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 Rv1961/-:

update plot	correlation	link to info on gene
Rv0829/-	(cc=0.4921)	info on Rv0829/-
Rv0731c/-	(cc=0.4837)	info on Rv0731c/-
Rv1686c/-	(cc=0.4795)	info on Rv1686c/-
Rv2425c/-	(cc=0.4769)	info on Rv2425c/-
Rv1830/-	(cc=0.4741)	info on Rv1830/-
Rv2896c/-	(cc=0.4625)	info on Rv2896c/-
Rv0858c/dapC	(cc=0.4557)	info on Rv0858c/dapC
Rv0142/-	(cc=0.4538)	info on Rv0142/-
Rv0620/galK	(cc=0.4532)	info on Rv0620/galK
Rv0222/echA1	(cc=0.4519)	info on Rv0222/echA1

Correlation of Rv1961/- with Rv2896c/-

Normalized LFCs for Rv1961/-:
(description and provenance of datasets)

	Rv1961/-	Rv2896c/-
Fe_supp_jason_reseq	-2.406	-0.685
low_pH_jason_reseq	-2.08	-0.932
NO_jason_reseq	0.184	0.263
B6_jason_reseq	-1.989	-0.482
MHCII_jason_reseq	-1.677	-0.754
Isoniazid02	0.236	0.764
Rifampicin4	-0.06	-0.181
Ethambutol3	-0.407	0.188
Meropenem3	-0.386	0.114
Vancomycin16	-0.114	0.058
Rv2680_day32	-1.231	-0.456
H37Rv_KO_MarP	-0.188	-0.051
hypoxia_3wks	-0.929	-0.287
hypoxia_6wks	-0.411	-0.624
glycerol	0.13	1.546
cholesterol	-0.233	0.503
AJ	0.533	-0.128
Bibs02	0.242	0.654
Bibs02c	-0.399	-0.115
BL6	0.758	0.637
BL6a	-0.118	0.103
BXD01	-0.901	-0.299
BXD010	-0.906	-0.223
BXD011	-0.524	-0.269
BXD03	-0.369	-0.562
BXD04	-0.494	0.256
BXD05	0.076	0.261
BXD06	-0.241	-0.173
BXD07	0.272	0.082
BXD08	0.156	0.117
BXD09	-0.147	-0.182
CAST	0.287	-0.108
CCcont	-0.33	-0.035
DS01	0.527	0.674
DS02	0.158	0.767
DS04	0.843	0.706
DS0c	-0.789	0.607
GP01	0.532	0.022
GP02	1.445	0.98
GP0c	1.337	0.465
NOD	-0.496	0.792
NZO	0.92	-0.078
PWK	-1.091	-0.413
H37Rv_KO_CtpC	0.04	0.386
H37Rv_KO_CtpD	-0.241	0.78
H37Rv_KO_Rv1272	-0.254	-0.435
H37Rv_KO_SugABC	0.123	-1.474
H37Rv_KO_MbtN	-0.052	0.529
Trans05	-0.223	-0.377
macrophage_unactivated	-1.225	0.18
IL1	-0.219	0.516
Rapamycin	0.031	0.206
Tcell	-0.277	-0.329
GMCSF	0.264	-0.351
IFNab	0.184	-0.121
IFNg	-0.377	0.489
IFNg_GMCSF1	0.063	0.179
Rv1432_day32	0.331	0.738
Rv1565c_day32	-0.595	0.491
secA2_input	0.13	0.435
delta_Rv3594	0.171	-0.286
delta_Rv3717	0.858	0.083
delta_Rv3811	1.316	0.0
delta_Rv0954	0.51	-0.261
PonA1	-0.609	-0.485
EccD1_KO	-0.158	-0.145
EspI_KO	-0.511	-0.083
PE35_KO	-0.618	0.545
PPE68_KO	-0.154	0.518
glycerol2	-0.118	-0.303
lignocerate	0.587	0.558
oleate	-1.456	-0.072
phosphatidylcholine	0.182	0.31
acetate	1.076	0.472
glucAc	1.194	0.304
Rv0950ko	0.917	0.172
Rv1096ko	0.66	0.829
Rv3684ko	0.357	0.576
delta_otsA_trehalose	-0.152	-0.416