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Module #290, TG: 2.4, TC: 2.4, 94 probes, 94 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.
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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:0000050 | 1.830e-02 | 0.03487 | 2 HTT, OTC | 2 | urea cycle |
GO:0019627 | 1.830e-02 | 0.03487 | 2 HTT, OTC | 2 | urea metabolic process |
GO:0043604 | 1.830e-02 | 0.03487 | 2 HTT, OTC | 2 | amide biosynthetic process |
GO:0060011 | 1.830e-02 | 0.03487 | 2 ACVR2A, FSHB | 2 | Sertoli cell proliferation |
GO:2000021 | 2.996e-02 | 0.401 | 4 AVPR1A, BDKRB1, GCLM, IBTK | 23 | regulation of ion homeostasis |
GO:0042713 | 4.063e-02 | 0.0523 | 2 ACVR2A, AVPR1A | 3 | sperm ejaculation |
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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:0070761 | 1.607e-02 | 0.05127 | 2 NOP58, ZNHIT6 | 3 | pre-snoRNP 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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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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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
ACER3alkaline ceramidase 3 (ENSG00000078124), score: 0.73
ACVR2Aactivin A receptor, type IIA (ENSG00000121989), score: 0.75
AKR1D1aldo-keto reductase family 1, member D1 (delta 4-3-ketosteroid-5-beta-reductase) (ENSG00000122787), score: 0.65
ANKRD40ankyrin repeat domain 40 (ENSG00000154945), score: -0.68
ARFIP1ADP-ribosylation factor interacting protein 1 (ENSG00000164144), score: 0.64
ASAH1N-acylsphingosine amidohydrolase (acid ceramidase) 1 (ENSG00000104763), score: 0.64
AVPR1Aarginine vasopressin receptor 1A (ENSG00000166148), score: 0.68
BDKRB1bradykinin receptor B1 (ENSG00000100739), score: 0.81
C18orf8chromosome 18 open reading frame 8 (ENSG00000141452), score: 0.62
C6orf62chromosome 6 open reading frame 62 (ENSG00000112308), score: 0.68
CA6carbonic anhydrase VI (ENSG00000131686), score: 0.62
CCDC127coiled-coil domain containing 127 (ENSG00000164366), score: -0.69
CCNHcyclin H (ENSG00000134480), score: -0.67
CD86CD86 molecule (ENSG00000114013), score: 0.68
CDKN2AIPCDKN2A interacting protein (ENSG00000168564), score: -0.74
CHRNA9cholinergic receptor, nicotinic, alpha 9 (ENSG00000174343), score: 0.65
CLK4CDC-like kinase 4 (ENSG00000113240), score: -0.71
CLPXClpX caseinolytic peptidase X homolog (E. coli) (ENSG00000166855), score: 0.68
COL4A3BPcollagen, type IV, alpha 3 (Goodpasture antigen) binding protein (ENSG00000113163), score: 0.65
COPAcoatomer protein complex, subunit alpha (ENSG00000122218), score: -0.77
CUEDC2CUE domain containing 2 (ENSG00000107874), score: -0.68
CYSLTR1cysteinyl leukotriene receptor 1 (ENSG00000173198), score: 0.63
DBR1debranching enzyme homolog 1 (S. cerevisiae) (ENSG00000138231), score: 0.62
DIRC2disrupted in renal carcinoma 2 (ENSG00000138463), score: 0.71
DPP8dipeptidyl-peptidase 8 (ENSG00000074603), score: 0.64
EDEM3ER degradation enhancer, mannosidase alpha-like 3 (ENSG00000116406), score: 0.69
EEF1E1eukaryotic translation elongation factor 1 epsilon 1 (ENSG00000124802), score: -0.69
EREGepiregulin (ENSG00000124882), score: 0.65
EXOC8exocyst complex component 8 (ENSG00000116903), score: 0.63
FAM63Bfamily with sequence similarity 63, member B (ENSG00000128923), score: 0.66
FSHBfollicle stimulating hormone, beta polypeptide (ENSG00000131808), score: 0.89
GCLMglutamate-cysteine ligase, modifier subunit (ENSG00000023909), score: 0.64
GPN1GPN-loop GTPase 1 (ENSG00000198522), score: 0.72
HNF4Ghepatocyte nuclear factor 4, gamma (ENSG00000164749), score: 0.65
HTThuntingtin (ENSG00000197386), score: -0.74
IBTKinhibitor of Bruton agammaglobulinemia tyrosine kinase (ENSG00000005700), score: 0.62
ITGA4integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor) (ENSG00000115232), score: 0.68
KIAA0907KIAA0907 (ENSG00000132680), score: 0.67
KLHL8kelch-like 8 (Drosophila) (ENSG00000145332), score: 0.7
LRIG3leucine-rich repeats and immunoglobulin-like domains 3 (ENSG00000139263), score: 0.7
LRRC15leucine rich repeat containing 15 (ENSG00000172061), score: 0.7
LRRC31leucine rich repeat containing 31 (ENSG00000114248), score: 0.83
MAP2K5mitogen-activated protein kinase kinase 5 (ENSG00000137764), score: -0.75
MBNL2muscleblind-like 2 (Drosophila) (ENSG00000139793), score: -0.8
MED23mediator complex subunit 23 (ENSG00000112282), score: 0.66
MTA1metastasis associated 1 (ENSG00000182979), score: -0.71
MTAPmethylthioadenosine phosphorylase (ENSG00000099810), score: 0.66
MYNNmyoneurin (ENSG00000085274), score: 0.69
NOP58NOP58 ribonucleoprotein homolog (yeast) (ENSG00000055044), score: 0.62
NPC1Niemann-Pick disease, type C1 (ENSG00000141458), score: 0.66
NRBP1nuclear receptor binding protein 1 (ENSG00000115216), score: -0.69
NT5E5'-nucleotidase, ecto (CD73) (ENSG00000135318), score: 0.81
OTCornithine carbamoyltransferase (ENSG00000036473), score: 0.68
PARP6poly (ADP-ribose) polymerase family, member 6 (ENSG00000137817), score: -0.75
PEX11Aperoxisomal biogenesis factor 11 alpha (ENSG00000166821), score: 0.69
PGM3phosphoglucomutase 3 (ENSG00000013375), score: 0.88
PIGXphosphatidylinositol glycan anchor biosynthesis, class X (ENSG00000163964), score: 0.62
POLR3Fpolymerase (RNA) III (DNA directed) polypeptide F, 39 kDa (ENSG00000132664), score: 0.63
QPCTglutaminyl-peptide cyclotransferase (ENSG00000115828), score: 0.71
RAB11ARAB11A, member RAS oncogene family (ENSG00000103769), score: 0.73
RANBP3RAN binding protein 3 (ENSG00000031823), score: -0.71
RECKreversion-inducing-cysteine-rich protein with kazal motifs (ENSG00000122707), score: 0.71
SCUBE3signal peptide, CUB domain, EGF-like 3 (ENSG00000146197), score: 0.62
SERINC5serine incorporator 5 (ENSG00000164300), score: 0.66
SETD5SET domain containing 5 (ENSG00000168137), score: -0.77
SLC17A5solute carrier family 17 (anion/sugar transporter), member 5 (ENSG00000119899), score: 0.73
SLC39A9solute carrier family 39 (zinc transporter), member 9 (ENSG00000029364), score: 0.92
SRSF5serine/arginine-rich splicing factor 5 (ENSG00000100650), score: -0.72
STOML2stomatin (EPB72)-like 2 (ENSG00000165283), score: -0.72
TARSL2threonyl-tRNA synthetase-like 2 (ENSG00000185418), score: -0.72
TCF12transcription factor 12 (ENSG00000140262), score: 0.66
TECtec protein tyrosine kinase (ENSG00000135605), score: 0.62
TMEM33transmembrane protein 33 (ENSG00000109133), score: 0.67
TUBGCP2tubulin, gamma complex associated protein 2 (ENSG00000130640), score: -0.71
TWISTNBTWIST neighbor (ENSG00000105849), score: 0.66
TXNDC15thioredoxin domain containing 15 (ENSG00000113621), score: 0.62
UBA6ubiquitin-like modifier activating enzyme 6 (ENSG00000033178), score: 0.67
UBL3ubiquitin-like 3 (ENSG00000122042), score: 0.68
UNC50unc-50 homolog (C. elegans) (ENSG00000115446), score: 0.63
USP20ubiquitin specific peptidase 20 (ENSG00000136878), score: -0.78
VAT1vesicle amine transport protein 1 homolog (T. californica) (ENSG00000108828), score: 0.66
VGLL1vestigial like 1 (Drosophila) (ENSG00000102243), score: 0.71
VPS4Bvacuolar protein sorting 4 homolog B (S. cerevisiae) (ENSG00000119541), score: 0.66
WDR3WD repeat domain 3 (ENSG00000065183), score: 0.63
WDR44WD repeat domain 44 (ENSG00000131725), score: 0.63
XKR9XK, Kell blood group complex subunit-related family, member 9 (ENSG00000221947), score: 0.78
XRCC6BP1XRCC6 binding protein 1 (ENSG00000166896), score: 0.66
YTHDC2YTH domain containing 2 (ENSG00000047188), score: -0.72
ZBTB49zinc finger and BTB domain containing 49 (ENSG00000168826), score: -0.72
ZC3H12Dzinc finger CCCH-type containing 12D (ENSG00000178199), score: 1
ZMPSTE24zinc metallopeptidase (STE24 homolog, S. cerevisiae) (ENSG00000084073), score: 0.62
ZNF326zinc finger protein 326 (ENSG00000162664), score: 0.75
ZNHIT6zinc finger, HIT type 6 (ENSG00000117174), score: -0.74
ZW10ZW10, kinetochore associated, homolog (Drosophila) (ENSG00000086827), score: 0.66
Non-Entrez genes
Unknown, score:
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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 |
oan_kd_m_ca1 | oan | kd | m | _ |
oan_kd_f_ca1 | oan | kd | f | _ |
oan_lv_f_ca1 | oan | lv | f | _ |
oan_lv_m_ca1 | oan | lv | m | _ |
© 2008-2010 Computational Biology Group, Department of Medical Genetics,
University of Lausanne, Switzerland