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Module #17, TG: 3, TC: 1, 99 probes, 95 Entrez genes, 13 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
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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.
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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:0007603 | 3.486e-02 | 0.05739 | 2
ABCA4, GNAT1 | 8 | phototransduction, visible light |
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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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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.
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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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| Id | Pvalue | ExpCount | Count | Size | Term |
| 00590 | 3.285e-02 | 0.2503 | 3
ALOX12, GGT5, PLA2G2D | 40 | Arachidonic acid metabolism |
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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
ABCA4ATP-binding cassette, sub-family A (ABC1), member 4 (ENSG00000198691), score: 0.7
ACER1alkaline ceramidase 1 (ENSG00000167769), score: 0.84
ADAM12ADAM metallopeptidase domain 12 (ENSG00000148848), score: 0.91
AFPalpha-fetoprotein (ENSG00000081051), score: 0.78
AIM1Labsent in melanoma 1-like (ENSG00000176092), score: 0.73
AKR1CL1aldo-keto reductase family 1, member C-like 1 (ENSG00000196326), score: 0.79
ALOX12arachidonate 12-lipoxygenase (ENSG00000108839), score: 0.79
APOA4apolipoprotein A-IV (ENSG00000110244), score: 0.9
ARCN1archain 1 (ENSG00000095139), score: 0.71
ATP8ATP synthase F0 subunit 8 (ENSG00000228253), score: -0.81
BIRC7baculoviral IAP repeat-containing 7 (ENSG00000101197), score: 0.75
C14orf126chromosome 14 open reading frame 126 (ENSG00000129480), score: 0.71
C17orf49chromosome 17 open reading frame 49 (ENSG00000161939), score: 0.71
C1orf177chromosome 1 open reading frame 177 (ENSG00000162398), score: 0.87
C20orf7chromosome 20 open reading frame 7 (ENSG00000101247), score: -0.77
C22orf15chromosome 22 open reading frame 15 (ENSG00000169314), score: 0.86
C22orf39chromosome 22 open reading frame 39 (ENSG00000242259), score: -0.73
C2orf43chromosome 2 open reading frame 43 (ENSG00000118961), score: 0.71
C3orf26chromosome 3 open reading frame 26 (ENSG00000184220), score: -0.7
C6orf108chromosome 6 open reading frame 108 (ENSG00000112667), score: -0.76
C6orf52chromosome 6 open reading frame 52 (ENSG00000137434), score: 0.73
C9orf152chromosome 9 open reading frame 152 (ENSG00000188959), score: 0.92
CBARA1calcium binding atopy-related autoantigen 1 (ENSG00000107745), score: -0.75
CBY1chibby homolog 1 (Drosophila) (ENSG00000100211), score: -0.69
CCDC142coiled-coil domain containing 142 (ENSG00000135637), score: 0.8
CCL25chemokine (C-C motif) ligand 25 (ENSG00000131142), score: 0.86
CD1ECD1e molecule (ENSG00000158488), score: 0.77
CDK5cyclin-dependent kinase 5 (ENSG00000164885), score: -0.77
CDKN2AIPNLCDKN2A interacting protein N-terminal like (ENSG00000237190), score: -0.86
CDV3CDV3 homolog (mouse) (ENSG00000091527), score: -0.87
CHCHD2coiled-coil-helix-coiled-coil-helix domain containing 2 (ENSG00000106153), score: -0.85
CPA6carboxypeptidase A6 (ENSG00000165078), score: 0.71
CRYBA2crystallin, beta A2 (ENSG00000163499), score: 0.85
DGUOKdeoxyguanosine kinase (ENSG00000114956), score: -0.69
DKK2dickkopf homolog 2 (Xenopus laevis) (ENSG00000155011), score: 0.73
DNAJC7DnaJ (Hsp40) homolog, subfamily C, member 7 (ENSG00000168259), score: -0.7
DSC3desmocollin 3 (ENSG00000134762), score: 0.84
F2RL2coagulation factor II (thrombin) receptor-like 2 (ENSG00000164220), score: 0.87
FAM189Bfamily with sequence similarity 189, member B (ENSG00000160767), score: -0.72
FKTNfukutin (ENSG00000106692), score: 0.74
FLJ35220hypothetical protein FLJ35220 (ENSG00000173818), score: -0.71
FOXP3forkhead box P3 (ENSG00000049768), score: 0.76
FXC1fracture callus 1 homolog (rat) (ENSG00000132286), score: 0.71
GGT5gamma-glutamyltransferase 5 (ENSG00000099998), score: -0.7
GLYATL3glycine-N-acyltransferase-like 3 (ENSG00000203972), score: 0.72
GNAT1guanine nucleotide binding protein (G protein), alpha transducing activity polypeptide 1 (ENSG00000114349), score: 0.72
GPR113G protein-coupled receptor 113 (ENSG00000173567), score: 0.76
GTF2F1general transcription factor IIF, polypeptide 1, 74kDa (ENSG00000125651), score: -0.88
HNRNPLheterogeneous nuclear ribonucleoprotein L (ENSG00000104824), score: -0.91
HRASLS2HRAS-like suppressor 2 (ENSG00000133328), score: 0.8
IFIT1Binterferon-induced protein with tetratricopeptide repeats 1B (ENSG00000204010), score: 0.92
INO80EINO80 complex subunit E (ENSG00000169592), score: -0.73
KRT28keratin 28 (ENSG00000173908), score: 0.93
LOC100127905family with sequence similarity 165, member B pseudogene (ENSG00000198738), score: 0.93
LUC7LLUC7-like (S. cerevisiae) (ENSG00000007392), score: -0.71
LYPD3LY6/PLAUR domain containing 3 (ENSG00000124466), score: 0.7
MAKmale germ cell-associated kinase (ENSG00000111837), score: 0.73
MCM10minichromosome maintenance complex component 10 (ENSG00000065328), score: 0.72
MEFVMediterranean fever (ENSG00000103313), score: 0.81
NAA40N(alpha)-acetyltransferase 40, NatD catalytic subunit, homolog (S. cerevisiae) (ENSG00000110583), score: -0.8
NGRNneugrin, neurite outgrowth associated (ENSG00000182768), score: -0.89
NUDT15nudix (nucleoside diphosphate linked moiety X)-type motif 15 (ENSG00000136159), score: -0.81
OR10H3olfactory receptor, family 10, subfamily H, member 3 (ENSG00000171936), score: 0.85
PAEPprogestagen-associated endometrial protein (ENSG00000122133), score: 0.8
PARP15poly (ADP-ribose) polymerase family, member 15 (ENSG00000173200), score: 0.73
PLA2G2Dphospholipase A2, group IID (ENSG00000117215), score: 0.85
PLEKHB2pleckstrin homology domain containing, family B (evectins) member 2 (ENSG00000115762), score: -0.77
PRHOXNBparahox cluster neighbor (ENSG00000183463), score: 0.89
PRSSL1protease, serine-like 1 (ENSG00000185198), score: 0.86
PSKH2protein serine kinase H2 (ENSG00000147613), score: 0.92
RAB1BRAB1B, member RAS oncogene family (ENSG00000174903), score: -0.91
RBM6RNA binding motif protein 6 (ENSG00000004534), score: -0.78
RGS13regulator of G-protein signaling 13 (ENSG00000127074), score: 0.8
RNASE1ribonuclease, RNase A family, 1 (pancreatic) (ENSG00000129538), score: -0.76
RPL36ALribosomal protein L36a-like (ENSG00000165502), score: -0.9
SCLT1sodium channel and clathrin linker 1 (ENSG00000151466), score: 0.9
SEPT12septin 12 (ENSG00000140623), score: 0.71
SERINC4serine incorporator 4 (ENSG00000184716), score: 0.98
SERPINA12serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 12 (ENSG00000165953), score: 0.86
SIP1survival of motor neuron protein interacting protein 1 (ENSG00000092208), score: -0.84
SNRPFsmall nuclear ribonucleoprotein polypeptide F (ENSG00000139343), score: -0.69
SRD5A3steroid 5 alpha-reductase 3 (ENSG00000128039), score: 0.7
SRP14signal recognition particle 14kDa (homologous Alu RNA binding protein) (ENSG00000140319), score: -0.9
TBX19T-box 19 (ENSG00000143178), score: 0.78
TLR6toll-like receptor 6 (ENSG00000174130), score: 0.78
TNNtenascin N (ENSG00000120332), score: 0.8
TRPM5transient receptor potential cation channel, subfamily M, member 5 (ENSG00000070985), score: 0.78
TTC24tetratricopeptide repeat domain 24 (ENSG00000187862), score: 0.74
YAP1Yes-associated protein 1 (ENSG00000137693), score: -0.69
ZBTB3zinc finger and BTB domain containing 3 (ENSG00000185670), score: 0.77
ZNF114zinc finger protein 114 (ENSG00000178150), score: 0.81
ZNF146zinc finger protein 146 (ENSG00000167635), score: -0.83
ZNF16zinc finger protein 16 (ENSG00000170631), score: 0.73
ZNHIT3zinc finger, HIT type 3 (ENSG00000108278), score: -0.73
ZSWIM3zinc finger, SWIM-type containing 3 (ENSG00000132801), score: 0.73
Non-Entrez genes
ENSG00000131142Unknown, score: 0.69
ENSG00000007392Unknown, score: 1
ENSG00000091527Unknown, score: 0.81
ENSG00000170631Unknown, score: 0.88
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 |
| mml_br_m2_ca1 | mml | br | m | 2 |
| mml_br_m1_ca1 | mml | br | m | 1 |
| mml_br_f_ca1 | mml | br | f | _ |
| mml_cb_m_ca1 | mml | cb | m | _ |
| mml_cb_f_ca1 | mml | cb | f | _ |
| mml_ts_m2_ca1 | mml | ts | m | 2 |
| mml_ht_f_ca1 | mml | ht | f | _ |
| mml_ts_m1_ca1 | mml | ts | m | 1 |
| mml_ht_m_ca1 | mml | ht | m | _ |
| mml_kd_m_ca1 | mml | kd | m | _ |
| mml_kd_f_ca1 | mml | kd | f | _ |
| 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
