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 Rv3900c/-:

update plot	correlation	link to info on gene
Rv3537/kstD	(cc=0.5508)	info on Rv3537/kstD
Rv1729c/-	(cc=0.4953)	info on Rv1729c/-
Rv3762c/-	(cc=0.4834)	info on Rv3762c/-
Rv0250c/-	(cc=0.4772)	info on Rv0250c/-
Rv1059/-	(cc=0.4726)	info on Rv1059/-
Rv2929/-	(cc=0.4714)	info on Rv2929/-
Rv3429/PPE59	(cc=0.4696)	info on Rv3429/PPE59
Rv3146/nuoB	(cc=0.4689)	info on Rv3146/nuoB
Rv1870c/-	(cc=0.461)	info on Rv1870c/-
Rv1207/folP2	(cc=0.4518)	info on Rv1207/folP2

Correlation of Rv3900c/- with Rv3762c/-

Normalized LFCs for Rv3900c/-:
(description and provenance of datasets)

	Rv3900c/-	Rv3762c/-
Fe_supp_jason_reseq	-0.406	-0.243
low_pH_jason_reseq	0.632	0.054
NO_jason_reseq	-0.352	-0.218
B6_jason_reseq	-0.285	-0.8
MHCII_jason_reseq	-0.876	-1.219
Isoniazid02	-0.226	-0.258
Rifampicin4	0.544	-0.019
Ethambutol3	0.946	1.102
Meropenem3	1.216	0.109
Vancomycin16	0.228	0.188
Rv2680_day32	-0.763	-0.848
H37Rv_KO_MarP	0.679	0.306
hypoxia_3wks	0.49	0.255
hypoxia_6wks	-0.077	0.399
glycerol	-0.24	0.155
cholesterol	-0.243	0.289
AJ	-0.439	0.291
Bibs02	-0.631	0.083
Bibs02c	-0.878	0.0
BL6	0.272	0.664
BL6a	-0.105	0.26
BXD01	0.446	0.66
BXD010	0.597	0.107
BXD011	0.116	0.16
BXD03	0.236	0.515
BXD04	0.63	1.163
BXD05	0.225	0.169
BXD06	0.749	0.483
BXD07	0.413	0.306
BXD08	0.497	0.437
BXD09	0.7	0.326
CAST	0.117	0.22
CCcont	0.838	0.151
DS01	-0.021	0.077
DS02	-0.884	0.154
DS04	0.748	-0.247
DS0c	-0.671	0.085
GP01	0.801	0.343
GP02	-0.257	-0.317
GP0c	0.689	-0.062
NOD	0.094	0.41
NZO	-0.712	0.319
PWK	-0.196	0.257
H37Rv_KO_CtpC	-0.042	0.021
H37Rv_KO_CtpD	1.454	1.191
H37Rv_KO_Rv1272	0.336	-0.057
H37Rv_KO_SugABC	0.8	0.694
H37Rv_KO_MbtN	0.202	0.397
Trans05	-0.034	-0.118
macrophage_unactivated	0.451	0.442
IL1	0.311	0.255
Rapamycin	0.368	-0.377
Tcell	-0.137	0.544
GMCSF	0.214	0.441
IFNab	0.339	0.175
IFNg	0.0	0.468
IFNg_GMCSF1	-0.647	0.44
Rv1432_day32	-0.469	0.177
Rv1565c_day32	-0.058	-0.776
secA2_input	0.177	0.025
delta_Rv3594	-0.054	-0.314
delta_Rv3717	-0.736	-0.082
delta_Rv3811	0.241	0.07
delta_Rv0954	-0.261	0.295
PonA1	-0.07	0.072
EccD1_KO	-0.582	-0.497
EspI_KO	-0.884	-0.684
PE35_KO	-0.137	-0.828
PPE68_KO	-0.086	-0.614
glycerol2	0.294	0.275
lignocerate	0.203	0.224
oleate	0.089	0.713
phosphatidylcholine	-0.057	0.359
acetate	-0.361	0.0
glucAc	-0.205	0.306
Rv0950ko	0.109	0.706
Rv1096ko	-0.802	0.519
Rv3684ko	-0.098	0.203
delta_otsA_trehalose	-0.73	-1.242