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Module #617, TG: 2.8, TC: 2, 99 probes, 99 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:0048583 | 1.563e-02 | 1.214 | 7
CALCA, ERAP1, F11, IL12A, IL6R, SCG2, TNFSF13 | 123 | regulation of response to stimulus |
| GO:0051707 | 3.268e-02 | 1.026 | 6
CCDC130, ERAP1, IL12A, IL6R, S100A12, TICAM1 | 104 | response to other organism |
| GO:0030595 | 3.427e-02 | 0.1678 | 3
EDNRB, IL6R, SCG2 | 17 | leukocyte chemotaxis |
| GO:0060326 | 3.427e-02 | 0.1678 | 3
EDNRB, IL6R, SCG2 | 17 | cell chemotaxis |
| GO:0045909 | 3.433e-02 | 0.03947 | 2
CALCA, NOS1 | 4 | positive regulation of vasodilation |
| GO:0009617 | 3.612e-02 | 0.3947 | 4
ERAP1, IL12A, IL6R, S100A12 | 40 | response to bacterium |
| GO:0002682 | 3.674e-02 | 1.47 | 7
AQP3, CALCA, ERAP1, IL12A, IL6R, TNFSF13, ZNF675 | 149 | regulation of immune system process |
| GO:0042742 | 4.774e-02 | 0.1974 | 3
IL12A, IL6R, S100A12 | 20 | defense response to bacterium |
| GO:0031638 | 4.809e-02 | 0.04934 | 2
F11, MMP14 | 5 | zymogen activation |
| GO:0001501 | 4.934e-02 | 1.589 | 7
CALCA, FGFR3, HOXB9, IL6R, MMP14, TBX1, ZNF675 | 161 | skeletal system development |
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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.
— 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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A list of all genes in the current module, in alphabetical order. The
size of the text corresponds to the gene scores.
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
ABCA7ATP-binding cassette, sub-family A (ABC1), member 7 (219577_s_at), score: -0.53
ADAMTS12ADAM metallopeptidase with thrombospondin type 1 motif, 12 (221421_s_at), score: -0.64
ADAMTSL4ADAMTS-like 4 (220578_at), score: 0.44
AQP3aquaporin 3 (Gill blood group) (39248_at), score: -0.46
ARID3AAT rich interactive domain 3A (BRIGHT-like) (205865_at), score: 0.46
ARL15ADP-ribosylation factor-like 15 (219842_at), score: 0.5
BADBCL2-associated agonist of cell death (209364_at), score: 0.46
BAHD1bromo adjacent homology domain containing 1 (203051_at), score: -0.51
BAZ1Bbromodomain adjacent to zinc finger domain, 1B (208445_s_at), score: -0.5
BEANbrain expressed, associated with Nedd4 (214068_at), score: 0.58
BRAFv-raf murine sarcoma viral oncogene homolog B1 (206044_s_at), score: 0.53
C13orf15chromosome 13 open reading frame 15 (218723_s_at), score: 0.44
C18orf1chromosome 18 open reading frame 1 (209574_s_at), score: 0.51
C1orf114chromosome 1 open reading frame 114 (206721_at), score: -0.49
CALCAcalcitonin-related polypeptide alpha (217561_at), score: 0.44
CATSPER2cation channel, sperm associated 2 (217588_at), score: -0.49
CCBP2chemokine binding protein 2 (206887_at), score: 0.55
CCDC130coiled-coil domain containing 130 (208094_s_at), score: 0.49
CLEC1AC-type lectin domain family 1, member A (219761_at), score: 0.42
COPS7BCOP9 constitutive photomorphogenic homolog subunit 7B (Arabidopsis) (219997_s_at), score: -0.53
DKFZp434H1419hypothetical protein DKFZp434H1419 (214717_at), score: -0.6
EDNRBendothelin receptor type B (204271_s_at), score: 0.68
ERAP1endoplasmic reticulum aminopeptidase 1 (214012_at), score: 0.47
ETNK2ethanolamine kinase 2 (219268_at), score: -0.47
F11coagulation factor XI (206610_s_at), score: -0.49
FAM46Cfamily with sequence similarity 46, member C (220306_at), score: 0.45
FGFR3fibroblast growth factor receptor 3 (204379_s_at), score: 0.54
FHITfragile histidine triad gene (206492_at), score: 0.42
FZD3frizzled homolog 3 (Drosophila) (219683_at), score: -0.55
GCNT1glucosaminyl (N-acetyl) transferase 1, core 2 (beta-1,6-N-acetylglucosaminyltransferase) (205505_at), score: 0.45
GNRHRgonadotropin-releasing hormone receptor (216341_s_at), score: 0.42
GRB10growth factor receptor-bound protein 10 (210999_s_at), score: -0.48
GSDMBgasdermin B (215659_at), score: 0.66
GSTA1glutathione S-transferase alpha 1 (215766_at), score: 0.44
HIST1H2AChistone cluster 1, H2ac (215071_s_at), score: 0.44
HOXB9homeobox B9 (216417_x_at), score: -0.49
IFT140intraflagellar transport 140 homolog (Chlamydomonas) (204792_s_at), score: -0.54
IL12Ainterleukin 12A (natural killer cell stimulatory factor 1, cytotoxic lymphocyte maturation factor 1, p35) (207160_at), score: -0.56
IL6Rinterleukin 6 receptor (205945_at), score: 0.53
IPPintracisternal A particle-promoted polypeptide (219843_at), score: 0.48
ISOC2isochorismatase domain containing 2 (218893_at), score: -0.48
KCNQ3potassium voltage-gated channel, KQT-like subfamily, member 3 (206573_at), score: 1
KIAA0892KIAA0892 (212505_s_at), score: -0.53
KLK13kallikrein-related peptidase 13 (205783_at), score: 0.66
KMOkynurenine 3-monooxygenase (kynurenine 3-hydroxylase) (205307_s_at), score: 0.44
KSR1kinase suppressor of ras 1 (213769_at), score: -0.48
LOC645139hypothetical LOC645139 (209064_x_at), score: -0.47
MMP14matrix metallopeptidase 14 (membrane-inserted) (202827_s_at), score: -0.58
MOCS3molybdenum cofactor synthesis 3 (206141_at), score: -0.54
MRPS18Amitochondrial ribosomal protein S18A (221693_s_at), score: -0.49
MRPS6mitochondrial ribosomal protein S6 (213167_s_at), score: -0.5
MTMR12myotubularin related protein 12 (220953_s_at), score: -0.47
NAG18NAG18 mRNA (210496_at), score: -0.49
NAV2neuron navigator 2 (218330_s_at), score: -0.47
NCRNA00115non-protein coding RNA 115 (220399_at), score: 0.52
NOS1nitric oxide synthase 1 (neuronal) (207309_at), score: 0.58
PAK1p21 protein (Cdc42/Rac)-activated kinase 1 (209615_s_at), score: -0.46
PDE1Cphosphodiesterase 1C, calmodulin-dependent 70kDa (207303_at), score: -0.61
PEX13peroxisomal biogenesis factor 13 (205246_at), score: 0.41
PEX16peroxisomal biogenesis factor 16 (221604_s_at), score: -0.5
POM121L2POM121 membrane glycoprotein-like 2 (rat) (216582_at), score: -0.55
PTPN21protein tyrosine phosphatase, non-receptor type 21 (40524_at), score: -0.47
PTPN9protein tyrosine phosphatase, non-receptor type 9 (202958_at), score: -0.52
RBM12BRNA binding motif protein 12B (51228_at), score: 0.45
RPAP2RNA polymerase II associated protein 2 (219504_s_at), score: -0.49
RPUSD2RNA pseudouridylate synthase domain containing 2 (221940_at), score: -0.55
S100A12S100 calcium binding protein A12 (205863_at), score: -0.46
S100A2S100 calcium binding protein A2 (204268_at), score: -0.59
SAPS2SAPS domain family, member 2 (202792_s_at), score: -0.56
SCG2secretogranin II (chromogranin C) (204035_at), score: 0.5
SCLYselenocysteine lyase (221575_at), score: 0.7
SLC27A3solute carrier family 27 (fatty acid transporter), member 3 (222217_s_at), score: 0.64
SLC9A8solute carrier family 9 (sodium/hydrogen exchanger), member 8 (212947_at), score: -0.49
SNCAsynuclein, alpha (non A4 component of amyloid precursor) (204466_s_at), score: -0.5
SUV39H2suppressor of variegation 3-9 homolog 2 (Drosophila) (219262_at), score: 0.47
TASP1taspase, threonine aspartase, 1 (219443_at), score: 0.48
TBX1T-box 1 (211273_s_at), score: 0.48
TBX10T-box 10 (207689_at), score: -0.56
TGIF2TGFB-induced factor homeobox 2 (216262_s_at), score: -0.89
THAP11THAP domain containing 11 (212910_at), score: 0.41
TICAM1toll-like receptor adaptor molecule 1 (213191_at), score: -0.71
TMEM144transmembrane protein 144 (219750_at), score: 0.44
TMEM204transmembrane protein 204 (219315_s_at), score: -0.47
TNFSF13tumor necrosis factor (ligand) superfamily, member 13 (209499_x_at), score: 0.5
TOM1L2target of myb1-like 2 (chicken) (214840_at), score: -0.48
TPK1thiamin pyrophosphokinase 1 (221218_s_at), score: 0.64
TRAF4TNF receptor-associated factor 4 (202871_at), score: -0.53
TSC22D1TSC22 domain family, member 1 (215111_s_at), score: 0.45
USP20ubiquitin specific peptidase 20 (203965_at), score: -0.57
VCPIP1valosin containing protein (p97)/p47 complex interacting protein 1 (219810_at), score: -0.6
WFS1Wolfram syndrome 1 (wolframin) (202908_at), score: 0.41
XYLBxylulokinase homolog (H. influenzae) (214776_x_at), score: -0.55
YPEL1yippee-like 1 (Drosophila) (206063_x_at), score: -0.48
ZBED4zinc finger, BED-type containing 4 (204799_at), score: -0.5
ZBTB3zinc finger and BTB domain containing 3 (220391_at), score: -0.51
ZNF215zinc finger protein 215 (220214_at), score: -0.48
ZNF467zinc finger protein 467 (214746_s_at), score: 0.58
ZNF675zinc finger protein 675 (217547_x_at), score: 0.44
ZNF839zinc finger protein 839 (221709_s_at), score: -0.51
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 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 experiments that were part of the study, are separated
by dashed vertical lines.
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| Id | sample | Experiment | ExpName | Array | Syndrome | Cell.line |
| 47C.CEL | 5 | 3 | DS-mosaic | hgu133plus2 | Down mosaic | DS-mosaic 5 |
| E-TABM-263-raw-cel-1515485991.cel | 18 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| H652_WBS.CEL | 17 | 8 | WBS | hgu133plus2 | WBS | WBS 1 |
| E-TABM-263-raw-cel-1515486111.cel | 24 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
© 2008-2010 Computational Biology Group, Department of Medical Genetics,
University of Lausanne, Switzerland
