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 Rv1424c/-:

update plot	correlation	link to info on gene
Rv2083/-	(cc=0.5161)	info on Rv2083/-
Rv0011c/-	(cc=0.5133)	info on Rv0011c/-
Rv2136c/-	(cc=0.5107)	info on Rv2136c/-
Rv3475/-	(cc=0.4888)	info on Rv3475/-
Rv3022A/PE29	(cc=0.4808)	info on Rv3022A/PE29
Rv2355/-	(cc=0.4798)	info on Rv2355/-
Rv2270/lppN	(cc=0.4734)	info on Rv2270/lppN
Rv1554/frdC	(cc=0.4731)	info on Rv1554/frdC
Rv1984c/cfp21	(cc=0.4666)	info on Rv1984c/cfp21
Rv2649/-	(cc=0.4647)	info on Rv2649/-

Correlation of Rv1424c/- with Rv3475/-

Normalized LFCs for Rv1424c/-:
(description and provenance of datasets)

	Rv1424c/-	Rv3475/-
Fe_supp_jason_reseq	0.554	-0.456
low_pH_jason_reseq	0.035	-0.413
NO_jason_reseq	0.108	0.179
B6_jason_reseq	0.256	-0.671
MHCII_jason_reseq	0.154	-0.15
Isoniazid02	0.226	0.0
Rifampicin4	0.726	0.942
Ethambutol3	0.039	0.591
Meropenem3	0.255	-0.201
Vancomycin16	0.602	0.117
Rv2680_day32	-0.576	0.249
H37Rv_KO_MarP	-0.044	-0.253
hypoxia_3wks	-0.722	0.439
hypoxia_6wks	0.777	0.161
glycerol	-0.434	-0.549
cholesterol	-0.054	0.198
AJ	0.413	1.348
Bibs02	0.128	1.098
Bibs02c	0.373	1.491
BL6	-0.111	0.014
BL6a	0.528	0.897
BXD01	-0.36	0.73
BXD010	0.594	0.761
BXD011	0.784	0.827
BXD03	-0.231	0.847
BXD04	0.073	0.477
BXD05	0.281	1.002
BXD06	0.168	0.547
BXD07	-0.051	0.881
BXD08	0.574	0.53
BXD09	0.375	0.673
CAST	0.055	1.17
CCcont	-0.389	-0.026
DS01	0.084	0.922
DS02	-0.027	0.934
DS04	0.915	1.107
DS0c	0.883	1.039
GP01	0.641	1.169
GP02	1.001	1.477
GP0c	0.672	0.835
NOD	0.054	1.334
NZO	0.532	1.006
PWK	0.31	1.216
H37Rv_KO_CtpC	0.753	0.741
H37Rv_KO_CtpD	0.728	0.814
H37Rv_KO_Rv1272	1.669	0.492
H37Rv_KO_SugABC	1.084	0.875
H37Rv_KO_MbtN	0.682	0.553
Trans05	0.714	0.771
macrophage_unactivated	0.0	-0.95
IL1	-0.629	-0.217
Rapamycin	0.531	-0.638
Tcell	-0.355	-0.981
GMCSF	0.169	-0.103
IFNab	-0.46	-0.674
IFNg	1.066	-0.42
IFNg_GMCSF1	0.0	-0.295
Rv1432_day32	1.701	0.837
Rv1565c_day32	0.782	0.167
secA2_input	1.071	0.072
delta_Rv3594	0.408	-0.066
delta_Rv3717	0.239	-0.109
delta_Rv3811	0.253	-0.156
delta_Rv0954	0.27	0.41
PonA1	0.173	0.122
EccD1_KO	0.395	0.155
EspI_KO	1.184	1.184
PE35_KO	1.345	1.05
PPE68_KO	1.123	0.819
glycerol2	-0.789	-0.771
lignocerate	-0.66	-0.728
oleate	-0.196	-0.767
phosphatidylcholine	-0.508	-0.718
acetate	-1.122	0.0
glucAc	-0.931	-0.168
Rv0950ko	-0.703	-0.178
Rv1096ko	-0.703	0.057
Rv3684ko	-0.963	-0.783
delta_otsA_trehalose	-0.303	0.549