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 Rv3772/hisC2

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

	Rv3432c/gadB	Rv3772/hisC2
Fe_supp_jason_reseq	0.26	0.81
low_pH_jason_reseq	0.156	0.467
NO_jason_reseq	-0.541	-0.672
B6_jason_reseq	-0.496	0.276
MHCII_jason_reseq	0.08	-0.236
Isoniazid02	-0.102	-0.258
Rifampicin4	-0.068	-0.479
Ethambutol3	0.793	0.054
Meropenem3	0.553	-0.013
Vancomycin16	-0.05	0.573
Rv2680_day32	0.454	0.427
H37Rv_KO_MarP	0.243	0.037
hypoxia_3wks	-0.171	-1.14
hypoxia_6wks	-0.169	-1.906
glycerol	0.275	-0.6
cholesterol	-0.12	0.244
AJ	-0.234	-0.592
Bibs02	0.229	-0.321
Bibs02c	0.39	-0.341
BL6	0.42	0.741
BL6a	0.342	-0.505
BXD01	-0.21	0.45
BXD010	0.278	0.328
BXD011	0.229	0.118
BXD03	-0.093	-0.074
BXD04	-0.042	-0.125
BXD05	0.754	0.19
BXD06	0.272	0.028
BXD07	0.169	0.155
BXD08	-0.171	0.028
BXD09	0.134	0.0
CAST	0.018	0.532
CCcont	0.125	1.0
DS01	0.198	0.149
DS02	0.165	-0.381
DS04	0.285	-0.391
DS0c	-0.393	-0.523
GP01	-0.465	-0.077
GP02	0.996	1.556
GP0c	0.563	0.195
NOD	-0.43	-0.176
NZO	0.152	0.735
PWK	-0.05	-1.4
H37Rv_KO_CtpC	-0.186	-0.265
H37Rv_KO_CtpD	0.672	0.727
H37Rv_KO_Rv1272	-0.222	-0.708
H37Rv_KO_SugABC	0.39	-0.514
H37Rv_KO_MbtN	0.148	-1.129
Trans05	0.284	0.491
macrophage_unactivated	-0.246	0.407
IL1	0.19	-0.985
Rapamycin	0.227	-0.301
Tcell	-0.443	-1.026
GMCSF	-0.222	-0.375
IFNab	0.239	0.121
IFNg	0.267	-0.037
IFNg_GMCSF1	-0.119	-0.588
Rv1432_day32	0.46	0.224
Rv1565c_day32	0.201	1.199
secA2_input	0.894	0.758
delta_Rv3594	-0.153	0.262
delta_Rv3717	-0.062	-0.982
delta_Rv3811	-0.062	-0.152
delta_Rv0954	0.31	1.092
PonA1	1.094	0.401
EccD1_KO	0.168	-0.197
EspI_KO	0.066	-0.876
PE35_KO	-0.187	-0.493
PPE68_KO	-0.15	-0.694
glycerol2	0.171	1.366
lignocerate	0.235	0.452
oleate	0.233	1.243
phosphatidylcholine	0.296	0.423
acetate	-0.08	-0.106
glucAc	-0.239	-0.093
Rv0950ko	0.871	0.163
Rv1096ko	0.944	1.167
Rv3684ko	0.531	1.091
delta_otsA_trehalose	-0.909	-1.383