TnSeqCorr

• These are correlations of TnSeq responses across 82 experimental conditions.
• LFCs (log2-fold-changes) were computed for each gene in each condition relative to a relevant control condition (e.g. H37Rv grown on 7H9).
• The LFCs were normalized by dividing by the standard deviation for each condition. (so roughly, |LFC|>2 are the outliers, i.e. tails of the distribution)
• Note that essential genes often have LFCs around 0.
• Data for some genes is not available if they have less than 3 TA sites, or the dynamic range of LFCs is less than 2.0 across all conditions. (This is the case for many essential genes.)
• 'leverage' on each plot is a statistical score that indicates how much the regression is influenced by a few outlier points; the traditional threshold is indicated on the plots (3p/n, which is about 0.07 for this dataset), but in practice, cases with leverage > ~0.2 seem to be the least reliable (most misleading) correlation coefficients.

Top 10 genes with highest correlation to Rv2352c/PPE38:

update plot	correlation	link to info on gene
Rv0160c/PE4	(cc=0.5845)	info on Rv0160c/PE4
Rv3161c/-	(cc=0.5722)	info on Rv3161c/-
Rv0354c/PPE7	(cc=0.5707)	info on Rv0354c/PPE7
Rv1504c/-	(cc=0.5614)	info on Rv1504c/-
Rv2947c/pks15	(cc=0.5506)	info on Rv2947c/pks15
Rv1278/-	(cc=0.5437)	info on Rv1278/-
Rv3919c/gid	(cc=0.5421)	info on Rv3919c/gid
Rv0073/-	(cc=0.5416)	info on Rv0073/-
Rv0469/umaA	(cc=0.5381)	info on Rv0469/umaA
Rv2853/PE_PGRS48	(cc=0.5372)	info on Rv2853/PE_PGRS48

Correlation of Rv2352c/PPE38 with Rv2853/PE_PGRS48

Normalized LFCs for Rv2352c/PPE38:
(description and provenance of datasets)

	Rv2352c/PPE38	Rv2853/PE_PGRS48
Fe_supp_jason_reseq	0.35	0.641
low_pH_jason_reseq	-1.029	-0.269
NO_jason_reseq	-0.491	0.06
B6_jason_reseq	-0.488	-0.414
MHCII_jason_reseq	-0.46	-0.425
Isoniazid02	-1.043	-0.965
Rifampicin4	-0.208	0.095
Ethambutol3	-0.882	0.258
Meropenem3	-1.085	-1.22
Vancomycin16	-0.602	-0.788
Rv2680_day32	-0.611	-0.666
H37Rv_KO_MarP	-0.629	-0.206
hypoxia_3wks	-0.06	-0.335
hypoxia_6wks	-0.56	-0.72
glycerol	0.532	0.587
cholesterol	0.575	0.29
AJ	0.321	0.881
Bibs02	0.203	0.199
Bibs02c	0.297	0.273
BL6	0.173	0.488
BL6a	0.425	0.462
BXD01	0.346	0.269
BXD010	-0.031	0.324
BXD011	-0.232	0.519
BXD03	0.503	0.679
BXD04	0.661	0.39
BXD05	0.358	0.242
BXD06	0.167	0.507
BXD07	0.22	0.494
BXD08	0.298	0.497
BXD09	0.376	0.213
CAST	0.235	0.475
CCcont	-0.032	0.574
DS01	0.267	0.24
DS02	0.17	-0.408
DS04	0.554	0.623
DS0c	0.179	0.0
GP01	0.253	-0.129
GP02	0.349	0.108
GP0c	0.348	-0.182
NOD	-0.184	0.61
NZO	0.393	0.344
PWK	0.06	0.078
H37Rv_KO_CtpC	0.169	0.235
H37Rv_KO_CtpD	0.659	0.174
H37Rv_KO_Rv1272	1.248	0.811
H37Rv_KO_SugABC	0.005	-0.084
H37Rv_KO_MbtN	0.457	0.659
Trans05	1.088	1.389
macrophage_unactivated	0.511	-0.262
IL1	-0.11	-0.196
Rapamycin	0.037	-0.227
Tcell	-0.495	-0.381
GMCSF	0.533	-0.404
IFNab	0.054	-0.435
IFNg	0.088	-0.043
IFNg_GMCSF1	0.364	-0.182
Rv1432_day32	0.407	-0.018
Rv1565c_day32	-0.141	1.512
secA2_input	-0.626	-0.747
delta_Rv3594	0.583	-0.017
delta_Rv3717	-0.374	0.169
delta_Rv3811	0.268	0.271
delta_Rv0954	0.289	-0.42
PonA1	0.085	0.667
EccD1_KO	-0.566	0.0
EspI_KO	-0.031	0.493
PE35_KO	0.105	0.175
PPE68_KO	0.275	-0.134
glycerol2	0.167	-0.078
lignocerate	-0.169	0.444
oleate	-0.004	-0.016
phosphatidylcholine	-0.224	0.245
acetate	-0.047	0.053
glucAc	0.016	0.15
Rv0950ko	0.277	0.283
Rv1096ko	-0.012	0.654
Rv3684ko	-0.134	0.845
delta_otsA_trehalose	0.184	0.127