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 Rv2740/ephG:

update plot	correlation	link to info on gene
Rv3165c/-	(cc=0.4995)	info on Rv3165c/-
Rv2060/-	(cc=0.4512)	info on Rv2060/-
Rv2308/-	(cc=0.4399)	info on Rv2308/-
Rv1218c/-	(cc=0.4285)	info on Rv1218c/-
Rv2040c/-	(cc=0.4014)	info on Rv2040c/-
Rv1954A/-	(cc=0.3991)	info on Rv1954A/-
Rv1353c/-	(cc=0.3983)	info on Rv1353c/-
Rv2408/PE24	(cc=0.3907)	info on Rv2408/PE24
Rv1496/-	(cc=0.3907)	info on Rv1496/-
Rv2252/-	(cc=0.3881)	info on Rv2252/-

Correlation of Rv2740/ephG with Rv1353c/-

Normalized LFCs for Rv2740/ephG:
(description and provenance of datasets)

	Rv2740/ephG	Rv1353c/-
Fe_supp_jason_reseq	0.23	0.423
low_pH_jason_reseq	-0.579	0.683
NO_jason_reseq	-0.735	0.226
B6_jason_reseq	-0.318	0.125
MHCII_jason_reseq	0.109	-0.151
Isoniazid02	-0.389	-0.567
Rifampicin4	-0.127	0.504
Ethambutol3	-0.264	-0.51
Meropenem3	-0.299	-0.399
Vancomycin16	-0.631	0.029
Rv2680_day32	1.128	-0.354
H37Rv_KO_MarP	-0.292	0.406
hypoxia_3wks	-0.67	-0.734
hypoxia_6wks	-0.238	-0.04
glycerol	-0.307	-1.463
cholesterol	-0.285	-0.055
AJ	-0.183	0.894
Bibs02	-0.585	-1.011
Bibs02c	-0.77	-0.906
BL6	-0.372	1.039
BL6a	0.281	0.432
BXD01	-0.235	0.416
BXD010	0.365	0.916
BXD011	0.709	0.198
BXD03	0.492	0.374
BXD04	-0.043	0.825
BXD05	0.429	1.163
BXD06	0.072	1.175
BXD07	0.409	0.654
BXD08	0.616	0.53
BXD09	0.427	0.76
CAST	0.327	-0.998
CCcont	-0.113	0.966
DS01	-1.258	-0.77
DS02	-1.3	0.158
DS04	0.066	-1.556
DS0c	-0.757	1.15
GP01	0.403	0.885
GP02	0.014	0.759
GP0c	0.834	0.689
NOD	-0.135	-1.801
NZO	0.428	0.246
PWK	-0.675	-0.037
H37Rv_KO_CtpC	-0.598	0.354
H37Rv_KO_CtpD	0.479	1.43
H37Rv_KO_Rv1272	0.103	0.0
H37Rv_KO_SugABC	-2.096	-1.297
H37Rv_KO_MbtN	-0.306	0.24
Trans05	0.053	0.934
macrophage_unactivated	-0.227	0.682
IL1	0.448	1.092
Rapamycin	0.672	1.203
Tcell	-0.635	0.433
GMCSF	0.734	0.121
IFNab	0.36	0.23
IFNg	0.222	-0.043
IFNg_GMCSF1	-0.544	0.55
Rv1432_day32	-0.327	0.888
Rv1565c_day32	0.826	0.013
secA2_input	-2.057	-2.069
delta_Rv3594	0.217	0.843
delta_Rv3717	1.121	0.237
delta_Rv3811	-0.311	1.164
delta_Rv0954	-1.55	-0.384
PonA1	0.187	-0.039
EccD1_KO	1.217	0.095
EspI_KO	0.704	1.286
PE35_KO	0.933	1.736
PPE68_KO	1.094	1.232
glycerol2	0.404	0.356
lignocerate	0.479	0.843
oleate	-0.713	0.608
phosphatidylcholine	0.625	0.945
acetate	0.356	1.368
glucAc	0.869	0.929
Rv0950ko	0.241	0.323
Rv1096ko	0.47	0.682
Rv3684ko	-0.174	1.742
delta_otsA_trehalose	0.404	-2.4