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 Rv0872c/PE_PGRS15

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

	Rv3198c/uvrD2	Rv0872c/PE_PGRS15
Fe_supp_jason_reseq	-0.096	0.14
low_pH_jason_reseq	-0.323	-1.631
NO_jason_reseq	-0.331	-0.32
B6_jason_reseq	0.604	0.24
MHCII_jason_reseq	0.192	0.762
Isoniazid02	-0.135	-0.473
Rifampicin4	-0.43	0.671
Ethambutol3	-0.113	-0.406
Meropenem3	0.628	0.059
Vancomycin16	0.157	-0.194
Rv2680_day32	-0.312	0.061
H37Rv_KO_MarP	-0.185	-0.045
hypoxia_3wks	-0.387	-0.175
hypoxia_6wks	-0.497	-0.76
glycerol	0.282	0.581
cholesterol	0.518	0.441
AJ	0.899	0.197
Bibs02	0.709	0.228
Bibs02c	1.099	0.782
BL6	0.053	0.332
BL6a	0.552	0.74
BXD01	0.081	0.276
BXD010	0.054	-0.058
BXD011	0.475	-0.107
BXD03	0.263	0.133
BXD04	0.15	-0.047
BXD05	0.237	0.468
BXD06	0.135	-0.06
BXD07	-0.446	0.117
BXD08	0.592	0.412
BXD09	0.322	0.148
CAST	0.752	0.637
CCcont	1.098	0.106
DS01	0.373	-0.161
DS02	0.711	0.17
DS04	0.968	0.447
DS0c	0.22	-0.218
GP01	-0.577	0.25
GP02	0.629	0.146
GP0c	-0.346	-0.039
NOD	0.552	0.236
NZO	1.402	-0.201
PWK	0.641	-0.104
H37Rv_KO_CtpC	-0.345	0.265
H37Rv_KO_CtpD	1.436	0.351
H37Rv_KO_Rv1272	0.795	0.952
H37Rv_KO_SugABC	1.151	0.895
H37Rv_KO_MbtN	0.105	0.369
Trans05	0.525	0.419
macrophage_unactivated	0.186	1.004
IL1	0.0	0.225
Rapamycin	0.522	0.847
Tcell	0.0	0.534
GMCSF	0.449	0.069
IFNab	0.0	0.378
IFNg	0.158	0.313
IFNg_GMCSF1	-0.192	0.214
Rv1432_day32	0.541	0.272
Rv1565c_day32	0.355	-0.351
secA2_input	0.0	0.094
delta_Rv3594	-0.379	-0.162
delta_Rv3717	-0.238	-0.646
delta_Rv3811	0.214	-0.47
delta_Rv0954	-0.963	-0.885
PonA1	-0.03	-0.247
EccD1_KO	0.293	0.02
EspI_KO	-0.088	-0.128
PE35_KO	-0.277	-0.248
PPE68_KO	0.192	-0.294
glycerol2	0.611	1.338
lignocerate	1.112	1.169
oleate	-0.549	1.262
phosphatidylcholine	0.611	1.195
acetate	0.618	0.281
glucAc	0.944	0.554
Rv0950ko	-0.247	0.208
Rv1096ko	-0.513	0.208
Rv3684ko	0.95	0.226
delta_otsA_trehalose	1.056	-0.152