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 Rv0746/PE_PGRS9:

update plot	correlation	link to info on gene
Rv0332/-	(cc=0.4071)	info on Rv0332/-
Rv1060/-	(cc=0.4057)	info on Rv1060/-
Rv1691/-	(cc=0.3945)	info on Rv1691/-
Rv0747/PE_PGRS10	(cc=0.387)	info on Rv0747/PE_PGRS10
Rv1647/-	(cc=0.3855)	info on Rv1647/-
Rv3508/PE_PGRS54	(cc=0.3846)	info on Rv3508/PE_PGRS54
Rv1180/pks3	(cc=0.3818)	info on Rv1180/pks3
Rv2645/-	(cc=0.3685)	info on Rv2645/-
Rv0428c/-	(cc=0.3647)	info on Rv0428c/-
Rv3766/-	(cc=0.3644)	info on Rv3766/-

Correlation of Rv0746/PE_PGRS9 with Rv3508/PE_PGRS54

Normalized LFCs for Rv0746/PE_PGRS9:
(description and provenance of datasets)

	Rv0746/PE_PGRS9	Rv3508/PE_PGRS54
Fe_supp_jason_reseq	1.321	-0.532
low_pH_jason_reseq	1.84	0.0
NO_jason_reseq	-1.089	0.0
B6_jason_reseq	1.7	-0.103
MHCII_jason_reseq	2.165	0.591
Isoniazid02	-0.212	-2.021
Rifampicin4	0.073	0.772
Ethambutol3	0.221	-1.28
Meropenem3	-0.25	-1.748
Vancomycin16	-0.91	-0.727
Rv2680_day32	-0.177	0.046
H37Rv_KO_MarP	-0.289	-0.103
hypoxia_3wks	0.104	-0.215
hypoxia_6wks	0.186	-0.616
glycerol	0.439	1.028
cholesterol	0.295	0.648
AJ	1.163	0.726
Bibs02	1.187	0.73
Bibs02c	0.964	0.415
BL6	-0.809	-0.269
BL6a	0.555	0.27
BXD01	1.277	0.259
BXD010	-0.175	-0.276
BXD011	-0.519	-0.236
BXD03	0.536	-0.033
BXD04	1.072	0.03
BXD05	0.292	0.397
BXD06	-0.544	0.182
BXD07	-0.14	0.408
BXD08	0.513	0.947
BXD09	-0.046	0.162
CAST	0.143	0.364
CCcont	-0.233	-0.193
DS01	-0.157	-0.058
DS02	-0.145	0.104
DS04	1.39	0.607
DS0c	-0.107	-0.28
GP01	0.683	1.149
GP02	0.562	1.255
GP0c	1.072	1.092
NOD	-0.35	-0.169
NZO	1.115	0.272
PWK	0.426	0.783
H37Rv_KO_CtpC	0.552	-0.209
H37Rv_KO_CtpD	-0.27	0.441
H37Rv_KO_Rv1272	0.543	0.934
H37Rv_KO_SugABC	-1.076	-0.243
H37Rv_KO_MbtN	-0.051	0.184
Trans05	0.231	0.361
macrophage_unactivated	-0.41	-0.287
IL1	0.074	-0.365
Rapamycin	-0.399	-1.126
Tcell	0.951	-1.072
GMCSF	-0.135	-0.158
IFNab	-0.916	-1.345
IFNg	-2.061	-1.082
IFNg_GMCSF1	0.654	-0.698
Rv1432_day32	0.113	0.855
Rv1565c_day32	-0.766	-0.52
secA2_input	0.067	0.131
delta_Rv3594	0.174	-0.402
delta_Rv3717	0.294	-0.352
delta_Rv3811	-0.677	-0.269
delta_Rv0954	-0.416	-1.151
PonA1	-0.06	0.032
EccD1_KO	1.72	-0.207
EspI_KO	1.155	0.043
PE35_KO	-0.245	-0.28
PPE68_KO	0.666	-0.525
glycerol2	0.144	0.347
lignocerate	0.242	0.157
oleate	0.315	0.296
phosphatidylcholine	0.553	0.451
acetate	0.213	0.474
glucAc	-0.085	0.753
Rv0950ko	-0.22	-0.057
Rv1096ko	0.784	0.226
Rv3684ko	0.393	-0.193
delta_otsA_trehalose	0.0	-0.026