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MapMan: a la carte painting of profiling data onto a template of your own design. Transcript Scavenger Module. 23,000 genes. 35 ‚BINS‘ - major functional categories - subdivided into hierarchical subBINS. Mapping file (Excel file). A sketch of your favorite bit of biology (bmp file).

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Mapman a la carte painting of profiling data onto a template of your own design
MapMan: a la carte painting of profiling data onto a template of your own design

Transcript Scavenger Module

23,000 genes

35 ‚BINS‘ - major functional categories- subdivided into hierarchical subBINS

Mapping file (Excel file)

A sketch of your favorite bit of biology

(bmp file)

Experimental data,

e.g 22k Affy chip,

(Excel file)

Automatic display onto your sketch

Oliver Thimm

Oliver Blaesing

Yves Gibon

Axel Nagel

Svenya Meyer

Peter Krüger

Joachim Selbig

Image Annotator Module


Sorting genes into rubbish bins with the scavenger module

1310 entries

Assignment

to BINS

2812 entries

- Screen Tigr3 gene descriptions with text search algorithms

using Kegg enzyme

and alternative names

3080 entries

Assignment

toBINS

16213 entries

keywords

user defined keywords

- Manual correction of binned gene annotations

21918 entries

19584 unique

master file

Manually corrected file

- Import existing categorised genes

Sorting genes into (rubbish) BINS, with the SCAVENGER module


Excerpt from a mapping file

A mouse over action revealss the assignment, illustrated for 249804_at (encodes galactinol synthase, as is displayed at the bottom of the screen)

Excerpt from a mapping file

BIN 3 is expanded to show its sub-BINS

Sub-BIN 3.1 (raffinose metabolism) is expanded to the level of single genes.

- identified by a ‚unique identifier

(Affy number blablablablabla_at)

- will carry the numeric code ‚3.1‘

The mapping file

(i)Re-organises the experimental data file.

- Groups together all the genes that have a

particular numeric code (i.e., are in the

same BIN/sub-BIN).

(ii)Provides the code via which the resulting sets

of data are painted onto your pretty diagrams


The user takes a diagram of his her choice and decides what data is displayed where and how

Mouse click at a selected position on the picture

Frequency

histogramm

presentation

default :

shows each gene

Mouse over

The User takes a diagram of his/her choice, and decides what data is displayed, where, and how ....

What data do you

want to paint here ?

Data files

Type in

BIN identifier

maps

+

Mapping files

Blue = increase

Red = decrease

Grey = no call

White = no change

How do you

want to show it ?


Example of a map

Syn-

thesis

Break-

down

Ascorbate, Glutathione

Misc. kin-ases

Myo-Ins

Callose.

Sugar alcohol

Misc

Treh-alose

Raffi-nose

Pectin-esterases

Break-

down

Syn-

thesis

UDP-sugar metabolism

Calvin cycle

Cellulose and hemicellulose synthesis

Pectin lyases, polygalacturonases

Hemi-cellose

Cellu-lases

XETs,

Expansins

Photo-respiration

Cell wall breakdown

gluconeogenesis

FA synthesis

Fermentation

Desaturation

Phospho-

and galacto-

lipids

TAG

Glyoxalate cycle

beta oxidation

(lyso)phos

pholipases

GDSL

lipisaes

lipases

Other organic acid

trans-formations

Sterols and sulpholipid

Lipid breakdown

Carbonic anhydrases

Tetrapyrrole

Branched chain amino acid AT

GABA metabolism

Ammonium

assimilation

Nitrate reduction

Asp AT

Ala AT

Asn

Ammonium release

Ser

Val

Phe

His

Thr

Asn

Leu

Pro

Ser

Phe

Val

Tyr

His

Gly

Ileu

Pro

Thr

Tryp

Gly

Tyr

C-1 metabolism

Met

Arg

Cys

Arg

Ileu

Tryp

Cys

Salvage

Lys

Leu

Hyp

Hyp

Synthesis

Breakdown

Deoxy-nucleotide

Met

Chorismate synthesis

Homoserine synthesis

Lys

Phosphotransfer

pyrophosphases

Amino acid synthesis

Amino acid breakdown

Nucleotides

Example of a ‚map‘

Glycolysis

Mitochondrial electron transport and ATP synthesis


Extension of the night for 2h

4h,

6h,

and 8h

Extension of the night for 2h,

Transcripts


Selective changes of expression of genes involved in cell wall synthesis breakdown and modification

Pectin *esterases

Selective changes of expression of genes involved in cell wall synthesis, breakdown and modification

synthesis

pectin lyases

polygalacturonases

XET‘s

Expansins

Break down

Transcripts


2h ext night

Painting at the pathway level

2h ext night

2 h into the

extended night

A few genes induced

No genes repressed


4h ext night

Induction of two PFP family members and cytosolic FBPase

Tho‘ many genes for pyruvate kinases are slightly repressed, one is induced

4h ext night

4 h into the

extended night

Some genes for glycolytic enzymes are being repressed


6h ext night

Reciprocal changes of specific PFK/PFP and FBP family members

Many genes for pyruvate kinases are slightly repressed, but three are is induced

6h ext night

6 h into the

extended night

Some genes for glycolytic enzymes are being repressed


8h ext night

Reciprocal changes of specific PFK/PFP and FBP family members

Many genes for pyruvate kinases are slightly repressed, but one is induced

8h ext night

8 h into the

extended night -

Repression becomes stronger and spreads to more genes


Cellular functions in an extended night after 2h

Looking for changes members

in general functions

4h,

6h,

and 8h

Cellular functions in an extended night after 2h,


Sugars regulate expression of 100 s of genes
Sugars regulate expression of 100’s of genes members

Nucleotide

metabolism

23.1 Synthesis

23.2 Breakdown

11.4 Phospho- & galactolipid synthesis

11.2 FA desaturation

11.1 FA synthesis

Lipid

metabolism

11.9.2

Lipases

11.9.3

(lyso)-phos-

pholipases

11.9.4

ß-oxidation

10.5 Pectin *esterases

10.2 + 10.3

Cellulose & hemicellulose synthesis

10.6.2

Matrix breakdown

Cell wall

10.7

XET‘s

Expansins

10.6.3

Pectin lyases

Polygalacturonases

  • - Central carbon metabolism

  • Nitrate, ammonium, amino acid

  • and nucleotide metabolism

  • RNA and protein synthesis

  • - Lipid metabolism

  • Cell wall metabolism and

  • modification

  • - Secondary metabolism

  • Hormone synthesis and sensing

  • Signalling pathways

  • Transcription factors


Integration with further experiments comparison with other nutrient challenges
Integration with further experiments members- comparison with other nutrient challenges

Overlay plots

Arabidopsis grown in liquid culture under continuous light with full nutrients, or with one limiting ...

Treatments:

Resupply 3mM sucrose to sugar-depleted seedlings.

Resupply 3mM nitrate to nitrate-depleted seedlings.

Resupply 3mM phosphate to phosphate-depleted seedlings

Resupply 3mM sulphate to

sulphate-depleted seedlings


Overlay the responses to identify similarities and differences on a gene to gene basis

6h Extended night members

vs.

End of normal night

pgm at end of night

vs.

WT at end of night

in pgm

vs.

in Extended Night

Paint out the result for each individual gene onto the map

Increase by > 1.0 in both

Increase by > 0.5 in both

Change by < 0.5 in both

Decrease by > 0.5 in both

Decrease by > 1.0 in both

Opposing Responses

Overlay the responses to identify similarities and differences on a gene-to-gene basis

Mathematical correlation plot

for all the genes


Direct overlay of the responses 6h extended night vs pgm

Light harvesting proteins etc members.

Direct overlay of the responses: 6h extended night vs. pgm


Overlay plot comparing the response of metabolism to carbon and nitrate deficiency

Many members

non-shared responses

Overlay plot comparing the response of metabolism tocarbon and nitratedeficiency

Shared: Repress

- Pectinesterases

- Expansins,

- XET‘s

- PolyGalUAases

Shared: Induce many genes for

amino acid breakdown


Overlay plot comparing the response of metabolism to nitrate and phosphate deficiency

Repression of photosynthesis members

Repression of chlorophyll synthesis

Many

shared responses

Overlay plot comparing the response of metabolism tonitrate and phosphatedeficiency

Induction of phenylpropanoid and flavanoid metabolism


Overlay plot comparing the response of metabolism to nitrate and sulphate deficiency

Many members

shared responses

Overlay plot comparing the response of metabolism tonitrate and sulphatedeficiency

Repression of photosynthesis

Repression of chlorophyll synthesis

Induction of phenylpropanoid and flavanoid metabolism


Current work
Current Work members

Ongoing correction of assignments by mining public sites

Establish pipelines to import updates of annotation, and expert advice

Display clusters or other statistictically-generated groupings of genes

Visualisation of metabolite profiling data sets

Combination of data-sets at different levels

Statistical treatment of the responses of different BINS

- rigorous support for conclusions

- data condensation to aid compariosn of different treatments

- support automatic identification of co-regulated processes

Adapt display to give information about the expression level as well as the change of expression

Extend to visualise the expression of a small set of genes-of-interest

across a large collection of arrays for different developmental stages,

organs , or treatments.

Use to organise and display data sets from crop plants


Mapman a la carte painting of profiling data onto a template of your own design

pgm members

PCA Analysis of transcript profiles:- diurnal cycles in wildtype (biological triplicates) - extended night in wildtype (biological duplicates) - diurnal cycles in pgm (biological duplicates)

WildtypeDark

Wildtype Extended night

Wildtype

Light

Component 1: treatments lie on an axis from high to low sugar

total of 40 arrays in 20 conditions


Mapman a la carte painting of profiling data onto a template of your own design

Response of starved seedlings to added sugar: members

starved of

sugar

3hrs after

adding sugar

Weighting in the 1st component,

in PCA of diurnal rhythms and extended night treatments

Correlation plot for ~14,000 genes betweenWeightingsoftranscripts in the first principle component andChanges of transcripts in the first 3 hrs after adding sugar to sugar-starved seedlings in liquid culture


Changes after adding sugar to starved seedlings

Several cell wall degrading membersenzymes

Several cell wall degradingenzymes

Several TPS‘s

Several TPS‘s

SO4

assimi-lation

SO4

assimi-lation

Phenyl-propanoid and flavonoid metabolism

Phenyl-propanoid and flavonoid metabolism

ASN1

ASN1

Amino acid break-down

Amino acid break-down

GDH1 GDH2

GDH1 GDH2

Amino acid synthesis

Amino acid synthesis

1st component for diurnal changes and extended night

Changes after adding sugar to starved seedlings

Reciprocal plot


Mapman a la carte painting of profiling data onto a template of your own design1
MapMan: membersa la carte painting of profiling data onto a template of your own design

Transcript Scavenger Module

Metabolite Scavenger Module

23,000 genes

100‘s of metabolites

35 ‚BINS‘ - major functional categories- subdivided into hierarchical subBINS

35 ‚BINS‘ - major functional categories- subdivided into hierarchical subBINS

Mapping file

A sketch of your favorite bit of biology –bmp file

Experimental data,

e.g 22k Affy array, as an Excel file

Experimental data,

e.g GC-MS profile, as an Excel file

Automatic display onto your sketch

Oliver Thimm

Oliver Blaesing

Yves Gibon

Axel Nagel

Svenya Meyer

Peter Krüger

Joachim Selbig

Image Annotator Module


L penelli metabolite profile painted out with mapman
L. penelli members metabolite profile painted out with Mapman

In work

Changes are shown in false color relative to L. esculentum


An introgression line with improved nitrogen assimilation
An introgression line with improved nitrogen assimilation ....

In work

Changes are shown in false color relative to L. esculentum


An introgression line with improved amino acid biosynthesis
An introgression line with improved amino acid biosynthesis....

In work

Changes are shown in false color relative to L. esculentum


An introgression line with high levels of stress related metabolites
An introgression line with high levels of stress-related metabolites

In work

Changes are shown in false color relative to L. esculentum


Reprogrammning of metabolism after adding nitrate back to deficient seedlings in liquid culture

Induce metabolites

glycolysis and the TCA cycle

30 min

Induce sucrose breakdown

Induce OPP cycle

Reprogrammning of metabolism after adding nitrate back to deficient seedlings in liquid culture

Induce nitrate reduction


Responses can be resolved to the pathway level

Repress enzymes for gluconeogenesis metabolites

Induce specific members of the families for each enzyme needed to move carbon from the end of glycolysis through to 2-oxoglutarate –the acceptor for ammonium

TCA cycle

Repress

non-phosphory-lating NADH dehydrogenases

Mitochondrial electron transport & ATP synthesis

Responses can be resolved to the pathway level


Reprogrammning of metabolism after adding nitrate back to deficient seedlings in liquid culture1

Induce metabolites

glycolysis and the TCA cycle

Inhibition ofphenylpropanoid and flavonoid metabolism

Inhibit amino acid and nucleotide breakdown

3 hours

30 min

Induce sucrose breakdown

Induce OPP cycle

Induce several XET‘s and expansins

Induce several FA desaturases

Reprogrammning of metabolism after adding nitrate back to deficient seedlings in liquid culture

Induce

photosynthesis

Why is Phe synthesis inhibited

Induce nitrate reduction

Induce sulphate reduction

Induce nucleotide synthesis and salvage

Induce amino acid synthesis


Mapman a la carte painting of profiling data onto a template of your own design
Nitrate readdition leads to major changes of transcripts for large enzyme families involved in biosynthetic and secondary metabolism

after 30 min,

3 hours

and 2 days

Many glucosyltransferases are repressed

Very widespread changes


Cellular responses to nitrate resupply after 30 min

... and 3 hours large enzyme families involved in biosynthetic and secondary metabolism

Cellular responses to nitrate resupply .. after 30 min