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 Rv3432c/gadB:

update plot	correlation	link to info on gene
Rv3772/hisC2	(cc=0.5061)	info on Rv3772/hisC2
Rv3736/-	(cc=0.4302)	info on Rv3736/-
Rv0834c/PE_PGRS14	(cc=0.4097)	info on Rv0834c/PE_PGRS14
Rv3523/ltp3	(cc=0.4093)	info on Rv3523/ltp3
Rv0110/-	(cc=0.4091)	info on Rv0110/-
Rv3171c/hpx	(cc=0.4049)	info on Rv3171c/hpx
Rv1177/fdxC	(cc=0.3936)	info on Rv1177/fdxC
Rv0597c/-	(cc=0.3918)	info on Rv0597c/-
Rv2571c/-	(cc=0.3898)	info on Rv2571c/-
Rv3785/-	(cc=0.3863)	info on Rv3785/-

Correlation of Rv3432c/gadB with Rv2571c/-

Normalized LFCs for Rv3432c/gadB:
(description and provenance of datasets)

	Rv3432c/gadB	Rv2571c/-
Fe_supp_jason_reseq	0.26	-1.208
low_pH_jason_reseq	0.156	-0.967
NO_jason_reseq	-0.541	-5.901
B6_jason_reseq	-0.496	-1.314
MHCII_jason_reseq	0.08	-0.468
Isoniazid02	-0.102	1.443
Rifampicin4	-0.068	-0.311
Ethambutol3	0.793	2.297
Meropenem3	0.553	0.576
Vancomycin16	-0.05	0.164
Rv2680_day32	0.454	-0.501
H37Rv_KO_MarP	0.243	0.854
hypoxia_3wks	-0.171	0.419
hypoxia_6wks	-0.169	-0.155
glycerol	0.275	0.736
cholesterol	-0.12	0.653
AJ	-0.234	-0.541
Bibs02	0.229	0.416
Bibs02c	0.39	0.092
BL6	0.42	-0.157
BL6a	0.342	-0.188
BXD01	-0.21	-0.275
BXD010	0.278	0.984
BXD011	0.229	-0.121
BXD03	-0.093	0.385
BXD04	-0.042	0.669
BXD05	0.754	0.083
BXD06	0.272	0.264
BXD07	0.169	0.061
BXD08	-0.171	0.726
BXD09	0.134	-0.266
CAST	0.018	0.422
CCcont	0.125	0.425
DS01	0.198	0.166
DS02	0.165	0.447
DS04	0.285	0.34
DS0c	-0.393	0.413
GP01	-0.465	-0.604
GP02	0.996	0.52
GP0c	0.563	1.039
NOD	-0.43	-0.524
NZO	0.152	-1.322
PWK	-0.05	-0.693
H37Rv_KO_CtpC	-0.186	-0.204
H37Rv_KO_CtpD	0.672	0.0
H37Rv_KO_Rv1272	-0.222	-0.134
H37Rv_KO_SugABC	0.39	-0.376
H37Rv_KO_MbtN	0.148	-0.566
Trans05	0.284	-0.822
macrophage_unactivated	-0.246	-2.948
IL1	0.19	-4.23
Rapamycin	0.227	-5.745
Tcell	-0.443	-4.161
GMCSF	-0.222	0.779
IFNab	0.239	0.701
IFNg	0.267	-1.109
IFNg_GMCSF1	-0.119	-2.69
Rv1432_day32	0.46	-1.491
Rv1565c_day32	0.201	-0.731
secA2_input	0.894	1.021
delta_Rv3594	-0.153	0.635
delta_Rv3717	-0.062	-0.25
delta_Rv3811	-0.062	0.702
delta_Rv0954	0.31	1.221
PonA1	1.094	1.091
EccD1_KO	0.168	-0.243
EspI_KO	0.066	-0.75
PE35_KO	-0.187	-1.403
PPE68_KO	-0.15	-1.43
glycerol2	0.171	-0.646
lignocerate	0.235	-0.933
oleate	0.233	-0.062
phosphatidylcholine	0.296	-0.48
acetate	-0.08	-1.481
glucAc	-0.239	-1.544
Rv0950ko	0.871	1.239
Rv1096ko	0.944	3.103
Rv3684ko	0.531	1.723
delta_otsA_trehalose	-0.909	0.355