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Module #46, TG: 2.8, TC: 1.2, 120 probes, 117 Entrez genes, 16 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.
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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:0021591 | 2.399e-02 | 0.0457 | 2
AQP1, MNAT1 | 5 | ventricular system development |
| GO:0015031 | 2.817e-02 | 6.123 | 15
AKTIP, ATG10, C11orf2, EXOC1, GIPC1, MIF, NDUFA13, PEX10, RAB11B, SNX13, SNX22, TRIP6, TRNT1, VPS35, YIPF5 | 670 | protein transport |
| GO:0045184 | 3.142e-02 | 6.215 | 15
AKTIP, ATG10, C11orf2, EXOC1, GIPC1, MIF, NDUFA13, PEX10, RAB11B, SNX13, SNX22, TRIP6, TRNT1, VPS35, YIPF5 | 680 | establishment of protein localization |
| GO:0033036 | 4.598e-02 | 8.646 | 18
AKTIP, ATG10, C11orf2, CLN8, EXOC1, GIPC1, MIF, NDUFA13, PEX10, PSAP, RAB11B, RBM8A, SNX13, SNX22, TRIP6, TRNT1, VPS35, YIPF5 | 946 | macromolecule localization |
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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:0031464 | 1.474e-02 | 0.053 | 2
CRBN, ERCC8 | 6 | Cul4A-RING ubiquitin ligase complex |
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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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| Id | Pvalue | ExpCount | Count | Size | Term |
| GO:0008135 | 2.856e-02 | 0.4786 | 4
EEF1G, EEF2, EIF4E, GSPT1 | 54 | translation factor activity, nucleic acid binding |
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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
ACOT8acyl-CoA thioesterase 8 (ENSG00000101473), score: 0.68
AIDAaxin interactor, dorsalization associated (ENSG00000186063), score: -0.73
AKTIPAKT interacting protein (ENSG00000166971), score: -0.66
ATG10ATG10 autophagy related 10 homolog (S. cerevisiae) (ENSG00000152348), score: 0.75
ATG12ATG12 autophagy related 12 homolog (S. cerevisiae) (ENSG00000145782), score: -0.65
BAT5HLA-B associated transcript 5 (ENSG00000204422), score: 1
C11orf2chromosome 11 open reading frame 2 (ENSG00000149823), score: 0.63
C12orf52chromosome 12 open reading frame 52 (ENSG00000139405), score: 0.66
C14orf80chromosome 14 open reading frame 80 (ENSG00000185347), score: 0.69
C2orf49chromosome 2 open reading frame 49 (ENSG00000135974), score: -0.75
C3orf16chromosome 3 open reading frame 16 (ENSG00000206199), score: 0.8
C5orf41chromosome 5 open reading frame 41 (ENSG00000164463), score: -0.64
C5orf45chromosome 5 open reading frame 45 (ENSG00000161010), score: 0.83
C6orf162chromosome 6 open reading frame 162 (ENSG00000111850), score: -0.65
C8orf38chromosome 8 open reading frame 38 (ENSG00000156170), score: -0.71
CD72CD72 molecule (ENSG00000137101), score: 0.77
CDC26cell division cycle 26 homolog (S. cerevisiae) (ENSG00000176386), score: -0.78
CECR5cat eye syndrome chromosome region, candidate 5 (ENSG00000069998), score: 0.71
CIITAclass II, major histocompatibility complex, transactivator (ENSG00000179583), score: 0.79
CITED4Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 4 (ENSG00000179862), score: 0.69
CLCC1chloride channel CLIC-like 1 (ENSG00000121940), score: -0.64
CLN8ceroid-lipofuscinosis, neuronal 8 (epilepsy, progressive with mental retardation) (ENSG00000182372), score: 0.72
CLUL1clusterin-like 1 (retinal) (ENSG00000079101), score: 0.69
CNIH4cornichon homolog 4 (Drosophila) (ENSG00000143771), score: -0.65
COASYCoA synthase (ENSG00000068120), score: 0.62
COMMD2COMM domain containing 2 (ENSG00000114744), score: -0.75
CRBNcereblon (ENSG00000113851), score: -0.65
CRIPTcysteine-rich PDZ-binding protein (ENSG00000119878), score: -0.71
DLEC1deleted in lung and esophageal cancer 1 (ENSG00000008226), score: 0.74
DOHHdeoxyhypusine hydroxylase/monooxygenase (ENSG00000129932), score: 0.65
DPH1DPH1 homolog (S. cerevisiae) (ENSG00000108963), score: 0.71
DUS4Ldihydrouridine synthase 4-like (S. cerevisiae) (ENSG00000105865), score: -0.64
DUSP11dual specificity phosphatase 11 (RNA/RNP complex 1-interacting) (ENSG00000144048), score: -0.68
EEF1Geukaryotic translation elongation factor 1 gamma (ENSG00000149016), score: 0.93
EEF2eukaryotic translation elongation factor 2 (ENSG00000167658), score: 0.65
ELAC2elaC homolog 2 (E. coli) (ENSG00000006744), score: 0.82
ERCC8excision repair cross-complementing rodent repair deficiency, complementation group 8 (ENSG00000049167), score: -0.64
EXOC1exocyst complex component 1 (ENSG00000090989), score: -0.65
FABP6fatty acid binding protein 6, ileal (ENSG00000170231), score: 0.7
FAM103A1family with sequence similarity 103, member A1 (ENSG00000169612), score: -0.83
FAM119Afamily with sequence similarity 119, member A (ENSG00000144401), score: -0.66
FAM156Afamily with sequence similarity 156, member A (ENSG00000182646), score: -0.82
FNTBfarnesyltransferase, CAAX box, beta (ENSG00000125954), score: 0.62
FRA10AC1fragile site, folic acid type, rare, fra(10)(q23.3) or fra(10)(q24.2) candidate 1 (ENSG00000148690), score: -0.65
GIPC1GIPC PDZ domain containing family, member 1 (ENSG00000123159), score: 0.63
GPR141G protein-coupled receptor 141 (ENSG00000187037), score: 0.8
GPR44G protein-coupled receptor 44 (ENSG00000183134), score: 0.62
GRWD1glutamate-rich WD repeat containing 1 (ENSG00000105447), score: 0.65
GSPT1G1 to S phase transition 1 (ENSG00000103342), score: -0.66
GUK1guanylate kinase 1 (ENSG00000143774), score: 0.75
HERC4hect domain and RLD 4 (ENSG00000148634), score: -0.64
HSPA1Lheat shock 70kDa protein 1-like (ENSG00000204390), score: -0.64
IL18BPinterleukin 18 binding protein (ENSG00000137496), score: 0.66
IL9Rinterleukin 9 receptor (ENSG00000124334), score: 0.92
INMTindolethylamine N-methyltransferase (ENSG00000106125), score: 0.7
KINKIN, antigenic determinant of recA protein homolog (mouse) (ENSG00000151657), score: -0.65
LGALS3BPlectin, galactoside-binding, soluble, 3 binding protein (ENSG00000108679), score: 0.62
LOC100131693eukaryotic translation initiation factor 4E pseudogene (ENSG00000151247), score: -0.71
LOC100133770hypothetical protein LOC100133770 (ENSG00000069329), score: -0.66
LOC652522similar to Werner syndrome protein (ENSG00000165392), score: -0.66
LPAR6lysophosphatidic acid receptor 6 (ENSG00000139679), score: -0.66
MIFmacrophage migration inhibitory factor (glycosylation-inhibiting factor) (ENSG00000133460), score: 0.83
MLST8MTOR associated protein, LST8 homolog (S. cerevisiae) (ENSG00000167965), score: 0.63
MNAT1menage a trois homolog 1, cyclin H assembly factor (Xenopus laevis) (ENSG00000020426), score: -0.66
MYL5myosin, light chain 5, regulatory (ENSG00000215375), score: 0.82
NDOR1NADPH dependent diflavin oxidoreductase 1 (ENSG00000188566), score: 0.65
NOL8nucleolar protein 8 (ENSG00000198000), score: -0.74
NPBneuropeptide B (ENSG00000183979), score: 0.79
NPRL3nitrogen permease regulator-like 3 (S. cerevisiae) (ENSG00000103148), score: 0.71
NT5DC25'-nucleotidase domain containing 2 (ENSG00000168268), score: 0.64
ODF2Louter dense fiber of sperm tails 2-like (ENSG00000122417), score: -0.7
PABPC1Lpoly(A) binding protein, cytoplasmic 1-like (ENSG00000101104), score: 0.66
PEX10peroxisomal biogenesis factor 10 (ENSG00000157911), score: 0.63
PHF14PHD finger protein 14 (ENSG00000106443), score: -0.64
PIGCphosphatidylinositol glycan anchor biosynthesis, class C (ENSG00000135845), score: -0.82
PIK3CDphosphoinositide-3-kinase, catalytic, delta polypeptide (ENSG00000171608), score: 0.72
PRICKLE4prickle homolog 4 (Drosophila) (ENSG00000124593), score: 0.65
PSAPprosaposin (ENSG00000197746), score: 0.67
RAB11BRAB11B, member RAS oncogene family (ENSG00000185236), score: 0.66
RABAC1Rab acceptor 1 (prenylated) (ENSG00000105404), score: 0.62
RBM8ARNA binding motif protein 8A (ENSG00000131795), score: -0.82
RSPO1R-spondin homolog (Xenopus laevis) (ENSG00000169218), score: 0.81
SCNN1Dsodium channel, nonvoltage-gated 1, delta (ENSG00000162572), score: 0.75
SCRIBscribbled homolog (Drosophila) (ENSG00000180900), score: 0.68
SETD6SET domain containing 6 (ENSG00000103037), score: -0.64
SFRS12splicing factor, arginine/serine-rich 12 (ENSG00000153914), score: -0.73
SLA2Src-like-adaptor 2 (ENSG00000101082), score: 0.67
SLC18A2solute carrier family 18 (vesicular monoamine), member 2 (ENSG00000165646), score: 0.88
SLC19A1solute carrier family 19 (folate transporter), member 1 (ENSG00000173638), score: 0.85
SNAPC5small nuclear RNA activating complex, polypeptide 5, 19kDa (ENSG00000174446), score: 0.62
SNX13sorting nexin 13 (ENSG00000071189), score: -0.72
SNX22sorting nexin 22 (ENSG00000157734), score: 0.92
SR140U2-associated SR140 protein (ENSG00000163714), score: -0.64
SURF6surfeit 6 (ENSG00000148296), score: 0.71
SUZ12suppressor of zeste 12 homolog (Drosophila) (ENSG00000178691), score: -0.66
TAS2R14taste receptor, type 2, member 14 (ENSG00000212127), score: 0.66
TBC1D8TBC1 domain family, member 8 (with GRAM domain) (ENSG00000204634), score: 0.77
TH1LTH1-like (Drosophila) (ENSG00000101158), score: 0.73
THUMPD1THUMP domain containing 1 (ENSG00000066654), score: -0.75
TMEM199transmembrane protein 199 (ENSG00000244045), score: -0.83
TMEM79transmembrane protein 79 (ENSG00000163472), score: 0.78
TMEM85transmembrane protein 85 (ENSG00000128463), score: 0.74
TRDMT1tRNA aspartic acid methyltransferase 1 (ENSG00000107614), score: -0.64
TRIM69tripartite motif-containing 69 (ENSG00000185880), score: 0.78
TRIP6thyroid hormone receptor interactor 6 (ENSG00000087077), score: 0.68
TRNT1tRNA nucleotidyl transferase, CCA-adding, 1 (ENSG00000072756), score: -0.71
TSPAN16tetraspanin 16 (ENSG00000130167), score: 0.8
UTS2urotensin 2 (ENSG00000049247), score: 0.85
WDR13WD repeat domain 13 (ENSG00000101940), score: 0.67
WDR83WD repeat domain 83 (ENSG00000123154), score: 0.63
YIPF5Yip1 domain family, member 5 (ENSG00000145817), score: -0.64
YJEFN3YjeF N-terminal domain containing 3 (ENSG00000186010), score: 0.62
ZACNzinc activated ligand-gated ion channel (ENSG00000186919), score: 0.66
ZC3H6zinc finger CCCH-type containing 6 (ENSG00000188177), score: -0.73
ZMAT1zinc finger, matrin type 1 (ENSG00000166432), score: -0.68
ZNF354Czinc finger protein 354C (ENSG00000177932), score: 0.7
ZNF581zinc finger protein 581 (ENSG00000171425), score: 0.72
Non-Entrez genes
ENSG00000204634Unknown, score: -0.97
ENSG00000129932Unknown, score: 0.71
ENSG00000123159Unknown, score: -0.64
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 |
| hsa_br_m1_ca1 | hsa | br | m | 1 |
| hsa_br_f_ca1 | hsa | br | f | _ |
| hsa_ht_m2_ca1 | hsa | ht | m | 2 |
| hsa_cb_m_ca1 | hsa | cb | m | _ |
| hsa_cb_f_ca1 | hsa | cb | f | _ |
| hsa_ht_f_ca1 | hsa | ht | f | _ |
| hsa_ts_m1_ca1 | hsa | ts | m | 1 |
| hsa_lv_m1_ca1 | hsa | lv | m | 1 |
| hsa_kd_m2_ca1 | hsa | kd | m | 2 |
| hsa_br_m6_ca1 | hsa | br | m | 6 |
| hsa_kd_f_ca1 | hsa | kd | f | _ |
| hsa_ht_m1_ca1 | hsa | ht | m | 1 |
| hsa_lv_m2_ca1 | hsa | lv | m | 2 |
| hsa_br_m3_ca1 | hsa | br | m | 3 |
| hsa_br_m7_ca1 | hsa | br | m | 7 |
| hsa_kd_m1_ca1 | hsa | kd | m | 1 |
© 2008-2010 Computational Biology Group, Department of Medical Genetics,
University of Lausanne, Switzerland
