Previous module |
Next module
Module #771, TG: 2.6, TC: 1.8, 133 probes, 133 Entrez genes, 8 conditions
HELP
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).
— Click on the Help button again to close this help window.
Under-expression is coded with green,
over-expression with red color.
Help |
Hide |
Top
Help |
Show |
Top
The GO tree — Biological processes
HELP
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.
— Click on the Help button again to close this help window.
Help |
Hide |
Top
Help |
Show |
Top
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.
Help |
Hide |
Top
Help |
Show |
Top
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.
Help |
Hide |
Top
Help |
Show |
Top
GO BP test for over-representation
HELP
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.
— Click on the Help button again to close this help window.
| Id | Pvalue | ExpCount | Count | Size | Term |
| GO:0048096 | 3.302e-02 | 0.04002 | 2
MLL4, SMARCD1 | 3 | chromatin-mediated maintenance of transcription |
Help |
Hide |
Top
Help |
Show |
Top
GO CC test for over-representation
HELP
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.
— Click on the Help button again to close this help window.
Help |
Hide |
Top
Help |
Show |
Top
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.
Help |
Hide |
Top
Help |
Show |
Top
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.
— Click on the Help button again to close this help window.
Help |
Hide |
Top
Help |
Show |
Top
miRNA test for over-representation
HELP
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.
— Click on the Help button again to close this help window.
Help |
Hide |
Top
Help |
Show |
Top
Chromosome test for over-representation
HELP
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.
| Id | Pvalue | ExpCount | Count | Size |
| 19 | 1.182e-02 | 8.152 | 22
BTBD2, CIC, CNOT3, DMWD, FBXO17, HNRNPUL1, LOC90379, MAP1S, MBD3, MLL4, PIP5K1C, PKN1, PNPLA6, POLRMT, PRKACA, SBNO2, SCAMP4, SF3A2, SIN3B, SIPA1L3, STRN4, XAB2 | 570 |
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.
— Click on the Help button again to close this help window.
Entrez genes
ADCY3adenylate cyclase 3 (209321_s_at), score: 0.66
AHDC1AT hook, DNA binding motif, containing 1 (205002_at), score: 0.69
AKAP10A kinase (PRKA) anchor protein 10 (205045_at), score: -0.74
ARFGAP1ADP-ribosylation factor GTPase activating protein 1 (217888_s_at), score: 0.65
ARSAarylsulfatase A (204443_at), score: 0.65
ATN1atrophin 1 (40489_at), score: 0.92
B3GAT3beta-1,3-glucuronyltransferase 3 (glucuronosyltransferase I) (203452_at), score: 0.76
BACE2beta-site APP-cleaving enzyme 2 (217867_x_at), score: 0.7
BAT2LHLA-B associated transcript 2-like (212068_s_at), score: 0.68
BCL7BB-cell CLL/lymphoma 7B (202518_at), score: 0.68
BIN1bridging integrator 1 (210201_x_at), score: 0.85
BRD9bromodomain containing 9 (220155_s_at), score: 0.72
BTBD2BTB (POZ) domain containing 2 (207722_s_at), score: 0.64
C16orf57chromosome 16 open reading frame 57 (218060_s_at), score: 0.71
CDC42BPBCDC42 binding protein kinase beta (DMPK-like) (217849_s_at), score: 0.82
CDR2Lcerebellar degeneration-related protein 2-like (213230_at), score: 0.87
CENPTcentromere protein T (218148_at), score: 0.67
CHST3carbohydrate (chondroitin 6) sulfotransferase 3 (209834_at), score: 0.79
CICcapicua homolog (Drosophila) (212784_at), score: 0.76
CIZ1CDKN1A interacting zinc finger protein 1 (205516_x_at), score: 0.73
CLIC4chloride intracellular channel 4 (201559_s_at), score: -0.72
CLIP2CAP-GLY domain containing linker protein 2 (211031_s_at), score: 0.81
CNOT3CCR4-NOT transcription complex, subunit 3 (203239_s_at), score: 0.64
COL8A1collagen, type VIII, alpha 1 (214587_at), score: -0.78
CORO2Bcoronin, actin binding protein, 2B (209789_at), score: 0.67
CRTC3CREB regulated transcription coactivator 3 (218648_at), score: 0.67
DMWDdystrophia myotonica, WD repeat containing (33768_at), score: 0.65
DOK4docking protein 4 (209691_s_at), score: 0.7
EIF2S3eukaryotic translation initiation factor 2, subunit 3 gamma, 52kDa (205321_at), score: -0.88
F11coagulation factor XI (206610_s_at), score: -0.76
FAM134Cfamily with sequence similarity 134, member C (212697_at), score: 0.66
FAM3Afamily with sequence similarity 3, member A (38043_at), score: 0.68
FASNfatty acid synthase (212218_s_at), score: 0.79
FBXL11F-box and leucine-rich repeat protein 11 (208989_s_at), score: 0.65
FBXO17F-box protein 17 (220233_at), score: 0.81
FCF1FCF1 small subunit (SSU) processome component homolog (S. cerevisiae) (219927_at), score: -0.74
FHL1four and a half LIM domains 1 (201539_s_at), score: -0.76
FKSG2apoptosis inhibitor (208588_at), score: -0.75
FLJ12529pre-mRNA cleavage factor I, 59 kDa subunit (217866_at), score: 0.8
FOXK2forkhead box K2 (203064_s_at), score: 0.9
FURINfurin (paired basic amino acid cleaving enzyme) (201945_at), score: 0.72
GOLGA3golgi autoantigen, golgin subfamily a, 3 (202106_at), score: 0.78
GRINAglutamate receptor, ionotropic, N-methyl D-aspartate-associated protein 1 (glutamate binding) (212090_at), score: 0.68
HECTD3HECT domain containing 3 (218632_at), score: 0.76
HNRNPUL1heterogeneous nuclear ribonucleoprotein U-like 1 (209675_s_at), score: 0.66
HSPA12Aheat shock 70kDa protein 12A (214434_at), score: 0.74
IDUAiduronidase, alpha-L- (205059_s_at), score: 0.83
KCTD13potassium channel tetramerisation domain containing 13 (45653_at), score: 0.65
KPNA6karyopherin alpha 6 (importin alpha 7) (212101_at), score: 0.69
LARP1La ribonucleoprotein domain family, member 1 (212193_s_at), score: 0.66
LEPREL2leprecan-like 2 (204854_at), score: 0.69
LOC100132540similar to LOC339047 protein (214870_x_at), score: 0.65
LOC100133105hypothetical protein LOC100133105 (214237_x_at), score: -0.73
LOC339047hypothetical protein LOC339047 (221501_x_at), score: 0.83
LOC90379hypothetical protein BC002926 (221849_s_at), score: 0.66
LRFN4leucine rich repeat and fibronectin type III domain containing 4 (219491_at), score: 0.77
LRP1low density lipoprotein-related protein 1 (alpha-2-macroglobulin receptor) (200785_s_at), score: 0.65
MAP1Smicrotubule-associated protein 1S (218522_s_at), score: 0.84
MAP3K6mitogen-activated protein kinase kinase kinase 6 (219278_at), score: 0.65
MAP7D1MAP7 domain containing 1 (217943_s_at), score: 0.79
MAST2microtubule associated serine/threonine kinase 2 (211593_s_at), score: 0.68
MBD3methyl-CpG binding domain protein 3 (41160_at), score: 0.67
MBNL2muscleblind-like 2 (Drosophila) (205018_s_at), score: -0.77
MICAL3microtubule associated monoxygenase, calponin and LIM domain containing 3 (212715_s_at), score: 0.64
MINK1misshapen-like kinase 1 (zebrafish) (214246_x_at), score: 0.66
MLL4myeloid/lymphoid or mixed-lineage leukemia 4 (203419_at), score: 0.75
MTA2metastasis associated 1 family, member 2 (203442_x_at), score: 0.73
MYST3MYST histone acetyltransferase (monocytic leukemia) 3 (202423_at), score: 0.64
NBL1neuroblastoma, suppression of tumorigenicity 1 (37005_at), score: 0.71
NCDNneurochondrin (209556_at), score: 0.64
NCOR2nuclear receptor co-repressor 2 (207760_s_at), score: 0.65
NOL9nucleolar protein 9 (218754_at), score: 0.7
NPIPnuclear pore complex interacting protein (204538_x_at), score: 0.75
OTUD3OTU domain containing 3 (213216_at), score: 0.68
PAFAH1B2platelet-activating factor acetylhydrolase, isoform Ib, beta subunit 30kDa (210160_at), score: -0.72
PARVBparvin, beta (37965_at), score: 0.73
PCDHG@protocadherin gamma cluster (215836_s_at), score: 0.77
PCDHGA1protocadherin gamma subfamily A, 1 (209079_x_at), score: 0.93
PDLIM4PDZ and LIM domain 4 (211564_s_at), score: 0.64
PEX26peroxisomal biogenesis factor 26 (219180_s_at), score: 0.7
PEX6peroxisomal biogenesis factor 6 (204545_at), score: 0.64
PIP5K1Cphosphatidylinositol-4-phosphate 5-kinase, type I, gamma (212518_at), score: 1
PKD1polycystic kidney disease 1 (autosomal dominant) (202328_s_at), score: 0.67
PKN1protein kinase N1 (202161_at), score: 0.76
PLAGL2pleiomorphic adenoma gene-like 2 (202925_s_at), score: 0.69
PNPLA6patatin-like phospholipase domain containing 6 (203718_at), score: 0.7
POLR2Apolymerase (RNA) II (DNA directed) polypeptide A, 220kDa (202725_at), score: 0.82
POLRMTpolymerase (RNA) mitochondrial (DNA directed) (203782_s_at), score: 0.66
POLSpolymerase (DNA directed) sigma (202466_at), score: 0.69
POM121POM121 membrane glycoprotein (rat) (212178_s_at), score: 0.74
POM121CPOM121 membrane glycoprotein C (213360_s_at), score: 0.67
POMZP3POM (POM121 homolog, rat) and ZP3 fusion (204148_s_at), score: 0.69
PPM1Fprotein phosphatase 1F (PP2C domain containing) (203063_at), score: 0.69
PRKACAprotein kinase, cAMP-dependent, catalytic, alpha (202801_at), score: 0.69
PTK7PTK7 protein tyrosine kinase 7 (207011_s_at), score: 0.69
PTPN9protein tyrosine phosphatase, non-receptor type 9 (202958_at), score: 0.7
RAB15RAB15, member RAS onocogene family (221810_at), score: 0.79
RAB5ARAB5A, member RAS oncogene family (206113_s_at), score: -0.74
RAD54L2RAD54-like 2 (S. cerevisiae) (213205_s_at), score: 0.78
RBBP9retinoblastoma binding protein 9 (221440_s_at), score: -0.8
RBM15BRNA binding motif protein 15B (202689_at), score: 0.76
RNF187ring finger protein 187 (212155_at), score: 0.71
RNF24ring finger protein 24 (204669_s_at), score: 0.66
RPL18AP6ribosomal protein L18a pseudogene 6 (216383_at), score: -0.83
RPRD2regulation of nuclear pre-mRNA domain containing 2 (212553_at), score: 0.64
SBNO2strawberry notch homolog 2 (Drosophila) (204166_at), score: 0.65
SCAMP1secretory carrier membrane protein 1 (206667_s_at), score: -0.97
SCAMP4secretory carrier membrane protein 4 (213244_at), score: 0.93
SDAD1SDA1 domain containing 1 (218607_s_at), score: 0.64
SENP5SUMO1/sentrin specific peptidase 5 (213184_at), score: 0.68
SF1splicing factor 1 (208313_s_at), score: 0.75
SF3A2splicing factor 3a, subunit 2, 66kDa (37462_i_at), score: 0.69
SIN3BSIN3 homolog B, transcription regulator (yeast) (209352_s_at), score: 0.64
SIPA1L3signal-induced proliferation-associated 1 like 3 (213600_at), score: 0.73
SLC6A8solute carrier family 6 (neurotransmitter transporter, creatine), member 8 (202219_at), score: 0.72
SLC9A1solute carrier family 9 (sodium/hydrogen exchanger), member 1 (209453_at), score: 0.63
SMARCD1SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1 (209518_at), score: 0.68
SMG7Smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans) (201794_s_at), score: 0.87
SMYD5SMYD family member 5 (209516_at), score: 0.64
SOLHsmall optic lobes homolog (Drosophila) (204275_at), score: 0.8
SPRY4sprouty homolog 4 (Drosophila) (221489_s_at), score: 0.65
SSBP3single stranded DNA binding protein 3 (217991_x_at), score: 0.76
STRN4striatin, calmodulin binding protein 4 (217903_at), score: 0.97
SUPT6Hsuppressor of Ty 6 homolog (S. cerevisiae) (208831_x_at), score: 0.77
TAPBPTAP binding protein (tapasin) (208829_at), score: 0.85
TBC1D10BTBC1 domain family, member 10B (220947_s_at), score: 0.71
TRIM33tripartite motif-containing 33 (210266_s_at), score: 0.64
TSKUtsukushin (218245_at), score: 0.65
TXLNAtaxilin alpha (212300_at), score: 0.83
VPS37Bvacuolar protein sorting 37 homolog B (S. cerevisiae) (221704_s_at), score: 0.89
XAB2XPA binding protein 2 (218110_at), score: 0.84
ZFP36L1zinc finger protein 36, C3H type-like 1 (211965_at), score: 0.64
ZNF282zinc finger protein 282 (212892_at), score: 0.63
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.
— Click on the Help button again to close this help window.
| Id | sample | Experiment | ExpName | Array | Syndrome | Cell.line |
| E-TABM-263-raw-cel-1515485771.cel | 7 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515485751.cel | 6 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515486091.cel | 23 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515486431.cel | 40 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-GEOD-3407-raw-cel-1437949557.cel | 1 | 4 | Cockayne | hgu133a | CS | eGFP |
| E-TABM-263-raw-cel-1515486031.cel | 20 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-GEOD-3860-raw-cel-1561690344.cel | 10 | 5 | HGPS | hgu133a | none | GM00038C |
| E-GEOD-3860-raw-cel-1561690304.cel | 8 | 5 | HGPS | hgu133a | none | GMO8398C |
© 2008-2010 Computational Biology Group, Department of Medical Genetics,
University of Lausanne, Switzerland
