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Module #738, TG: 2.8, TC: 1, 103 probes, 103 Entrez genes, 21 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:0051239 | 3.471e-02 | 3.436 | 11
ADORA2B, BDKRB2, BMP6, DMPK, FGF9, IRF1, NEFM, PPARG, SMAD3, TLR3, TP53 | 313 | regulation of multicellular organismal process |
| GO:0045595 | 3.998e-02 | 1.954 | 8
BMP6, FGF9, NEFM, PPARG, SIX2, SMAD3, TLR3, TP53 | 178 | regulation of cell differentiation |
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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
HELP
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
HELP
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.
— Click on the Help button again to close this help window.
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
ACTR3BARP3 actin-related protein 3 homolog B (yeast) (218868_at), score: -0.78
ADORA2Badenosine A2b receptor (205891_at), score: 0.86
AHI1Abelson helper integration site 1 (221569_at), score: -0.72
AIM1absent in melanoma 1 (212543_at), score: 0.83
AKR1C3aldo-keto reductase family 1, member C3 (3-alpha hydroxysteroid dehydrogenase, type II) (209160_at), score: 0.69
ANGPTL2angiopoietin-like 2 (213004_at), score: 0.77
ANXA10annexin A10 (210143_at), score: -0.76
APOL6apolipoprotein L, 6 (219716_at), score: 0.81
BDKRB2bradykinin receptor B2 (205870_at), score: 0.7
BMP6bone morphogenetic protein 6 (206176_at), score: -0.78
BTG2BTG family, member 2 (201236_s_at), score: 0.7
C13orf15chromosome 13 open reading frame 15 (218723_s_at), score: 0.72
CALB2calbindin 2 (205428_s_at), score: -0.76
CALCOCO1calcium binding and coiled-coil domain 1 (209002_s_at), score: 0.78
CCDC28Acoiled-coil domain containing 28A (209479_at), score: 0.71
CDC2L6cell division cycle 2-like 6 (CDK8-like) (212899_at), score: 0.69
CRTC3CREB regulated transcription coactivator 3 (218648_at), score: 0.86
DAPK1death-associated protein kinase 1 (203139_at), score: 0.73
DENND2ADENN/MADD domain containing 2A (53991_at), score: 0.84
DEPDC6DEP domain containing 6 (218858_at), score: 0.84
DMPKdystrophia myotonica-protein kinase (37996_s_at), score: 0.73
DNAJB9DnaJ (Hsp40) homolog, subfamily B, member 9 (202843_at), score: -0.79
DOCK10dedicator of cytokinesis 10 (219279_at), score: -0.7
DZIP3DAZ interacting protein 3, zinc finger (213186_at), score: 0.7
EDEM1ER degradation enhancer, mannosidase alpha-like 1 (203279_at), score: -0.67
EIF4Eeukaryotic translation initiation factor 4E (201436_at), score: -0.65
ESM1endothelial cell-specific molecule 1 (208394_x_at), score: -0.78
FBXL14F-box and leucine-rich repeat protein 14 (213145_at), score: 0.72
FGF9fibroblast growth factor 9 (glia-activating factor) (206404_at), score: 0.71
FICDFIC domain containing (219910_at), score: -0.68
FNBP1formin binding protein 1 (212288_at), score: 0.8
GFOD1glucose-fructose oxidoreductase domain containing 1 (219821_s_at), score: -0.74
GKglycerol kinase (207387_s_at), score: -0.77
GK3Pglycerol kinase 3 pseudogene (215966_x_at), score: -0.89
GMPRguanosine monophosphate reductase (204187_at), score: 0.73
GTF2A1Lgeneral transcription factor IIA, 1-like (213413_at), score: 0.98
HSPA12Aheat shock 70kDa protein 12A (214434_at), score: 0.74
IFIH1interferon induced with helicase C domain 1 (219209_at), score: 0.79
IRF1interferon regulatory factor 1 (202531_at), score: 0.85
KAL1Kallmann syndrome 1 sequence (205206_at), score: -0.83
KIAA1305KIAA1305 (220911_s_at), score: 0.76
LOC100132540similar to LOC339047 protein (214870_x_at), score: 0.79
LOC100133105hypothetical protein LOC100133105 (214237_x_at), score: -0.68
LOC339047hypothetical protein LOC339047 (221501_x_at), score: 0.82
LOC399491LOC399491 protein (214035_x_at), score: 0.76
LRP8low density lipoprotein receptor-related protein 8, apolipoprotein e receptor (205282_at), score: -0.72
MAN1C1mannosidase, alpha, class 1C, member 1 (218918_at), score: 0.84
MFAP3Lmicrofibrillar-associated protein 3-like (205442_at), score: -0.78
MMP10matrix metallopeptidase 10 (stromelysin 2) (205680_at), score: -0.79
MMP16matrix metallopeptidase 16 (membrane-inserted) (207012_at), score: -0.74
MSTO1misato homolog 1 (Drosophila) (218296_x_at), score: -0.73
MX2myxovirus (influenza virus) resistance 2 (mouse) (204994_at), score: 0.71
NCALDneurocalcin delta (211685_s_at), score: -0.71
NEFMneurofilament, medium polypeptide (205113_at), score: -0.94
NMIN-myc (and STAT) interactor (203964_at), score: 0.7
NOX4NADPH oxidase 4 (219773_at), score: -0.69
NPIPnuclear pore complex interacting protein (204538_x_at), score: 0.84
NPTX1neuronal pentraxin I (204684_at), score: -0.75
NTMneurotrimin (222020_s_at), score: -0.66
OAS12',5'-oligoadenylate synthetase 1, 40/46kDa (205552_s_at), score: 0.7
OAS22'-5'-oligoadenylate synthetase 2, 69/71kDa (204972_at), score: 0.85
OPCMLopioid binding protein/cell adhesion molecule-like (214111_at), score: -0.85
ORAI3ORAI calcium release-activated calcium modulator 3 (221864_at), score: 0.74
P2RY5purinergic receptor P2Y, G-protein coupled, 5 (218589_at), score: 0.69
PCDH9protocadherin 9 (219737_s_at), score: -1
PCYT2phosphate cytidylyltransferase 2, ethanolamine (209577_at), score: 0.75
PDE5Aphosphodiesterase 5A, cGMP-specific (206757_at), score: 0.84
PIGLphosphatidylinositol glycan anchor biosynthesis, class L (213889_at), score: 0.7
PITX1paired-like homeodomain 1 (208502_s_at), score: 0.72
PPARGperoxisome proliferator-activated receptor gamma (208510_s_at), score: 0.78
PPATphosphoribosyl pyrophosphate amidotransferase (209433_s_at), score: -0.65
RAB1ARAB1A, member RAS oncogene family (213440_at), score: -0.69
RASSF2Ras association (RalGDS/AF-6) domain family member 2 (203185_at), score: 0.74
REREarginine-glutamic acid dipeptide (RE) repeats (200940_s_at), score: 0.69
RNF44ring finger protein 44 (203286_at), score: 0.74
ROR2receptor tyrosine kinase-like orphan receptor 2 (205578_at), score: 0.85
SAV1salvador homolog 1 (Drosophila) (218276_s_at), score: 0.78
SCG5secretogranin V (7B2 protein) (203889_at), score: -0.7
SDF2L1stromal cell-derived factor 2-like 1 (218681_s_at), score: -0.7
SECTM1secreted and transmembrane 1 (213716_s_at), score: 0.71
SERPINB9serpin peptidase inhibitor, clade B (ovalbumin), member 9 (209723_at), score: 0.7
SIX2SIX homeobox 2 (206510_at), score: 0.7
SLC25A13solute carrier family 25, member 13 (citrin) (203775_at), score: -0.65
SLC4A7solute carrier family 4, sodium bicarbonate cotransporter, member 7 (209884_s_at), score: -0.8
SMAD3SMAD family member 3 (218284_at), score: 0.84
SNNstannin (218032_at), score: 0.79
SSTR1somatostatin receptor 1 (208482_at), score: -0.7
ST5suppression of tumorigenicity 5 (202440_s_at), score: 0.7
STARD5StAR-related lipid transfer (START) domain containing 5 (213820_s_at), score: 0.72
TBC1D8TBC1 domain family, member 8 (with GRAM domain) (204526_s_at), score: 0.78
TENC1tensin like C1 domain containing phosphatase (tensin 2) (212494_at), score: 0.74
TGDSTDP-glucose 4,6-dehydratase (208249_s_at), score: -0.66
THSD7Athrombospondin, type I, domain containing 7A (214920_at), score: 0.82
TLR3toll-like receptor 3 (206271_at), score: 0.86
TMEM2transmembrane protein 2 (218113_at), score: -0.72
TP53tumor protein p53 (201746_at), score: 0.74
TRIM21tripartite motif-containing 21 (204804_at), score: 0.8
TSPAN13tetraspanin 13 (217979_at), score: -0.69
ULBP2UL16 binding protein 2 (221291_at), score: -0.71
VWA5Avon Willebrand factor A domain containing 5A (210102_at), score: 0.78
WDR4WD repeat domain 4 (221632_s_at), score: -0.72
XYLT1xylosyltransferase I (213725_x_at), score: -0.65
ZDHHC7zinc finger, DHHC-type containing 7 (218606_at), score: 0.76
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-1515485811.cel | 9 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515486371.cel | 37 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515485891.cel | 13 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515485771.cel | 7 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515485671.cel | 2 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515486351.cel | 36 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515486431.cel | 40 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515485751.cel | 6 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-GEOD-3860-raw-cel-1561690199.cel | 1 | 5 | HGPS | hgu133a | none | GM0316B |
| 47B.CEL | 4 | 3 | DS-mosaic | hgu133plus2 | Down mosaic | DS-mosaic 4 |
| E-TABM-263-raw-cel-1515485691.cel | 3 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515485871.cel | 12 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| 46B.CEL | 2 | 3 | DS-mosaic | hgu133plus2 | none | DS-mosaic 2 |
| E-TABM-263-raw-cel-1515486331.cel | 35 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515486211.cel | 29 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-GEOD-3407-raw-cel-1437949721.cel | 5 | 4 | Cockayne | hgu133a | CS | CSB |
| E-TABM-263-raw-cel-1515485831.cel | 10 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515486271.cel | 32 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515485791.cel | 8 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515486311.cel | 34 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515486291.cel | 33 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
© 2008-2010 Computational Biology Group, Department of Medical Genetics,
University of Lausanne, Switzerland
