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The left side of the screen shows the module hierarchy, constructed from the subset relationship of the module genes. E.g. from module 54 there is an edge that goes to module 119, because the genes in module 54 are all included in module 119. Edges always point upward, so supersets of a module are always above it.
The diagram only shows direct subset relationships, e.g. module 54 is also a subset module 192, but this connection is not shown, because there is another module containing module 54 (module 119), and this module is included completely in module 192.
Move the mouse cursor over the module boxes to see summary information about the modules. Clicking on the module boxes takes you to a more detailed module information page.
The figure is interactive, in that modules can be highlighted and searched based on a number of criteria. The figure always has an active module, the one circled with red color. The active module can be changed by selecting another module from the module list at the right hand side.
If the Highlight subsets and supersets option is turned on, then the direct subsets and superset of the active module are marked with green circles. This makes it easier to find supersets and subsets, without the need of following the connections.
If the Overlap size option is turned on, then for all modules, their overlap (number of genes) with the active module is shown at the top left corner. For the active module, its number of genes is shown.
It is also possible to highlight modules based on their various properties. Stars with three different colors can be used for this purpose and the selection criteria can be chosen independently for the three colors. It is possible to select the modules that contain hemizygous (or flanking) genes; modules that were replicated in lymphoblastoid cell lines; extracellular region related modules, modules that are enriched for some GO category; or modules that are enriched for a given GO category or a specific KEGG pathway.
It is possible to query the modules that contain a given gene (or any of the genes in a given gene list). For this please select genes from the gene symbol list on the bottom right. Multiple selection is possible, usually by holding the CTRL button, and then click on the Select button. The selected genes are shown below the selection box. It is possible to build the list of marked genes incrementally.
The modules that contain any of the selected genes are marked with the letter G at the bottom right corner or their box.
When looking for a given gene, the user can directly type in a substring of the gene symbol into the filter field, and then the gene list is restricted to gene symbols containing the given substring. This makes it easier to find the genes in the long selection list.
The genes that were incorporated in a dysregulated module (i.e. a module that appears in the diagram on the left), are marked with an asterisk in the gene list.
The gene list can be cleared by clicking on the Clear button.
Clicking on the names of the genes in list of selected genes links to the GeneCard page of the gene.
M2-40 — 13 genes, 6 samples
Enriched GO categories:
None.
Enriched KEGG pathways:
None.
Genes:
AGBL5, C9orf127, DBC1, EGFL6, FGF9, GOLSYN, IGF1, IL27RA, ITIH5, NRCAM, SPON1, STARD5, VAMP1
M2-54 — 12 genes, 5 samples
Enriched GO categories:
None.
Enriched KEGG pathways:
None.
Genes:
AGBL5, C9orf127, DBC1, EGFL6, FGF9, GOLSYN, IL27RA, NME3, NRCAM, SPON1, STARD5, VAMP1
M2-80 — 12 genes, 18 samples
Enriched GO categories:
None.
Enriched KEGG pathways:
None.
Genes:
C15orf5, DBC1, EGFL6, FGF9, FLG, GABRE, GOLSYN, ITIH5, NRCAM, PLGLB2, RALGPS2, SPON1
M2-119 — 17 genes, 5 samples
Enriched GO categories:
extracellular region (CC, p=0.020, 7/700)
extracellular region part (CC, p=0.048, 5/387)
Enriched KEGG pathways:
None.
Genes:
AGBL5, C9orf127, CDH8, DBC1, EGFL6, F10, FGF9, GOLSYN, IGF1, IL27RA, ITIH5, NME3, NRCAM, PRELP, SPON1, STARD5, VAMP1
M2-192 — 27 genes, 5 samples
Enriched GO categories:
extracellular region (CC, p=0.0079, 9/700)
extracellular region part (CC, p=0.0403, 6/387)
Enriched KEGG pathways:
None.
Genes:
AGBL5, AKAP6, B3GNT1, BTD, BTN3A2, C9orf127, CDH8, CRYL1, DBC1, EGFL6, F10, FGF9, GOLSYN, GSTT2, HSPB3, IGF1, IL27RA, ITIH5, KLF5, NME3, NRCAM, PLGLB2, PRELP, SPON1, STARD5, VAMP1, VCAM1
M2-284 — 41 genes, 5 samples
Enriched GO categories:
extracellular region (CC, p=0.0057, 12/700)
Enriched KEGG pathways:
None.
Genes:
AGBL5, AKAP6, B3GNT1, BTD, BTN3A2, C9orf127, CDH8, CHST7, CRYL1, CYP26B1, DBC1, EGFL6, F10, FAM13B, FGF9, GABRE, GOLSYN, GSTT2, HSPB3, ID1, IGF1, IL27RA, ITIH5, KLF5, LMOD1, MR1, NME3, NRCAM, PAPPA2, PEX6, …
M2-323 — 32 genes, 8 samples
Enriched GO categories:
extracellular region (CC, p=0.0077, 10/700)
Enriched KEGG pathways:
None.
Genes:
AGBL5, B3GNT1, BTD, BTN3A2, C15orf5, C9orf127, CDH8, DBC1, EGFL6, ENDOD1, F10, FAM13B, FGF9, FLG, GABRE, GOLSYN, HOXA7, HSPB3, IGF1, IL27RA, ITIH5, KLF5, NME3, NRCAM, PAPPA2, PEX6, PLGLB2, PRELP, RALGPS2, SPON1, …
M2-410 — 60 genes, 5 samples
Enriched GO categories:
extracellular region (CC, p=0.011, 14/700)
retinoic acid metabolic process (BP, p=0.044, 2/3)
Enriched KEGG pathways:
None.
Genes:
AGBL5, AKAP6, ALDH1A3, B3GNT1, BTD, BTN3A2, C15orf5, C1orf115, C7orf58, C9orf127, CDH8, CHST7, CRYL1, CYP26B1, DBC1, DDIT3, DNAJC4, EGFL6, ENDOD1, F10, FAM13B, FGF9, FLG, GABRE, GDPD5, GOLSYN, GSTT2, HOXA7, HSPB3, ID1, …
M2-500 — 41 genes, 20 samples
Enriched GO categories:
extracellular region (CC, p=0.014, 11/700)
Enriched KEGG pathways:
None.
Genes:
ABHD14A, ADAMTS6, AGBL5, B3GNT1, BTD, BTN3A2, C15orf5, C1orf115, C9orf127, CHST7, CYP26B1, DBC1, DNAJC4, EGFL6, ENDOD1, F10, FGF9, FLG, GABRE, GDPD5, GOLSYN, HOXA7, IGF1, ITGB8, ITIH5, KLF5, LEPREL2, LMOD1, LPCAT4, NME3, …
M2-607 — 103 genes, 6 samples
Enriched GO categories:
extracellular region (CC, p=0.013, 19/700)
integral to membrane (CC, p=0.032, 37/2022)
intrinsic to membrane (CC, p=0.040, 37/2051)
Enriched KEGG pathways:
None.
Genes:
ABHD14A, ACCN2, AGBL5, AKAP6, ALDH1A3, ARNT2, B3GALT4, B3GNT1, BTD, BTN3A1, BTN3A2, C10orf116, C14orf94, C15orf5, C1orf115, C4orf30, C7orf58, C9orf127, CDH8, CHAC1, CHST7, CRYL1, CYP26B1, DBC1, DDIT3, DNAJC4, DPYSL4, EGFL6, EIF4H, ENDOD1, …
M2-702 — 163 genes, 5 samples
Enriched GO categories:
MHC class I peptide loading complex (CC, p=0.00043, 4/6)
intrinsic to membrane (CC, p=0.00255, 58/2051)
TAP complex (CC, p=0.00273, 3/4)
integral to membrane (CC, p=0.00513, 56/2022)
extracellular region (CC, p=0.00874, 26/700)
Enriched KEGG pathways:
None.
Genes:
ABHD10, ABHD14A, ACCN2, AGBL5, AKAP6, ALDH1A3, ALDH3B1, ARNT2, B3GALT4, B3GNT1, BCL7B, BST1, BTD, BTN3A1, BTN3A2, BTN3A3, C10orf116, C14orf94, C15orf5, C1orf115, C4orf30, C7orf58, C9orf125, C9orf127, CALB2, CAND2, CDH8, CHAC1, CHST7, CLEC3B, …
M2-711 — 155 genes, 6 samples
Enriched GO categories:
extracellular region (CC, p=0.0033, 27/700)
intrinsic to membrane (CC, p=0.0057, 55/2051)
integral to membrane (CC, p=0.0067, 54/2022)
MHC class I peptide loading complex (CC, p=0.0067, 3/6)
membrane part (CC, p=0.0282, 59/2426)
Enriched KEGG pathways:
None.
Genes:
ABHD14A, ACCN2, AGBL5, AKAP6, ALDH1A3, AMPH, ARNT2, B3GALT4, B3GNT1, BAZ1B, BCL7B, BST1, BTD, BTN3A1, BTN3A2, C10orf116, C14orf94, C15orf5, C1orf115, C4orf30, C4orf31, C7orf58, C9orf125, C9orf127, CALB2, CDH8, CHAC1, CHST7, CLEC11A, CLGN, …
M2-741 — 159 genes, 8 samples
Enriched GO categories:
extracellular region (CC, p=0.00086, 30/700)
intrinsic to membrane (CC, p=0.00230, 59/2051)
integral to membrane (CC, p=0.00409, 57/2022)
membrane part (CC, p=0.00642, 64/2426)
MHC class I peptide loading complex (CC, p=0.00711, 3/6)
Enriched KEGG pathways:
None.
Genes:
AGBL5, AKAP6, ALDH1A3, ALDH3B1, ARNT2, B3GNT1, BCL7B, BST1, BTD, BTN3A1, BTN3A2, BTN3A3, C10orf116, C15orf5, C1orf115, C7orf10, C7orf58, C9orf125, C9orf127, CALB2, CDH8, CHST7, CLEC3B, CLGN, COL8A1, CRELD1, CRYL1, CTSC, CTSO, CYP26B1, …
M2-770 — 149 genes, 9 samples
Enriched GO categories:
intrinsic to membrane (CC, p=0.0011, 57/2051)
integral to membrane (CC, p=0.0013, 56/2022)
extracellular region (CC, p=0.0026, 27/700)
membrane part (CC, p=0.0067, 60/2426)
Enriched KEGG pathways:
None.
Genes:
ABCC9, ABHD14A, ACCN2, AGBL5, AKAP6, ALDH1A3, B3GALT4, B3GNT1, BAZ1B, BCL7B, BST1, BTD, BTN3A1, BTN3A2, C10orf116, C14orf94, C15orf5, C1orf115, C4orf31, C7orf58, C9orf127, CDH8, CHST7, CLEC11A, CLEC3B, CLGN, CNTNAP1, CRELD1, CRYBB2, CRYL1, …
M2-806 — 239 genes, 5 samples
Enriched GO categories:
intrinsic to membrane (CC, p=2.1e-05, 89/2051)
integral to membrane (CC, p=3.7e-05, 87/2022)
membrane part (CC, p=8.6e-04, 94/2426)
MHC class I peptide loading complex (CC, p=1.3e-03, 4/6)
extracellular region (CC, p=2.7e-03, 37/700)
Enriched KEGG pathways:
None.
Genes:
ABCC9, ABHD10, ABHD14A, ACCN2, ACVR2A, ADAMTS6, AGBL5, AKAP6, ALDH1A3, ALDH3B1, AMPH, ANKRD28, ARNT2, B3GALT4, B3GNT1, BAZ1B, BCL7B, BST1, BTD, BTN3A1, BTN3A2, BTN3A3, C10orf116, C10orf57, C10orf72, C14orf94, C15orf5, C17orf85, C1orf115, C4orf30, …
M2-809 — 191 genes, 5 samples
Enriched GO categories:
extracellular region (CC, p=0.00019, 36/700)
intrinsic to membrane (CC, p=0.00255, 69/2051)
integral to membrane (CC, p=0.00409, 67/2022)
antigen processing and presentation of peptide antigen (BP, p=0.02167, 5/21)
extracellular region part (CC, p=0.03137, 19/387)
Enriched KEGG pathways:
None.
Genes:
ABCC9, ABHD14A, ADCY9, ADRA2A, AGBL5, AKAP6, ALDH1A3, ALDH1B1, ALDH3B1, ALDH6A1, ALDH9A1, ANKRD28, ARHGEF6, ASPN, ATF4, ATP2A2, B3GNT1, BAG1, BAZ1B, BST1, BTN3A1, BTN3A2, C10orf116, C10orf57, C10orf72, C1orf115, C2orf68, C4orf18, C4orf30, C4orf31, …
M2-827 — 226 genes, 7 samples
Enriched GO categories:
MHC class I peptide loading complex (CC, p=0.0012, 4/6)
intrinsic to membrane (CC, p=0.0013, 78/2051)
integral to membrane (CC, p=0.0014, 77/2022)
TAP complex (CC, p=0.0055, 3/4)
extracellular region (CC, p=0.0060, 34/700)
Enriched KEGG pathways:
None.
Genes:
ABCC9, ABHD10, ABHD14A, ACCN2, ACVR2A, ADAMTS6, AGBL5, AK5, AKAP6, ALDH1A3, AMPH, ARHGEF6, ARNT2, B3GALT4, B3GNT1, BAG1, BAZ1B, BCL7B, BST1, BTD, BTN3A1, BTN3A2, BZW2, C10orf116, C14orf94, C15orf5, C1orf115, C4orf30, C4orf31, C7orf58, …
M2-328 — 12 genes, 14 samples
Enriched GO categories:
None.
Enriched KEGG pathways:
None.
Genes:
CDKN1C, CRTC3, CTDSP2, DHRS3, LOC100132540, LOC339047, LOC399491, PELI2, RERE, ROR2, TBC1D8, ZHX2
M2-379 — 16 genes, 29 samples
Enriched GO categories:
None.
Enriched KEGG pathways:
None.
Genes:
CDKN1C, CRTC3, DMWD, FBXL11, FLJ12529, FNBP4, LHFPL2, LOC100132540, LOC339047, LOC399491, NPIP, PTPN9, RERE, SF1, SLC25A37, TCF20
M2-503 — 73 genes, 28 samples
Enriched GO categories:
extracellular region (CC, p=1.4e-11, 30/700)
extracellular space (CC, p=1.3e-09, 18/246)
extracellular region part (CC, p=2.9e-09, 21/387)
cytokine activity (MF, p=2.7e-08, 11/73)
inflammatory response (BP, p=5.3e-07, 14/153)
Enriched KEGG pathways:
Cytokine-cytokine receptor interaction (0.00075, 10/122)
Genes:
ABCA5, ABCA8, ANKRD1, ANXA3, BMP2, C1orf54, C3, CADPS2, CCL2, CD200, CFH, CFHR1, COL15A1, CREG1, CXCL1, CXCL2, CXCL3, DACT1, DMD, EPHA5, FGF1, FOXN3, HIVEP1, ICAM1, IER3, IFI27, IL1A, IL1B, IL6, IL8, …
M2-852 — 165 genes, 11 samples
Enriched GO categories:
activation of plasma proteins during acute inflammatory response (BP, p=0.048, 4/17)
complement activation (BP, p=0.048, 4/17)
Enriched KEGG pathways:
None.
Genes:
ADAMTS6, AGBL5, AHCTF1, ALDH1A3, ANKRD28, ANKRD36B, ANXA10, APH1B, APOBEC3F, ARL17, ARL2, ARNT2, ASB1, B3GNTL1, B9D1, BAX, BCCIP, BRE, BTD, BTN3A2, C14orf138, C17orf39, C1orf115, C1orf9, C3, C9orf127, CCDC93, CCNT2, CD320, CD55, …
M2-877 — 339 genes, 6 samples
Enriched GO categories:
MHC class I peptide loading complex (CC, p=0.0029, 4/6)
extracellular region (CC, p=0.0029, 47/700)
intrinsic to membrane (CC, p=0.0058, 104/2051)
integral to membrane (CC, p=0.0073, 102/2022)
TAP complex (CC, p=0.0113, 3/4)
Enriched KEGG pathways:
None.
Genes:
ABCC9, ABHD10, ABHD14A, ACCN2, ACVR2A, ACYP1, ADAMTS6, AGBL5, AK5, AKAP6, ALDH1A3, ALDH1B1, ALDH3B1, ALDH6A1, ALDOC, ALG13, AMPH, ANKRD28, APOD, ARHGEF6, ARL6IP5, ARNT2, ARNTL2, ATF4, ATG16L1, B3GALT4, B3GNT1, BAG1, BAZ1B, BCL7B, …
M2-991 — 373 genes, 12 samples
Enriched GO categories:
extracellular region (CC, p=1.8e-12, 73/700)
extracellular region part (CC, p=3.7e-05, 38/387)
immune response (BP, p=2.4e-03, 30/295)
interleukin-1 receptor activity (MF, p=2.7e-03, 4/4)
extracellular space (CC, p=2.9e-03, 24/246)
Enriched KEGG pathways:
None.
Genes:
ABCA1, ABCA5, ABCC3, ABCC9, ABHD10, ABLIM1, ACSL1, ACVR2A, ADAMTS6, ADH1B, ADK, AKAP2, AKR1A1, AKR1C3, ALDH1A3, ALMS1, ANKMY2, ANKRD36B, APOD, ARHGAP26, ARHGEF11, ARPC1B, ATF5, ATG16L1, ATP2B1, BICC1, BMP2K, BRWD1, BTD, C10orf18, …