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 Rv3198c/uvrD2:

update plot	correlation	link to info on gene
Rv3388/PE_PGRS52	(cc=0.4981)	info on Rv3388/PE_PGRS52
Rv3512/PE_PGRS56	(cc=0.4684)	info on Rv3512/PE_PGRS56
Rv3428c/-	(cc=0.4532)	info on Rv3428c/-
Rv0213c/-	(cc=0.4522)	info on Rv0213c/-
Rv0515/-	(cc=0.4202)	info on Rv0515/-
Rv0787/-	(cc=0.4037)	info on Rv0787/-
Rv0814c/sseC2	(cc=0.4002)	info on Rv0814c/sseC2
Rv0260c/-	(cc=0.3973)	info on Rv0260c/-
Rv0963c/-	(cc=0.3904)	info on Rv0963c/-
Rv0872c/PE_PGRS15	(cc=0.3889)	info on Rv0872c/PE_PGRS15

Correlation of Rv3198c/uvrD2 with Rv3512/PE_PGRS56

Normalized LFCs for Rv3198c/uvrD2:
(description and provenance of datasets)

	Rv3198c/uvrD2	Rv3512/PE_PGRS56
Fe_supp_jason_reseq	-0.096	-0.587
low_pH_jason_reseq	-0.323	-1.091
NO_jason_reseq	-0.331	-0.176
B6_jason_reseq	0.604	-0.322
MHCII_jason_reseq	0.192	0.123
Isoniazid02	-0.135	-1.909
Rifampicin4	-0.43	-0.647
Ethambutol3	-0.113	-0.537
Meropenem3	0.628	-0.737
Vancomycin16	0.157	-0.963
Rv2680_day32	-0.312	0.529
H37Rv_KO_MarP	-0.185	0.0
hypoxia_3wks	-0.387	-0.183
hypoxia_6wks	-0.497	-1.13
glycerol	0.282	1.981
cholesterol	0.518	1.209
AJ	0.899	2.276
Bibs02	0.709	1.27
Bibs02c	1.099	1.576
BL6	0.053	0.263
BL6a	0.552	0.914
BXD01	0.081	0.695
BXD010	0.054	1.102
BXD011	0.475	0.49
BXD03	0.263	0.573
BXD04	0.15	0.859
BXD05	0.237	0.764
BXD06	0.135	0.075
BXD07	-0.446	0.291
BXD08	0.592	0.341
BXD09	0.322	0.36
CAST	0.752	0.484
CCcont	1.098	0.24
DS01	0.373	0.38
DS02	0.711	0.922
DS04	0.968	0.11
DS0c	0.22	-0.129
GP01	-0.577	0.561
GP02	0.629	0.553
GP0c	-0.346	0.738
NOD	0.552	0.0
NZO	1.402	1.326
PWK	0.641	0.674
H37Rv_KO_CtpC	-0.345	0.261
H37Rv_KO_CtpD	1.436	0.584
H37Rv_KO_Rv1272	0.795	1.177
H37Rv_KO_SugABC	1.151	0.381
H37Rv_KO_MbtN	0.105	-0.271
Trans05	0.525	1.157
macrophage_unactivated	0.186	-0.537
IL1	0.0	-1.978
Rapamycin	0.522	-1.795
Tcell	0.0	-1.652
GMCSF	0.449	-0.779
IFNab	0.0	-2.283
IFNg	0.158	-1.157
IFNg_GMCSF1	-0.192	-0.349
Rv1432_day32	0.541	0.252
Rv1565c_day32	0.355	-1.275
secA2_input	0.0	0.0
delta_Rv3594	-0.379	0.272
delta_Rv3717	-0.238	-0.629
delta_Rv3811	0.214	-0.253
delta_Rv0954	-0.963	-2.288
PonA1	-0.03	0.714
EccD1_KO	0.293	0.418
EspI_KO	-0.088	-0.451
PE35_KO	-0.277	-0.916
PPE68_KO	0.192	-0.685
glycerol2	0.611	0.109
lignocerate	1.112	0.505
oleate	-0.549	-0.515
phosphatidylcholine	0.611	0.0
acetate	0.618	1.225
glucAc	0.944	1.367
Rv0950ko	-0.247	-0.63
Rv1096ko	-0.513	0.115
Rv3684ko	0.95	-0.065
delta_otsA_trehalose	1.056	0.366