733291,SRX2733291,SRX2733292,SRX2733292,SRX2733293,SRX2733293,SRX2733294,SRX2733294,SRX2733295,SRX2733295,SRX2733303,SRX2733303,SRX2733305,SRX2733305,SRX2733316,SRX2733316,SRX2733317,SRX2733317:beta;SRX2733100,SRX2733101,SRX2733102,SRX2733103,SRX2733105,SRX2733106,SRX2733107,SRX2733108,SRX2733109,SRX2733114,SRX2733116,SRX2733118,SRX2733120,SRX2733121,SRX2733122,SRX2733124,SRX2733125,SRX2733127,SRX2733129,SRX2733131,SRX2733134,SRX2733136,SRX2733137,SRX2733138,SRX2733139,SRX2733142,SRX2733144,SRX2733145,SRX2733148,SRX2733152,SRX2733154,SRX2733155,SRX2733165,SRX2733166,SRX2733167,SRX2733168,SRX2733169,SRX2733171,SRX2733172,SRX2733173,SRX2733174,SRX2733175,SRX2733176,SRX2733178,SRX2733179,SRX2733181,SRX2733182,SRX2733185,SRX2733186,SRX2733188,SRX2733193,SRX2733194,SRX2733195,SRX2733196,SRX2733197,SRX2733198,SRX2733199,SRX2733200,SRX2733201,SRX2733202,SRX2733203,SRX2733204,SRX2733207,SRX2733208,SRX2733209,SRX2733214,SRX2733214,SRX2733219,SRX2733219,SRX2733220,SRX2733220,SRX2733226,SRX2733226,SRX2733227,SRX2733227,SRX2733230,SRX2733230,SRX2733236,SRX2733236,SRX2733239,SRX2733239,SRX2733240,SRX2733240,SRX2733241,SRX2733241,SRX2733242,SRX2733242,SRX2733244,SRX2733244,SRX2733245,SRX2733245,SRX2733246,SRX2733246,SRX2733254,SRX2733254,SRX2733267,SRX2733267,SRX2733284,SRX2733284,SRX2733288,SRX2733288,SRX2733296,SRX2733296,SRX2733297,SRX2733297,SRX2733298,SRX2733298,SRX2733299,SRX2733299,SRX2733300,SRX2733300,SRX2733301,SRX2733301,SRX2733302,SRX2733302,SRX2733304,SRX2733304,SRX2733306,SRX2733306,SRX2733307,SRX2733307,SRX2733308,SRX2733308,SRX2733309,SRX2733309,SRX2733310,SRX2733310,SRX2733311,SRX2733311,SRX2733312,SRX2733312,SRX2733313,SRX2733313,SRX2733314,SRX2733314,SRX2733315,SRX2733315,SRX2733318,SRX2733318,SRX2733319,SRX2733319,SRX2733320,SRX2733320,SRX2733321,SRX2733321;

SRP106195:human insulin-producing EndoC-βH1 cell line exposed to control (siCTL) versus knockdown (SRp55):siCTL;SRX2779450,SRX2779451,SRX2779452,SRX2779453,SRX2779454:SRp55;SRX2779455,SRX2779456,SRX2779457,SRX2779458,SRX2779459;

SRP121445:non-diabetic control versus type 1 diabetes (T1D):control;SRX3325355,SRX3325356,SRX3325357, SRX3325358,SRX3325359:T1D;SRX3325360,SRX3325361,SRX3325362;age,sex

SRP127362:control vs cytokine treatment:control;SRX3503795,SRX3503797,SRX3503799,SRX3503801,SRX3503803:cytokine treatment; SRX3503796,SRX3503798,SRX3503800,SRX35038002,SRX3503804;

SRP128998:high glucose versus high glucose VPA (valproic acid):high glucose;SRX3557428,SRX3557429, SRX3557430:high glucose VPA;SRX3557431,SRX3557432,SRX3557433;

SRP128998:low glucose versus low glucose VPA (valproic acid):low glucose;SRX3557434,SRX3557435,SRX3557436: low glucose VPA;SRX3557437,SRX3557438,SRX3557439;

SRP135788:CD3+ T cells of nondiabetic individuals vs type 1 diabetes:nondiabetic;SRX3797556SRX3797557,SRX3797558,SRX3797559,SRX3797560,SRX3797561,SRX3797562,SRX3797563,SRX3797564,SRX3797565,SRX3797566,SRX3797567,SRX3797568,SRX3797569,SRX3797570,SRX3797571,SRX3797572,SRX3797573,:type 1 diabetes;SRX3797574,SRX3797575,SRX3797576,SRX3797577,SRX3797578,SRX3797579,SRX3797580,SRX3797581,SRX3797582,SRX3797583,SRX3797584,SRX3797585,SRX3797585,SRX3797586,SRX3797587,SRX3797588,SRX3797589,SRX3797590,SRX3797591,SRX3797592,SRX3797593,SRX3797594,SRX3797595,SRX3797596,SRX3797597,SRX3797598,SRX3797599,SRX3797600,SRX3797601,SRX3797602,SRX3797603,SRX3797604;

SRP151530:BCL11A control vs BCL11A knockdown:control;SRX4317511,SRX4317512,SRX4317513,SRX4317514: knockdown;SRX4317515,SRX4317516,SRX4317517,SRX4317518;

SRP107327:control IL6Ra- versus IL6Ra+ in obese PBMC:IL6Ra-;SRX2833985,SRX2833986,SRX2833988:IL6Ra+;SRX2833984,SRX2833987,SRX2833989;

SRP107327:control IL6Ra- versus IL6Ra+ in lean PBMC:IL6Ra-;SRX2833991,SRX2833993,SRX2833995,SRX2833997:IL6Ra+;SRX2833990,SRX2833992,SRX2833994,SRX2833996;

**SRP107327: obese PBMC versus lean PBMC:obese;SRX2833984,SRX2833985,SRX2833986,SRX2833987,SRX2833988,SRX2833989:lean;SRX2833990,SRX2833991,SRX2833992,SRX2833993,SRX2833994,SRX2833995,SRX2833996,SRX2833997;

SRP111557:non-diabetic versus Type II diabetic:non-diabetic;SRX2996334,SRX2996335,SRX2996336,SRX2996337,SRX2996338,SRX3413848:Type II diabetic;SRX2996339,SRX2996340,SRX3413849;sex,age,BMI

SRP115040:normo-glycemic versus long duration type 1 diabetes:normo-glycemic;SRX3070956,SRX3070957,SRX3070958:long duration T1D;SRX3070959;

SRP115040:normo-glycemic versus long duration type 1 diabetes:normo-glycemic;SRX3070956,SRX3070957,SRX3070958:short duration T1D;SRX3070960;

**longT1D versus short T1D????

SRP144623:wild-type early stage pancreatic progenitors (PP1) versus wild-type late stage pancreatic progenitors (PP2):WP PP1;SRX4042188,SRX4042189:WT PP2;SRX4042190,SRX4042191,SRX4042192;

SRP144623:wild-type late stage pancreatic progenitors (PP2) versus GLIS3-/- PP2:WT PP2;SRX4042190,SRX4042191,SRX4042192:GLIS3-/- PP2;SRX4042193,SRX4042194,SRX4042195;

SRP144623:wild-type late stage pancreatic progenitors (PP2) versus WT INS-GFP+ PP2:WT PP2;SRX4042190,SRX4042191,SRX4042192:INS-GFP+ PP2;SRX4042198,SRX4042199;

SRP144623:wild-type early stage pancreatic progenitors (PP1) versus WT INS-GFP+ PP1:WP PP1;SRX4042188,SRX4042189:WT INS-GFP+ PP1;SRX4042196,SRX4042197;

SRP144623:GLIS3 PP2 versus GLIS3-/- INS-GFPT PP2:GLIS3 PP2;SRX4042193,SRX4042194,SRX4042195:GLIS3-/- INS-GFPT PP2;SRX4042200,SRX4042201;

SRP154717:pericytes cultured in control versus diabetic:control;SRX4415408,SRX4415409,SRX4415410,SRX4415417,SRX4415418,SRX4415419:diabetic;SRX4415423,SRX4415424,SRX4415425;sex

SRP154717:pericytes cultured in diabetic versus pDAPT:diabetic;SRX4415423,SRX4415424,SRX4415425:pDAPT;SRX4415429,SRX4415430,SRX4415431;sex

SRP154717:endothelial cell cultured in control versus diabetic:control;SRX4415405,SRX4415406,SRX4415407,SRX4415414,SRX4415415,SRX4415416:diabetic;SRX4415420,SRX4415421,SRX4415422;sex
,
SRP154717:endothelial cell cultured in diabetic versus pDAPT:diabetic;SRX4415420,SRX4415421,SRX4415422:pDAPT;SRX4415426,SRX4415427,SRX4415428;sex

SRP163900:UN (untreated) versus IL15 in ex vivo:UN;SRX4804447,SRX4804454,SRX4804461,SRX4804468,SRX4804475:IL15;SRX4804441,SRX4804448,SRX4804455,SRX4804462,SRX4804469;

SRP163900:IL15 versus IL15+BNZ in ex vivo:IL15;SRX4804441,SRX4804448,SRX4804455,SRX4804462,SRX4804469:IL15+BNZ;SRX4804442,SRX4804449,SRX4804456,SRX4804463,SRX4804470;

SRP163900:IL15 versus IL15+IL21 in ex vivo:IL15;SRX4804441,SRX4804448,SRX4804455,SRX4804462,SRX4804469:IL15+IL21;SRX4804443,SRX4804450,SRX4804457,SRX4804464,SRX4804471;

SRP163900:IL15+IL21 versus IL15+IL21+BNZ in ex vivo:IL15+IL21;SRX4804443,SRX4804450,SRX4804457,SRX4804464,SRX4804471:IL15+IL21+BNZ;SRX4804444,SRX4804451,SRX4804458,SRX4804465,SRX4804472;

SRP163900:UN versus IL21 in ex vivo:UN;SRX4804447,SRX4804454,SRX4804461,SRX4804468,SRX4804475:IL21;SRX4804445,SRX4804452,SRX4804459,SRX4804466,SRX4804473;

SRP163900:IL21 versus Il21+BNZ in ex vivo:IL21;SRX4804445,SRX4804452,SRX4804459,SRX4804466,SRX4804473:Il21+BNZ;SRX4804446,SRX4804453,SRX4804460,SRX4804467,SRX4804474;

SRP163900:UN versus IL15 in in vitro:UN;SRX4804485,SRX4804495,SRX4804505,SRX4804515,SRX4804519,SRX4804523,SRX4804527:IL15;SRX4804476,SRX4804486,SRX4804496,SRX4804506;

SRP163900:IL15 versus IL15+BNZ in in vitro:IL15;SRX4804476,SRX4804486,SRX4804496,SRX4804506:IL15+BNZ;SRX4804477,SRX4804487,SRX4804497,SRX4804507;

SRP163900:IL15 versus IL15+IL21 in in vitro:IL15;SRX4804476,SRX4804486,SRX4804496,SRX4804506:Il15+IL21;SRX4804479,SRX4804489,SRX4804499,SRX4804509;

SRP163900:IL15+IL21 versus IL15+IL21+BNZ in in vitro:IL15+IL21;SRX4804479,SRX4804489,SRX4804499,SRX4804509:IL15+IL21+BNZ;SRX4804480,SRX4804490,SRX4804500,SRX4804510;

SRP163900:UN versus IL21 in in vitro:UN;SRX4804485,SRX4804495,SRX4804505,SRX4804515,SRX4804519,SRX4804523,SRX4804527:IL21;SRX4804482,SRX4804492,SRX4804502,SRX4804512,SRX4804516,SRX4804520,SRX4804524;

SRP163900:IL21 versus Il21+BNZ in in vitro:IL21;SRX4804482,SRX4804492,SRX4804502,SRX4804512,SRX4804516,SRX4804520,SRX4804524:IL21+BNZ;SRX4804483,SRX4804493,SRX4804503,SRX4804513,SRX4804517,SRX4804521,SRX4804525;

SRP163900:IL21 versus IL21+CP in in vitro:IL21;SRX4804482,SRX4804492,SRX4804502,SRX4804512,SRX4804516,SRX4804520,SRX4804524:IL21+CP;SRX4804484,SRX4804494,SRX4804504,SRX4804514,SRX4804518,SRX4804522,SRX4804526;

SRP163900:IL15 versus Il15+CP in in vitro:IL15;SRX4804476,SRX4804486,SRX4804496,SRX4804506:IL15+CP;SRX4804478,SRX4804488,SRX4804498,SRX4804508;

SRP163900:IL15+IL21 versus IL15+IL21+CP in in vitro:IL15+IL21;SRX4804479,SRX4804489,SRX4804499,SRX4804509:IL15+IL21+CP;SRX4804481,SRX4804491,SRX4804501
,SRX4804511;

SRP029281:alpha versus beta cells:alpha;SRX340815,SRX340817,SRX340819:beta;SRX340816,SRX340818,SRX340820;

SRP029281:alpha versus exocrine cells:alpha;SRX340815,SRX340817,SRX340819:exocrine;SRX340821,SRX340822;

SRP029281:beta versus exocrine cells:beta;SRX340816,SRX340818,SRX340820:exocrine;SRX340821,SRX340822;

SRP121799:diabetic versus non-diabetic CMSC:diabetic;SRX3327085,SRX3327086,
SRX3327087,SRX3327088,SRX3327089,SRX3327090,SRX3327091:non-diabetic;SRX3327092,SRX3327093,SRX3327094,SRX3327095,SRX3327096,SRX3327097,SRX3327098;

lines which have issues unknown: 30, 50, 61, 79, 111

One thing to note here, is that we actually prefer the studies original gene identifiers (ensembl gene ids, microarray probes, etc) whenever possible. Since gene symbols can change over time, keeping these IDs as close to the source as possible makes it easier for us to keep them up to date. I only mention this because it looked like your sets were already in Gene Symbols.

I propose the following format in a text file. One line per contrast.

SRP096177:Genes altered by knockdown of expression of lysine methyltransferase Set7:ctrl;SRX2468679,SRX2468680,SRX2468681:KD;SRX2468682,SRX2468683,SRX2468684,covariates;

Will be using clusterprofiler for analysis
http://118.138.234.73/public/megan/clusterProfiler-useCase.html

Hi Aaron,
please take a look at what I have done with https://github.com/markziemann/gene_sig_commons/blob/master/epilepsy_de.Rmd
which generates the gene signatures for our epilepsy contrasts. The results are found here: http://118.138.234.73/public/gene_sig_commons/
Could you have a go at creating an Rmd file called "diabetes_de.Rmd" which processes the diabetes related studies?
If you have doubts, we can work through it during our next meeting.
Cheers,
Mark

Need to get an Rscript/Rmd to process each of the datasets to generate the gene signature information and send it to a central repository.

Issue with line 15

SRP253279: high binding to the RBD of the S protein versus low binding to the RBD of the S protein (fragments A and B): high binding RBD; SRX7950378, SRX7950380: low binding RBD; SRX7950382, SRX7950384;

Error in apply(yy, 2, function(x) { : dim(X) must have a positive length

All other contrasts seem to be working fine.

there are some duplicated names - need to check that they are not duplicated in the diabetes_de.Rmd

diab <- gmt_import("diabetes.gmt")
duplicated(names(diab)
diab <- diab[which(!duplicated(names(diab)))]
duplicated(names(diab)

Hi Mark, I am wondering how to extend gene signatures for other diseases? for example immunology disease?
Thanks
Shicheng

• Pathway analysis
• Gene sets
• background info

There are a few problems with the functions

• Omit runs that are failed
• Omit runs where there are fewer than 1000 genes expressed
• Omit contrasts with fewer than 2 replicates