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Module #44, TG: 2.8, TC: 1.8, 68 probes, 65 Entrez genes, 4 conditions
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The image plot shows the color-coded level of gene expression, for the
genes and conditions in a given transcription module. The genes are on
the horizontal, the conditions on the vertical axis.
The genes are ordered according to their ISA gene scores, similarly
the conditions are ordered according to their condition scores. The
score of a gene means the «degree of inclusion» in
the module: a high score gene is essential in the module.
Condition scores can also be negative, that means that the genes of
the module are all down-regulated in the condition. Here the absolute
value of the score gives the «degree of inclusion».
The plots above and beside the expression matrix show the gene scores
and condition scores, respectively.
Note that the plot is interactive, you can see the name of the gene
and condition under the mouse cursor.
The expression matrix was normalized to have mean zero and standard
deviation one for every gene separately across all conditions
(i.e. not just for the conditions in the module).
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Under-expression is coded with green,
over-expression with red color.
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The GO tree — Biological processes
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This is one of three sections showing Gene Ontology enrichment of the
current module: in this case for biological processes.
The graph shows the hierarchy of the GO categories, their enrichment
for the current module is color coded, and the blue number beside the
category is the minus log ten p-value of the enrichment. (Calculated
using the standard hypergeometric test.) The color of the arrows code
«is a» (cyan) and «part of» relationships.
The tree was built the following way. First all GO terms with more
significant enrichment p-value than 0.05 were collected. Then all
paths from these terms to the root node of the GO tree were included
too. If a GO term is included more than once in the tree, then the
green numbers show 1) the id of the node, this makes it easier to find
other appereances of the term, and 2) the number of appearences.
Note that the same GO category might show up on the graph many
times. This is because the GO was «straightened» for this
graph, i.e. if there are more paths from a GO term to the root node of
the tree, all of them are included. The green numbers
Move the mouse cursor over the terms to get their definition. Clicking
on them takes you to the corresponding Gene Ontology web page.
If you cannot see a graph here at all, that means that there were no
significantly enriched GO categories, at the 0.05 level.
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The GO tree — Cellular Components
HELP
This is one of three sections showing Gene Ontology enrichment of the
current module: in this case for cellular components.
The graph shows the hierarchy of the GO categories, their enrichment
for the current module is color coded, and the blue number beside the
category is the minus log ten p-value of the enrichment. (Calculated
using the standard hypergeometric test.) The color of the arrows code
«is a» (cyan) and «part of» relationships.
The tree was built the following way. First all GO terms with more
significant enrichment p-value than 0.05 were collected. Then all
paths from these terms to the root node of the GO tree were included
too. If a GO term is included more than once in the tree, then the
green numbers show 1) the id of the node, this makes it easier to find
other appereances of the term, and 2) the number of appearences.
Note that the same GO category might show up on the graph many
times. This is because the GO was «straightened» for this
graph, i.e. if there are more paths from a GO term to the root node of
the tree, all of them are included. The green numbers
Move the mouse cursor over the terms to get their definition. Clicking
on them takes you to the corresponding Gene Ontology web page.
If you cannot see a graph here at all, that means that there were no
significantly enriched GO categories, at the 0.05 level.
— Click on the Help button again to close this help window.
extracellular region
The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
cellular_component
The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
all
NA
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The GO tree — Molecular Function
HELP
This is one of three sections showing Gene Ontology enrichment of the
current module: in this case for molecular function.
The graph shows the hierarchy of the GO categories, their enrichment
for the current module is color coded, and the blue number beside the
category is the minus log ten p-value of the enrichment. (Calculated
using the standard hypergeometric test.) The color of the arrows code
«is a» (cyan) and «part of» relationships.
The tree was built the following way. First all GO terms with more
significant enrichment p-value than 0.05 were collected. Then all
paths from these terms to the root node of the GO tree were included
too. If a GO term is included more than once in the tree, then the
green numbers show 1) the id of the node, this makes it easier to find
other appereances of the term, and 2) the number of appearences.
Note that the same GO category might show up on the graph many
times. This is because the GO was «straightened» for this
graph, i.e. if there are more paths from a GO term to the root node of
the tree, all of them are included. The green numbers
Move the mouse cursor over the terms to get their definition. Clicking
on them takes you to the corresponding Gene Ontology web page.
If you cannot see a graph here at all, that means that there were no
significantly enriched GO categories, at the 0.05 level.
— Click on the Help button again to close this help window.
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GO BP test for over-representation
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List of all enriched GO categories (biological processes), at the 0.05
p-value level.
The columns:
- ExpCount is the expected count of genes in the
module annotated with the given GO term, just by chance.
- Count
is the number of genes in the module annotated with the given GO
term.
- Size is the total number of genes (in our universe)
annotated with the GO term.
Clicking on Count shows the genes that drive the
enrichment. You can also click on the individual numbers in
the Count column, to show the driving genes for that individual
GO category.
Clicking on the GO identifiers takes you to the Gene Ontology web
pages.
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| Id | Pvalue | ExpCount | Count | Size | Term |
| GO:0043604 | 1.853e-02 | 0.03715 | 2
OTC, PRHOXNB | 7 | amide biosynthetic process |
| GO:0030299 | 2.284e-02 | 0.04245 | 2
APOA4, SOAT2 | 8 | intestinal cholesterol absorption |
| GO:0034433 | 2.284e-02 | 0.04245 | 2
APOA4, SOAT2 | 8 | steroid esterification |
| GO:0034434 | 2.284e-02 | 0.04245 | 2
APOA4, SOAT2 | 8 | sterol esterification |
| GO:0034435 | 2.284e-02 | 0.04245 | 2
APOA4, SOAT2 | 8 | cholesterol esterification |
| GO:0044241 | 2.717e-02 | 0.04776 | 2
APOA4, SOAT2 | 9 | lipid digestion |
| GO:0034377 | 3.659e-02 | 0.05837 | 2
APOA4, SOAT2 | 11 | plasma lipoprotein particle assembly |
| GO:0065005 | 3.659e-02 | 0.05837 | 2
APOA4, SOAT2 | 11 | protein-lipid complex assembly |
| GO:0006952 | 3.782e-02 | 2.77 | 9
APOA4, CCL23, CCL24, CD209, CD5L, CFP, CXCR2, PLA2G2D, TNFAIP8L2 | 522 | defense response |
| GO:0050892 | 4.165e-02 | 0.06368 | 2
APOA4, SOAT2 | 12 | intestinal absorption |
| GO:0043603 | 4.677e-02 | 0.06899 | 2
OTC, PRHOXNB | 13 | cellular amide metabolic process |
| GO:0008202 | 4.914e-02 | 0.9233 | 5
AFP, APOA4, APOF, CYP1A1, SOAT2 | 174 | steroid metabolic process |
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GO CC test for over-representation
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List of all enriched GO categories (cellular components), at the 0.05
p-value level.
The columns:
- ExpCount is the expected count of genes in the
module annotated with the given GO term, just by chance.
- Count
is the number of genes in the module annotated with the given GO
term.
- Size is the total number of genes (in our universe)
annotated with the GO term.
Clicking on Count shows the genes that drive the
enrichment. You can also click on the individual numbers in
the Count column, to show the driving genes for that individual
GO category.
Clicking on the GO identifiers takes you to the Gene Ontology web
pages.
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| Id | Pvalue | ExpCount | Count | Size | Term |
| GO:0005576 | 8.863e-06 | 7.383 | 23
ADAM12, AFP, APOA4, APOF, BPIL1, CCL23, CCL24, CD209, CD5L, CFP, CPA6, DKK2, DNASE2B, FETUB, LIPM, PAEP, PLA2G2D, PROL1, PRSSL1, SERPINA12, TECTB, VMO1, VWCE | 1407 | extracellular region |
| GO:0034364 | 2.401e-02 | 0.06821 | 2
APOA4, APOF | 13 | high-density lipoprotein particle |
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GO MF test for over-representation
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List of all enriched GO categories (molecular function), at the 0.05
p-value level.
The columns:
- ExpCount is the expected count of genes in the
module annotated with the given GO term, just by chance.
- Count
is the number of genes in the module annotated with the given GO
term.
- Size is the total number of genes (in our universe)
annotated with the GO term.
Clicking on Count shows the genes that drive the
enrichment. You can also click on the individual numbers in
the Count column, to show the driving genes for that individual
GO category.
Clicking on the GO identifiers takes you to the Gene Ontology web
pages.
— Click on the Help button again to close this help window.
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KEGG Pathway test for over-representation
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List of all enriched KEGG pathways, at the 0.05
p-value level.
The columns:
- ExpCount is the expected count of genes in the
module annotated with the given KEGG pathway, just by chance.
- Count
is the number of genes in the module annotated with the given KEGG
pathway.
- Size is the total number of genes (in our universe)
annotated with the KEGG pathway.
Clicking on Count shows the genes that drive the
enrichment. You can also click on the individual numbers in
the Count column, to show the driving genes for that individual
KEGG pathway.
Clicking on the KEGG identifiers takes you to the KEGG web site.
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miRNA test for over-representation
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List of all enriched miRNA families, at the 0.05
p-value level.
The columns:
- ExpCount is the expected count of genes in the
module regulated by the given miRNA family, just by chance.
- Count
is the number of genes in the module regulated by the given miRNA
family.
- Size is the total number of genes (in our universe)
regulated with the given miRNA family.
Clicking on Count shows the genes that drive the
enrichment. You can also click on the individual numbers in
the Count column, to show the driving genes for that individual
miRNA family.
The miRNA regulation data was taken from the TargetScan database.
(Only the conserved sites were used for the current analysis.)
Clicking on the miRNA names takes you to the TargetScan web site.
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Chromosome test for over-representation
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List of all enriched Chromosomes, at the 0.05
p-value level.
The columns:
- ExpCount is the expected number of genes in the
module on the given chromosome, just by chance.
- Count
is the number of genes in the module on the given chromosome.
- Size is the total number of genes (in our universe)
on the given chromosome.
Clicking on Count shows the genes that drive the
enrichment. You can also click on the individual numbers in
the Count column, to show the driving genes for that individual
chromosome.
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HELP
A list of all genes in the current module, in alphabetical order. The
size of the text corresponds to the gene scores.
Text color indicates correlation and anti-correlation: genes of the
same color are correlated, both move up or down in the module samples
(listed below). Genes of different color are anti-correlated, they
have opposite behavior in the module samples.
Note, that text color of the individual genes should be interpreted
together with the coloring of the samples below. For
red samples,
red genes have a higher expression
(compared to the average gene expression level),
green genes have a lower
expression.
Green samples have opposite
behavior, in these red genes have a
lower expression, green genes
have a higher expression.
Note that some gene symbols may show up more than once, if many
probes match the same Entrez gene.
Genes with no Entrez mapping are given separately, with their
Affymetrics probe ID.
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Entrez genes
A4GNTalpha-1,4-N-acetylglucosaminyltransferase (ENSG00000118017), score: 0.85
ADAM12ADAM metallopeptidase domain 12 (ENSG00000148848), score: 0.83
AFPalpha-fetoprotein (ENSG00000081051), score: 0.69
AIM1Labsent in melanoma 1-like (ENSG00000176092), score: 0.71
AKR1CL1aldo-keto reductase family 1, member C-like 1 (ENSG00000196326), score: 0.76
ALG2asparagine-linked glycosylation 2, alpha-1,3-mannosyltransferase homolog (S. cerevisiae) (ENSG00000119523), score: 0.71
APOA4apolipoprotein A-IV (ENSG00000110244), score: 0.8
APOFapolipoprotein F (ENSG00000175336), score: 0.74
AQP8aquaporin 8 (ENSG00000103375), score: 0.82
ARL2BPADP-ribosylation factor-like 2 binding protein (ENSG00000102931), score: -0.7
B3GNT7UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7 (ENSG00000156966), score: 0.72
BPIL1bactericidal/permeability-increasing protein-like 1 (ENSG00000078898), score: 0.68
C17orf87chromosome 17 open reading frame 87 (ENSG00000161929), score: 0.87
C9orf152chromosome 9 open reading frame 152 (ENSG00000188959), score: 0.89
CCL23chemokine (C-C motif) ligand 23 (ENSG00000167236), score: 0.7
CCL24chemokine (C-C motif) ligand 24 (ENSG00000106178), score: 0.78
CD209CD209 molecule (ENSG00000090659), score: 0.77
CD33CD33 molecule (ENSG00000105383), score: 0.8
CD5LCD5 molecule-like (ENSG00000073754), score: 0.71
CDC42BPACDC42 binding protein kinase alpha (DMPK-like) (ENSG00000143776), score: -0.77
CDX2caudal type homeobox 2 (ENSG00000165556), score: 0.71
CFPcomplement factor properdin (ENSG00000126759), score: 0.7
CLDN14claudin 14 (ENSG00000159261), score: 0.7
CPA6carboxypeptidase A6 (ENSG00000165078), score: 0.69
CRYBA2crystallin, beta A2 (ENSG00000163499), score: 0.74
CXCR2chemokine (C-X-C motif) receptor 2 (ENSG00000180871), score: 0.88
CYP1A1cytochrome P450, family 1, subfamily A, polypeptide 1 (ENSG00000140465), score: 0.71
DKK2dickkopf homolog 2 (Xenopus laevis) (ENSG00000155011), score: 0.74
DNASE2Bdeoxyribonuclease II beta (ENSG00000137976), score: 0.7
DSC3desmocollin 3 (ENSG00000134762), score: 0.87
EMR1egf-like module containing, mucin-like, hormone receptor-like 1 (ENSG00000174837), score: 0.79
F2RL2coagulation factor II (thrombin) receptor-like 2 (ENSG00000164220), score: 0.73
FETUBfetuin B (ENSG00000090512), score: 0.73
FGD2FYVE, RhoGEF and PH domain containing 2 (ENSG00000146192), score: 0.78
FOXA1forkhead box A1 (ENSG00000129514), score: 0.7
FOXP3forkhead box P3 (ENSG00000049768), score: 0.94
GLYATL3glycine-N-acyltransferase-like 3 (ENSG00000203972), score: 0.84
GNAT1guanine nucleotide binding protein (G protein), alpha transducing activity polypeptide 1 (ENSG00000114349), score: 0.73
HRASLS2HRAS-like suppressor 2 (ENSG00000133328), score: 0.7
IL1R2interleukin 1 receptor, type II (ENSG00000115590), score: 0.73
KRT28keratin 28 (ENSG00000173908), score: 1
LIPMlipase, family member M (ENSG00000173239), score: 0.73
LYPD3LY6/PLAUR domain containing 3 (ENSG00000124466), score: 0.73
ONECUT1one cut homeobox 1 (ENSG00000169856), score: 0.73
OR10H3olfactory receptor, family 10, subfamily H, member 3 (ENSG00000171936), score: 0.73
OTCornithine carbamoyltransferase (ENSG00000036473), score: 0.71
PAEPprogestagen-associated endometrial protein (ENSG00000122133), score: 0.72
PFKFB16-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1 (ENSG00000158571), score: 0.69
PLA2G2Dphospholipase A2, group IID (ENSG00000117215), score: 0.77
PPAPDC1Bphosphatidic acid phosphatase type 2 domain containing 1B (ENSG00000147535), score: 0.78
PRHOXNBparahox cluster neighbor (ENSG00000183463), score: 1
PROL1proline rich, lacrimal 1 (ENSG00000171199), score: 0.69
PRSSL1protease, serine-like 1 (ENSG00000185198), score: 0.79
PSKH2protein serine kinase H2 (ENSG00000147613), score: 0.82
PTCRApre T-cell antigen receptor alpha (ENSG00000171611), score: 0.76
RGS13regulator of G-protein signaling 13 (ENSG00000127074), score: 0.89
SERPINA12serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 12 (ENSG00000165953), score: 0.84
SLC46A1solute carrier family 46 (folate transporter), member 1 (ENSG00000076351), score: 0.71
SOAT2sterol O-acyltransferase 2 (ENSG00000167780), score: 0.89
TECTBtectorin beta (ENSG00000119913), score: 0.79
TMEM154transmembrane protein 154 (ENSG00000170006), score: 0.69
TNFAIP8L2tumor necrosis factor, alpha-induced protein 8-like 2 (ENSG00000163154), score: 0.69
TRPM5transient receptor potential cation channel, subfamily M, member 5 (ENSG00000070985), score: 0.88
VMO1vitelline membrane outer layer 1 homolog (chicken) (ENSG00000182853), score: 0.69
VWCEvon Willebrand factor C and EGF domains (ENSG00000167992), score: 0.74
Non-Entrez genes
ENSG00000182853Unknown, score: 0.92
ENSG00000078898Unknown, score: 0.81
ENSG00000119523Unknown, score: 0.83
HELP
Conditions in the module, given in the same order as on the expression
plot above. Red color means over-expression, green under-expression in
the given condition.
The barplot below shows the condition (sample) scores. A separate bar
is shown for each sample, its height is the corresponding score of the
sample in the module. The red and green numbers on the bars are the
sample scores expressed in percents, i.e. 100% is 1.0.
The height of each bar corresponds to the weighted
mean expression of the module genes. The weights are the gene scores
of the module and they are positive for the genes listed in
red above and they are negative for
the genes that are listed in
green.
Bars going up correspond to samples listed in
red (the ones that are different
enough to included in the module). In these samples
the red module genes are highly
expressed, and the green
module genes are lowly expressed. The behavior of the genes is the
opposite for bars going down.
The red and green lines show the module thresholds, samples above
the red line and below the green line are included in the module.
The different species and tissues that were part of the study, are separated
by dashed vertical lines.
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| Id | species | tissue | sex | individual |
| ppy_lv_f_ca1 | ppy | lv | f | _ |
| ppy_lv_m_ca1 | ppy | lv | m | _ |
| mml_lv_f_ca1 | mml | lv | f | _ |
| mml_lv_m_ca1 | mml | lv | m | _ |
© 2008-2010 Computational Biology Group, Department of Medical Genetics,
University of Lausanne, Switzerland
