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Module #654, TG: 2.8, TC: 2, 103 probes, 103 Entrez genes, 6 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.
extracellular region
The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
cellular_component
The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
extracellular region part
Any constituent part of the extracellular region, the space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers constituent parts of the host cell environment outside an intracellular parasite.
all
This term is the most general term possible
extracellular region part
Any constituent part of the extracellular region, the space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers constituent parts of the host cell environment outside an intracellular parasite.
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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:0006349 | 2.698e-02 | 0.0346 | 2
DIRAS3, IGF2 | 3 | genetic imprinting |
| GO:0008544 | 3.999e-02 | 0.7151 | 5
COL5A3, COL7A1, CST6, KRT17, SOX9 | 62 | epidermis 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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| Id | Pvalue | ExpCount | Count | Size | Term |
| GO:0005576 | 3.731e-03 | 8.01 | 20
ACAN, ADAMTS6, CDCP1, CLCF1, CLEC3B, CLU, COL5A3, COL7A1, CST6, CXCL6, EMCN, HGF, IGF2, IL13RA2, IL33, KAL1, KIT, MSTP9, OLFML2A, PRSS3 | 673 | extracellular region |
| GO:0044421 | 4.726e-03 | 4.475 | 14
ACAN, ADAMTS6, CLCF1, CLU, COL5A3, COL7A1, CXCL6, IGF2, IL13RA2, IL33, KAL1, KIT, OLFML2A, PRSS3 | 376 | extracellular region part |
| GO:0005882 | 1.730e-02 | 0.3928 | 4
KRT17, KRT33A, NEFL, SYNM | 33 | intermediate filament |
| GO:0045111 | 1.730e-02 | 0.3928 | 4
KRT17, KRT33A, NEFL, SYNM | 33 | intermediate filament cytoskeleton |
| GO:0060053 | 2.299e-02 | 0.04761 | 2
NEFL, SYNM | 4 | neurofilament cytoskeleton |
| GO:0005615 | 4.539e-02 | 2.821 | 9
CLCF1, CLU, CXCL6, IGF2, IL13RA2, IL33, KAL1, KIT, PRSS3 | 237 | extracellular space |
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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:0030246 | 4.494e-02 | 1.449 | 7
ACAN, CLEC1A, CLEC3B, COL5A3, CXCL6, GAA, LMAN2L | 130 | carbohydrate 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.
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
ACANaggrecan (205679_x_at), score: -0.53
ADAMTS6ADAM metallopeptidase with thrombospondin type 1 motif, 6 (220866_at), score: 0.55
ANXA10annexin A10 (210143_at), score: 0.57
ARL17ADP-ribosylation factor-like 17 (210435_at), score: 0.46
ARNT2aryl-hydrocarbon receptor nuclear translocator 2 (202986_at), score: -0.6
ASTN2astrotactin 2 (209693_at), score: -0.54
B3GNTL1UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase-like 1 (213589_s_at), score: -0.59
BAXBCL2-associated X protein (208478_s_at), score: -0.52
BCCIPBRCA2 and CDKN1A interacting protein (218264_at), score: -0.55
C11orf67chromosome 11 open reading frame 67 (221600_s_at), score: -0.55
C17orf39chromosome 17 open reading frame 39 (220058_at), score: -0.56
C1orf9chromosome 1 open reading frame 9 (203429_s_at), score: 0.49
CD320CD320 molecule (218529_at), score: -0.63
CD55CD55 molecule, decay accelerating factor for complement (Cromer blood group) (201925_s_at), score: 0.55
CDCP1CUB domain containing protein 1 (218451_at), score: 0.49
CDH18cadherin 18, type 2 (206280_at), score: -0.53
CLCF1cardiotrophin-like cytokine factor 1 (219500_at), score: 0.63
CLEC1AC-type lectin domain family 1, member A (219761_at), score: 0.48
CLEC3BC-type lectin domain family 3, member B (205200_at), score: 0.69
CLUclusterin (208791_at), score: 0.56
CNNM2cyclin M2 (206818_s_at), score: -0.52
COL5A3collagen, type V, alpha 3 (52255_s_at), score: 0.69
COL7A1collagen, type VII, alpha 1 (217312_s_at), score: 0.47
CORO2Bcoronin, actin binding protein, 2B (209789_at), score: 0.48
CRYL1crystallin, lambda 1 (220753_s_at), score: 0.49
CST6cystatin E/M (206595_at), score: 0.58
CTSOcathepsin O (203758_at), score: 0.47
CXCL6chemokine (C-X-C motif) ligand 6 (granulocyte chemotactic protein 2) (206336_at), score: 0.49
DIRAS3DIRAS family, GTP-binding RAS-like 3 (215506_s_at), score: 0.62
DUSP5dual specificity phosphatase 5 (209457_at), score: 0.56
DUSP6dual specificity phosphatase 6 (208891_at), score: 0.61
EDNRBendothelin receptor type B (204271_s_at), score: 0.54
EGR3early growth response 3 (206115_at), score: 0.49
EMCNendomucin (219436_s_at), score: -0.66
EML1echinoderm microtubule associated protein like 1 (204797_s_at), score: 0.57
EVI2Becotropic viral integration site 2B (211742_s_at), score: -0.6
FAM29Afamily with sequence similarity 29, member A (218602_s_at), score: 0.48
FBXO31F-box protein 31 (219785_s_at), score: -0.54
FZD4frizzled homolog 4 (Drosophila) (218665_at), score: -0.6
GAAglucosidase, alpha; acid (202812_at), score: 0.52
GKglycerol kinase (207387_s_at), score: 0.51
GPM6Bglycoprotein M6B (209167_at), score: 0.63
GPR177G protein-coupled receptor 177 (221958_s_at), score: 0.51
GPRASP1G protein-coupled receptor associated sorting protein 1 (204793_at), score: -0.7
HGFhepatocyte growth factor (hepapoietin A; scatter factor) (209960_at), score: 0.54
HOXD1homeobox D1 (205975_s_at), score: 0.49
HSPB2heat shock 27kDa protein 2 (205824_at), score: -0.61
IER2immediate early response 2 (202081_at), score: 0.5
IGF2insulin-like growth factor 2 (somatomedin A) (202409_at), score: 0.55
IL13RA2interleukin 13 receptor, alpha 2 (206172_at), score: 0.58
IL33interleukin 33 (209821_at), score: 0.76
JUNBjun B proto-oncogene (201473_at), score: 0.48
KAL1Kallmann syndrome 1 sequence (205206_at), score: 0.49
KCNE4potassium voltage-gated channel, Isk-related family, member 4 (222379_at), score: -0.58
KITv-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog (205051_s_at), score: -0.56
KRT17keratin 17 (212236_x_at), score: 0.5
KRT33Akeratin 33A (208483_x_at), score: 0.56
LMAN2Llectin, mannose-binding 2-like (221274_s_at), score: -0.57
LOC388152hypothetical LOC388152 (220602_s_at), score: -0.63
MLPHmelanophilin (218211_s_at), score: -0.64
MSTP9macrophage stimulating, pseudogene 9 (213382_at), score: 0.54
NAGPAN-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (205090_s_at), score: -0.56
NEFLneurofilament, light polypeptide (221805_at), score: 0.62
NFATC2IPnuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2 interacting protein (217526_at), score: 0.53
NOL8nucleolar protein 8 (218244_at), score: -0.54
OLFML2Aolfactomedin-like 2A (213075_at), score: 0.51
OPCMLopioid binding protein/cell adhesion molecule-like (214111_at), score: 0.46
PAFAH1B3platelet-activating factor acetylhydrolase, isoform Ib, gamma subunit 29kDa (203228_at), score: -0.53
PIGLphosphatidylinositol glycan anchor biosynthesis, class L (213889_at), score: -0.58
PKIAprotein kinase (cAMP-dependent, catalytic) inhibitor alpha (204612_at), score: 0.47
PMAIP1phorbol-12-myristate-13-acetate-induced protein 1 (204285_s_at), score: 0.55
PNRC2proline-rich nuclear receptor coactivator 2 (217779_s_at), score: 0.52
POP1processing of precursor 1, ribonuclease P/MRP subunit (S. cerevisiae) (213449_at), score: -0.53
PRKG2protein kinase, cGMP-dependent, type II (207505_at), score: 0.63
PRSS3protease, serine, 3 (213421_x_at), score: 0.63
PSMB9proteasome (prosome, macropain) subunit, beta type, 9 (large multifunctional peptidase 2) (204279_at), score: -0.58
PTCD1pentatricopeptide repeat domain 1 (218956_s_at), score: -0.53
PTGS1prostaglandin-endoperoxide synthase 1 (prostaglandin G/H synthase and cyclooxygenase) (215813_s_at), score: 0.55
RAB8BRAB8B, member RAS oncogene family (219210_s_at), score: -0.59
RASA2RAS p21 protein activator 2 (206636_at), score: 0.53
RASSF2Ras association (RalGDS/AF-6) domain family member 2 (203185_at), score: 0.47
RBM4BRNA binding motif protein 4B (209497_s_at), score: -0.57
SAT1spermidine/spermine N1-acetyltransferase 1 (213988_s_at), score: 0.55
SETMARSET domain and mariner transposase fusion gene (206554_x_at), score: -0.61
SFRS12splicing factor, arginine/serine-rich 12 (212721_at), score: 0.48
SLC16A5solute carrier family 16, member 5 (monocarboxylic acid transporter 6) (206600_s_at), score: -0.61
SLC17A7solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 7 (204230_s_at), score: 0.47
SLC38A4solute carrier family 38, member 4 (220786_s_at), score: -0.78
SOX9SRY (sex determining region Y)-box 9 (202935_s_at), score: 0.46
SPRY4sprouty homolog 4 (Drosophila) (221489_s_at), score: 0.46
SYNMsynemin, intermediate filament protein (212730_at), score: -0.55
SYT11synaptotagmin XI (209198_s_at), score: -0.6
TFDP2transcription factor Dp-2 (E2F dimerization partner 2) (203588_s_at), score: -0.58
TMSB15Athymosin beta 15a (205347_s_at), score: -0.63
TPK1thiamin pyrophosphokinase 1 (221218_s_at), score: 0.6
TRIAP1TP53 regulated inhibitor of apoptosis 1 (218403_at), score: -0.56
TRIB2tribbles homolog 2 (Drosophila) (202478_at), score: -0.54
UCP2uncoupling protein 2 (mitochondrial, proton carrier) (208998_at), score: -1
VAMP1vesicle-associated membrane protein 1 (synaptobrevin 1) (213326_at), score: -0.53
VWA5Avon Willebrand factor A domain containing 5A (210102_at), score: -0.56
XPO4exportin 4 (218479_s_at), score: -0.56
ZNF219zinc finger protein 219 (219314_s_at), score: 0.63
ZNF22zinc finger protein 22 (KOX 15) (218005_at), score: -0.58
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 |
| E-TABM-263-raw-cel-1515486011.cel | 19 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515486191.cel | 28 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515486391.cel | 38 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515486051.cel | 21 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515485831.cel | 10 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515485991.cel | 18 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
© 2008-2010 Computational Biology Group, Department of Medical Genetics,
University of Lausanne, Switzerland
