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 Rv0017c/rodA:

update plot	correlation	link to info on gene
Rv0016c/pbpA	(cc=0.8416)	info on Rv0016c/pbpA
Rv3630/-	(cc=0.6746)	info on Rv3630/-
Rv2004c/-	(cc=0.6604)	info on Rv2004c/-
Rv2190c/-	(cc=0.6412)	info on Rv2190c/-
Rv1836c/-	(cc=0.6403)	info on Rv1836c/-
Rv1821/secA2	(cc=0.6302)	info on Rv1821/secA2
Rv0050/ponA1	(cc=0.6279)	info on Rv0050/ponA1
Rv0989c/grcC2	(cc=0.6156)	info on Rv0989c/grcC2
Rv0820/phoT	(cc=0.6061)	info on Rv0820/phoT
Rv1566c/-	(cc=0.6002)	info on Rv1566c/-

Correlation of Rv0017c/rodA with Rv2004c/-

Normalized LFCs for Rv0017c/rodA:
(description and provenance of datasets)

	Rv0017c/rodA	Rv2004c/-
Fe_supp_jason_reseq	2.392	0.655
low_pH_jason_reseq	2.923	0.592
NO_jason_reseq	-0.281	0.0
B6_jason_reseq	0.0	0.526
MHCII_jason_reseq	0.503	2.331
Isoniazid02	-1.005	-1.48
Rifampicin4	-2.32	-1.4
Ethambutol3	-2.802	-1.418
Meropenem3	-1.846	-1.157
Vancomycin16	-4.6	-1.149
Rv2680_day32	1.168	0.608
H37Rv_KO_MarP	-4.322	-0.936
hypoxia_3wks	0.447	0.969
hypoxia_6wks	0.656	0.236
glycerol	1.891	2.262
cholesterol	1.357	1.492
AJ	-0.866	0.598
Bibs02	1.507	0.898
Bibs02c	0.488	2.801
BL6	0.805	0.982
BL6a	0.769	2.218
BXD01	1.247	1.666
BXD010	-0.141	0.372
BXD011	0.54	0.896
BXD03	0.424	0.592
BXD04	0.236	1.385
BXD05	0.903	1.344
BXD06	0.254	0.995
BXD07	0.323	1.665
BXD08	0.653	2.226
BXD09	0.14	0.958
CAST	-0.39	-0.928
CCcont	2.042	1.202
DS01	0.83	2.281
DS02	-0.117	1.435
DS04	0.822	2.117
DS0c	0.217	1.788
GP01	1.006	1.367
GP02	-0.194	1.104
GP0c	1.008	0.996
NOD	-0.524	-0.905
NZO	-1.246	-1.065
PWK	-1.225	-1.189
H37Rv_KO_CtpC	0.571	1.486
H37Rv_KO_CtpD	1.363	1.305
H37Rv_KO_Rv1272	0.824	2.101
H37Rv_KO_SugABC	0.453	0.94
H37Rv_KO_MbtN	0.943	2.096
Trans05	0.642	2.198
macrophage_unactivated	0.385	1.158
IL1	-0.679	-0.872
Rapamycin	-1.363	0.114
Tcell	0.398	0.58
GMCSF	-1.658	0.38
IFNab	-0.13	0.834
IFNg	-1.344	0.198
IFNg_GMCSF1	0.258	-0.779
Rv1432_day32	2.066	1.51
Rv1565c_day32	0.0	0.0
secA2_input	-2.537	-0.294
delta_Rv3594	0.737	-0.171
delta_Rv3717	0.369	0.162
delta_Rv3811	1.068	-0.123
delta_Rv0954	-2.989	-1.835
PonA1	-2.28	-1.597
EccD1_KO	-0.921	-0.414
EspI_KO	-0.847	0.485
PE35_KO	0.505	0.572
PPE68_KO	0.349	1.254
glycerol2	-3.464	0.671
lignocerate	-1.587	0.381
oleate	-3.311	-1.184
phosphatidylcholine	-1.737	0.203
acetate	-0.504	0.106
glucAc	-0.083	0.324
Rv0950ko	-1.716	-0.087
Rv1096ko	-1.007	0.721
Rv3684ko	0.488	0.0
delta_otsA_trehalose	1.148	0.353