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Module #197, TG: 2.6, TC: 2.4, 102 probes, 102 Entrez genes, 10 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:0045017 | 1.385e-02 | 0.5651 | 5
CHPT1, PEX7, PIGK, PIGL, PIGS | 32 | glycerolipid biosynthetic process |
| GO:0046474 | 3.521e-02 | 0.4238 | 4
CHPT1, PIGK, PIGL, PIGS | 24 | glycerophospholipid biosynthetic process |
| GO:0016255 | 4.143e-02 | 0.05298 | 2
PIGK, PIGS | 3 | attachment of GPI anchor to protein |
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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:0042765 | 1.757e-02 | 0.05432 | 2
PIGK, PIGS | 3 | GPI-anchor transamidase 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:0003923 | 3.342e-02 | 0.05147 | 2
PIGK, PIGS | 3 | GPI-anchor transamidase activity |
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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 |
| 00563 | 3.182e-02 | 0.199 | 3
PIGK, PIGL, PIGS | 11 | Glycosylphosphatidylinositol(GPI)-anchor biosynthesis |
| 05012 | 4.160e-02 | 0.4885 | 4
COX1, CYTB, ND2, UBE2G1 | 27 | Parkinson's disease |
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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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| Id | Pvalue | ExpCount | Count | Size |
| MT | 3.823e-02 | 0.1097 | 3
COX1, CYTB, ND2 | 6 |
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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
AASDHPPTaminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase (ENSG00000149313), score: -0.62
AATFapoptosis antagonizing transcription factor (ENSG00000108270), score: -0.61
ACER2alkaline ceramidase 2 (ENSG00000177076), score: 0.61
ACYP2acylphosphatase 2, muscle type (ENSG00000170634), score: -0.9
ADCK1aarF domain containing kinase 1 (ENSG00000063761), score: -0.74
ALKBH2alkB, alkylation repair homolog 2 (E. coli) (ENSG00000189046), score: 0.72
AMBRA1autophagy/beclin-1 regulator 1 (ENSG00000110497), score: 0.72
ANAPC4anaphase promoting complex subunit 4 (ENSG00000053900), score: -0.61
ARSKarylsulfatase family, member K (ENSG00000164291), score: 0.65
ASB1ankyrin repeat and SOCS box-containing 1 (ENSG00000065802), score: 0.69
ATG16L1ATG16 autophagy related 16-like 1 (S. cerevisiae) (ENSG00000085978), score: 0.68
ATG4CATG4 autophagy related 4 homolog C (S. cerevisiae) (ENSG00000125703), score: 0.65
ATP13A3ATPase type 13A3 (ENSG00000133657), score: 0.67
ATP2B4ATPase, Ca++ transporting, plasma membrane 4 (ENSG00000058668), score: -0.84
BLVRAbiliverdin reductase A (ENSG00000106605), score: -0.64
C11orf46chromosome 11 open reading frame 46 (ENSG00000152219), score: 0.61
C11orf57chromosome 11 open reading frame 57 (ENSG00000150776), score: -0.63
C12orf66chromosome 12 open reading frame 66 (ENSG00000174206), score: 0.65
C13orf31chromosome 13 open reading frame 31 (ENSG00000179630), score: 0.81
C1orf123chromosome 1 open reading frame 123 (ENSG00000162384), score: 0.7
C20orf43chromosome 20 open reading frame 43 (ENSG00000022277), score: -0.73
C3orf39chromosome 3 open reading frame 39 (ENSG00000144647), score: 0.69
CCDC82coiled-coil domain containing 82 (ENSG00000149231), score: -0.63
CDC123cell division cycle 123 homolog (S. cerevisiae) (ENSG00000151465), score: -0.79
CDCA3cell division cycle associated 3 (ENSG00000111665), score: 0.82
CHD1Lchromodomain helicase DNA binding protein 1-like (ENSG00000131778), score: -0.63
CHPT1choline phosphotransferase 1 (ENSG00000111666), score: -0.65
COX1cytochrome c oxidase subunit I (ENSG00000198804), score: -0.88
CYLDcylindromatosis (turban tumor syndrome) (ENSG00000083799), score: -0.63
CYTBcytochrome b (ENSG00000198727), score: -1
CYTH1cytohesin 1 (ENSG00000108669), score: -0.65
DDX1DEAD (Asp-Glu-Ala-Asp) box polypeptide 1 (ENSG00000079785), score: 0.63
DDX47DEAD (Asp-Glu-Ala-Asp) box polypeptide 47 (ENSG00000213782), score: -0.61
ERCC6excision repair cross-complementing rodent repair deficiency, complementation group 6 (ENSG00000225830), score: -0.74
ERICH1glutamate-rich 1 (ENSG00000104714), score: -0.68
EXD2exonuclease 3'-5' domain containing 2 (ENSG00000081177), score: -0.62
FAM73Afamily with sequence similarity 73, member A (ENSG00000180488), score: 0.64
FAM82A2family with sequence similarity 82, member A2 (ENSG00000137824), score: 0.65
FBXO22F-box protein 22 (ENSG00000167196), score: 0.66
FBXO3F-box protein 3 (ENSG00000110429), score: 0.59
FRA10AC1fragile site, folic acid type, rare, fra(10)(q23.3) or fra(10)(q24.2) candidate 1 (ENSG00000148690), score: -0.63
FUT10fucosyltransferase 10 (alpha (1,3) fucosyltransferase) (ENSG00000172728), score: 0.81
GARSglycyl-tRNA synthetase (ENSG00000106105), score: 0.62
GBGT1globoside alpha-1,3-N-acetylgalactosaminyltransferase 1 (ENSG00000148288), score: 0.58
GCNT7glucosaminyl (N-acetyl) transferase family member 7 (ENSG00000124091), score: 0.61
GPR107G protein-coupled receptor 107 (ENSG00000148358), score: -0.69
GTF3Ageneral transcription factor IIIA (ENSG00000122034), score: -0.62
IKIK cytokine, down-regulator of HLA II (ENSG00000113141), score: -0.75
IKBIPIKBKB interacting protein (ENSG00000166130), score: 0.63
INVSinversin (ENSG00000119509), score: -0.6
IPPintracisternal A particle-promoted polypeptide (ENSG00000197429), score: 0.97
KCTD5potassium channel tetramerisation domain containing 5 (ENSG00000167977), score: -0.66
KIAA0174KIAA0174 (ENSG00000182149), score: -0.6
LYSMD4LysM, putative peptidoglycan-binding, domain containing 4 (ENSG00000183060), score: -0.69
ME2malic enzyme 2, NAD(+)-dependent, mitochondrial (ENSG00000082212), score: -0.69
METRNLmeteorin, glial cell differentiation regulator-like (ENSG00000176845), score: -0.62
MRPL19mitochondrial ribosomal protein L19 (ENSG00000115364), score: 0.67
N4BP1NEDD4 binding protein 1 (ENSG00000102921), score: 0.68
NAGAN-acetylgalactosaminidase, alpha- (ENSG00000198951), score: 0.59
NARFnuclear prelamin A recognition factor (ENSG00000141562), score: -0.65
ND2MTND2 (ENSG00000198763), score: -0.96
NIF3L1NIF3 NGG1 interacting factor 3-like 1 (S. pombe) (ENSG00000196290), score: 0.72
NOXO1NADPH oxidase organizer 1 (ENSG00000196408), score: 0.96
NSUN2NOP2/Sun domain family, member 2 (ENSG00000037474), score: -0.74
OTOL1otolin 1 homolog (zebrafish) (ENSG00000182447), score: 0.7
PDE6Gphosphodiesterase 6G, cGMP-specific, rod, gamma (ENSG00000185527), score: 0.65
PEX7peroxisomal biogenesis factor 7 (ENSG00000112357), score: 0.61
PFKFB36-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (ENSG00000170525), score: -0.61
PGRprogesterone receptor (ENSG00000082175), score: 0.66
PHF12PHD finger protein 12 (ENSG00000109118), score: 0.64
PHF21APHD finger protein 21A (ENSG00000135365), score: 0.65
PIGKphosphatidylinositol glycan anchor biosynthesis, class K (ENSG00000142892), score: 0.74
PIGLphosphatidylinositol glycan anchor biosynthesis, class L (ENSG00000108474), score: 0.74
PIGSphosphatidylinositol glycan anchor biosynthesis, class S (ENSG00000087111), score: 0.76
PODNpodocan (ENSG00000174348), score: 0.63
PYCRLpyrroline-5-carboxylate reductase-like (ENSG00000104524), score: 0.64
RBPJLrecombination signal binding protein for immunoglobulin kappa J region-like (ENSG00000124232), score: 0.64
RIC8Bresistance to inhibitors of cholinesterase 8 homolog B (C. elegans) (ENSG00000111785), score: 0.84
RPS6KA6ribosomal protein S6 kinase, 90kDa, polypeptide 6 (ENSG00000072133), score: 0.69
SAP30LSAP30-like (ENSG00000164576), score: 0.71
SFRS8splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot homolog, Drosophila) (ENSG00000061936), score: 0.71
SLC35B3solute carrier family 35, member B3 (ENSG00000124786), score: -0.65
SLC38A8solute carrier family 38, member 8 (ENSG00000166558), score: 0.96
SNX13sorting nexin 13 (ENSG00000071189), score: 0.63
SPG20spastic paraplegia 20 (Troyer syndrome) (ENSG00000133104), score: -0.65
STAMBPSTAM binding protein (ENSG00000124356), score: 0.66
STT3BSTT3, subunit of the oligosaccharyltransferase complex, homolog B (S. cerevisiae) (ENSG00000163527), score: 0.63
THYN1thymocyte nuclear protein 1 (ENSG00000151500), score: -0.74
TIAL1TIA1 cytotoxic granule-associated RNA binding protein-like 1 (ENSG00000151923), score: 0.59
TMCO6transmembrane and coiled-coil domains 6 (ENSG00000113119), score: 0.65
TMEM18transmembrane protein 18 (ENSG00000151353), score: -0.7
TMEM184Ctransmembrane protein 184C (ENSG00000164168), score: 0.88
TOE1target of EGR1, member 1 (nuclear) (ENSG00000132773), score: 0.67
UBE2G1ubiquitin-conjugating enzyme E2G 1 (UBC7 homolog, yeast) (ENSG00000132388), score: -0.96
UBXN2AUBX domain protein 2A (ENSG00000173960), score: 0.61
UNC50unc-50 homolog (C. elegans) (ENSG00000115446), score: -0.69
USP19ubiquitin specific peptidase 19 (ENSG00000172046), score: 0.64
UTP20UTP20, small subunit (SSU) processome component, homolog (yeast) (ENSG00000120800), score: 0.6
ZC3H15zinc finger CCCH-type containing 15 (ENSG00000065548), score: -1
ZNF346zinc finger protein 346 (ENSG00000113761), score: -0.61
ZNF512zinc finger protein 512 (ENSG00000243943), score: 0.73
ZWILCHZwilch, kinetochore associated, homolog (Drosophila) (ENSG00000174442), score: 0.7
Non-Entrez genes
Unknown, score:
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 |
| mdo_lv_f_ca1 | mdo | lv | f | _ |
| mdo_br_f_ca1 | mdo | br | f | _ |
| mdo_lv_m_ca1 | mdo | lv | m | _ |
| mdo_kd_m_ca1 | mdo | kd | m | _ |
| mdo_kd_f_ca1 | mdo | kd | f | _ |
| mdo_ht_m_ca1 | mdo | ht | m | _ |
| mdo_br_m_ca1 | mdo | br | m | _ |
| mdo_cb_f_ca1 | mdo | cb | f | _ |
| mdo_cb_m_ca1 | mdo | cb | m | _ |
| mdo_ht_f_ca1 | mdo | ht | f | _ |
© 2008-2010 Computational Biology Group, Department of Medical Genetics,
University of Lausanne, Switzerland
