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GO enrichment with GOrilla

We use GOrilla to compute GO enrichment of inferred genes: http://cbl-gorilla.cs.technion.ac.il/.

We performed all analysis below on January 5th, 2022. At this time, the GOrilla database had last been updated on March 6th, 2021 (using the GO database and other sources)

All results (list of genes and detailed GO enrichment) can be found in main repository in docs/data_and_resuls/haemochromatosis/networks_hemochromatosis.

Collecting the list of genes of interest

We obtained this list using our R markdown doing network analysis of E-G pairs starting from genes directly involved in hemochromatosis or involved in the regulation of iron metabolism.

We saved this list of 457 (13 known + 444 inferred) genes as new_genes_v7.list. For each one of the 13 initial genes, we also saved separately the corresponding inferred genes:

└── results
...
├── new_genes_v7.list # 457
└── separate
  ├── BMP6.list # 17
  ├── CIAPIN1.list # 56
  ├── CYBRD1.list # 35
  ├── HAMP.list # 35
  ├── HFE2.list # 27
  ├── HFE.list # 61
  ├── NEO1.list # 39
  ├── SLC11A2.list # 68
  ├── SLC39A14.list # 35
  ├── SLC40A1.list # 26
  ├── TFR2.list # 34
  ├── TFRC.list # 10
  └── TMPRSS6.list # 14

GO enrichment

All 457 genes (original + inferred)

Method

We provided GOrilla with two lists:

  • the list of background genes: their 23,221 RefSeq ids, which we saved as all_genes_in_eg_pairs_131_biosamples.list (note that GOrilla found only 21,304 of them, but this is still better than the number of default background genes used by our custom script)

The system has recognized 21304 genes out of 23545 gene terms entered by the user. 21304 genes were recognised by gene symbol and 0 genes by other gene IDs. 314 duplicate genes were removed (keeping the highest ranking instance of each gene) leaving a total of 20990 genes. Only 17621 of these genes are associated with a GO term.

  • the list of the 457 genes for which we want to test enrichment in GO terms, which we denoted new_genes_v7.list (note that GOrilla only found 430 of them, yet our custom script only found 336, so GOrilla did better than us. In other for GOrilla to give us this information, we had to run a separate analysis with this list as single list, ie without background)

The system has recognized 430 genes out of 457 gene terms entered by the user. 430 genes were recognized by gene symbol and 0 genes by other gene IDs . Only 388 of these genes are associated with a GO term.

Note that we set the p-value threshold to the largest possible value in GOrilla, which is 10^-3. The FDR q-value given by GOrilla are obtained by performing the Benjamini and Hochberg correction - the same as that performed by default in our custom script:

'P-value' is the enrichment p-value computed according to the mHG or HG model. This p-value is not corrected for multiple testing of 15373 GO terms.

'FDR q-value' is the correction of the above p-value for multiple testing using the Benjamini and Hochberg (1995) method. Namely, for the ith term (ranked according to p-value) the FDR q-value is (p-value * number of GO terms) / i.

Enrichment (N, B, n, b) is defined as follows: N - is the total number of genes B - is the total number of genes associated with a specific GO term n - is the number of genes in the top of the user's input list or in the target set when appropriate b - is the number of genes in the intersection Enrichment = (b/n) / (B/N)

Genes: For each GO term you can see the list of associated genes that appear in the optimal top of the list. Each gene name is specified by gene symbol followed by a short description of the gene

Results

We saved the results in: /work2/project/regenet/workspace/thoellinger/shared/2022/networks_hemochromatosis/results/GO_FDR/all_genes/GOrilla_all_genes.xls (private).

GO term Description P-value FDR q-value Enrichment (N, B, n, b)
GO:0006334 nucleosome assembly 2.44E-18 3.74E-14 9.45 (17621,125,388,26)
GO:0034728 nucleosome organization 2.05E-16 1.57E-12 7.57 (17621,162,388,27)
GO:0034723 DNA replication-dependent nucleosome organization 5.27E-16 2.7E-12 21.19 (17621,30,388,14)
GO:0006335 DNA replication-dependent nucleosome assembly 5.27E-16 2.03E-12 21.19 (17621,30,388,14)
GO:0055076 transition metal ion homeostasis 2.24E-15 6.88E-12 8.56 (17621,122,388,23)
GO:0065004 protein-DNA complex assembly 2.28E-15 5.85E-12 6.59 (17621,193,388,28)
GO:0046916 cellular transition metal ion homeostasis 5.87E-15 1.29E-11 9.35 (17621,102,388,21)
GO:0071824 protein-DNA complex subunit organization 3.83E-14 7.35E-11 5.68 (17621,232,388,29)
GO:0010273 detoxification of copper ion 6.5E-14 1.11E-10 30.28 (17621,15,388,10)
GO:0000183 chromatin silencing at rDNA 9.01E-14 1.39E-10 17.89 (17621,33,388,13)
GO:0061687 detoxification of inorganic compound 1.7E-13 2.38E-10 28.38 (17621,16,388,10)
GO:0060968 regulation of gene silencing 3.52E-13 4.51E-10 6.83 (17621,153,388,23)
GO:0006333 chromatin assembly or disassembly 4.51E-13 5.33E-10 8.72 (17621,99,388,19)
GO:0006342 chromatin silencing 1.09E-12 1.2E-9 8.98 (17621,91,388,18)
GO:0071280 cellular response to copper ion 7.87E-12 8.06E-9 17.84 (17621,28,388,11)
GO:0071294 cellular response to zinc ion 2.12E-11 2.03E-8 19.75 (17621,23,388,10)
GO:0046688 response to copper ion 2.51E-11 2.27E-8 13.97 (17621,39,388,12)
GO:0045814 negative regulation of gene expression, epigenetic 2.68E-11 2.29E-8 7.50 (17621,109,388,18)
GO:0006882 cellular zinc ion homeostasis 2.92E-11 2.36E-8 16.11 (17621,31,388,11)
GO:0060964 regulation of gene silencing by miRNA 7.84E-11 6.03E-8 7.05 (17621,116,388,18)
GO:0055069 zinc ion homeostasis 9.31E-11 6.81E-8 14.69 (17621,34,388,11)
GO:0060966 regulation of gene silencing by RNA 1.05E-10 7.34E-8 6.93 (17621,118,388,18)
GO:0060147 regulation of posttranscriptional gene silencing 1.05E-10 7.02E-8 6.93 (17621,118,388,18)
GO:0045652 regulation of megakaryocyte differentiation 1.08E-10 6.92E-8 8.85 (17621,77,388,15)
GO:0040029 regulation of gene expression, epigenetic 2.61E-10 1.6E-7 4.58 (17621,248,388,25)
GO:0016458 gene silencing 6.61E-10 3.91E-7 5.50 (17621,165,388,20)
GO:0071276 cellular response to cadmium ion 4.89E-9 2.79E-6 12.27 (17621,37,388,10)
GO:0006325 chromatin organization 6.28E-9 3.45E-6 2.72 (17621,684,388,41)
GO:0055072 iron ion homeostasis 7.27E-9 3.85E-6 7.98 (17621,74,388,13)
GO:0010043 response to zinc ion 2.1E-8 1.07E-5 9.25 (17621,54,388,11)
GO:0045653 negative regulation of megakaryocyte differentiation 2.29E-8 1.14E-5 19.87 (17621,16,388,7)
GO:0006879 cellular iron ion homeostasis 6.67E-8 3.2E-5 8.33 (17621,60,388,11)
GO:0046686 response to cadmium ion 4.86E-7 2.26E-4 7.83 (17621,58,388,10)
GO:0010038 response to metal ion 5.77E-7 2.61E-4 3.21 (17621,340,388,24)
GO:0016233 telomere capping 5.96E-7 2.62E-4 13.25 (17621,24,388,7)
GO:0045637 regulation of myeloid cell differentiation 6.11E-7 2.61E-4 3.68 (17621,247,388,20)
GO:0071248 cellular response to metal ion 6.41E-7 2.66E-4 4.22 (17621,183,388,17)
GO:0010039 response to iron ion 1.44E-6 5.84E-4 11.77 (17621,27,388,7)
GO:0032200 telomere organization 1.5E-6 5.92E-4 5.13 (17621,115,388,13)
GO:0034622 cellular protein-containing complex assembly 1.71E-6 6.57E-4 2.24 (17621,812,388,40)
GO:0065003 protein-containing complex assembly 1.92E-6 7.19E-4 1.94 (17621,1262,388,54)
GO:0022607 cellular component assembly 3.32E-6 1.22E-3 1.66 (17621,2162,388,79)
GO:0034755 iron ion transmembrane transport 3.52E-6 1.26E-3 18.92 (17621,12,388,5)
GO:0071241 cellular response to inorganic substance 4.29E-6 1.5E-3 3.68 (17621,210,388,17)
GO:0043933 protein-containing complex subunit organization 5.12E-6 1.75E-3 1.79 (17621,1544,388,61)
GO:0060586 multicellular organismal iron ion homeostasis 7.69E-6 2.57E-3 25.95 (17621,7,388,4)
GO:0010035 response to inorganic substance 1.06E-5 3.47E-3 2.53 (17621,485,388,27)
GO:0006336 DNA replication-independent nucleosome assembly 1.43E-5 4.58E-3 7.12 (17621,51,388,8)
GO:0045934 negative regulation of nucleobase-containing compound metabolic process 1.46E-5 4.58E-3 1.78 (17621,1457,388,57)
GO:0034724 DNA replication-independent nucleosome organization 1.66E-5 5.1E-3 6.99 (17621,52,388,8)
GO:0055065 metal ion homeostasis 1.8E-5 5.41E-3 2.32 (17621,587,388,30)
GO:0016584 nucleosome positioning 1.8E-5 5.33E-3 14.19 (17621,16,388,5)
GO:0045926 negative regulation of growth 2.23E-5 6.46E-3 3.24 (17621,238,388,17)
GO:0038111 interleukin-7-mediated signaling pathway 2.74E-5 7.8E-3 9.73 (17621,28,388,6)
GO:0034080 CENP-A containing nucleosome assembly 2.8E-5 7.83E-3 7.75 (17621,41,388,7)
GO:0055080 cation homeostasis 3.47E-5 9.52E-3 2.17 (17621,669,388,32)
GO:0006536 glutamate metabolic process 4.16E-5 1.12E-2 9.08 (17621,30,388,6)
GO:0006875 cellular metal ion homeostasis 4.4E-5 1.17E-2 2.33 (17621,526,388,27)
GO:0031936 negative regulation of chromatin silencing 4.55E-5 1.18E-2 11.95 (17621,19,388,5)
GO:0098771 inorganic ion homeostasis 4.61E-5 1.18E-2 2.14 (17621,679,388,32)
GO:0031055 chromatin remodeling at centromere 5.24E-5 1.32E-2 7.06 (17621,45,388,7)
GO:0007166 cell surface receptor signaling pathway 5.33E-5 1.32E-2 1.57 (17621,2109,388,73)
GO:0051276 chromosome organization 6.2E-5 1.51E-2 2.55 (17621,392,388,22)
GO:0030003 cellular cation homeostasis 7.83E-5 1.88E-2 2.18 (17621,605,388,29)
GO:0036017 response to erythropoietin 1.03E-4 2.42E-2 27.25 (17621,5,388,3)
GO:0006873 cellular ion homeostasis 1.13E-4 2.64E-2 2.13 (17621,618,388,29)
GO:0045892 negative regulation of transcription, DNA-templated 1.38E-4 3.16E-2 1.74 (17621,1224,388,47)
GO:0042592 homeostatic process 1.43E-4 3.23E-2 1.67 (17621,1438,388,53)
GO:1903507 negative regulation of nucleic acid-templated transcription 1.43E-4 3.19E-2 1.74 (17621,1226,388,47)
GO:0050801 ion homeostasis 1.44E-4 3.16E-2 1.99 (17621,754,388,33)
GO:1902679 negative regulation of RNA biosynthetic process 1.49E-4 3.22E-2 1.74 (17621,1228,388,47)
GO:0051252 regulation of RNA metabolic process 1.56E-4 3.32E-2 1.38 (17621,3595,388,109)
GO:0006303 double-strand break repair via nonhomologous end joining 1.8E-4 3.79E-2 5.05 (17621,72,388,8)
GO:0043486 histone exchange 1.94E-4 4.03E-2 5.78 (17621,55,388,7)
GO:0006826 iron ion transport 1.94E-4 3.98E-2 5.78 (17621,55,388,7)
GO:2001141 regulation of RNA biosynthetic process 2.16E-4 4.37E-2 1.39 (17621,3342,388,102)
GO:0000726 non-recombinational repair 2.18E-4 4.35E-2 4.91 (17621,74,388,8)
GO:0009889 regulation of biosynthetic process 2.69E-4 5.31E-2 1.33 (17621,4054,388,119)
GO:0048878 chemical homeostasis 2.78E-4 5.41E-2 1.77 (17621,1052,388,41)
GO:0019725 cellular homeostasis 2.79E-4 5.37E-2 1.89 (17621,815,388,34)
GO:0098754 detoxification 2.82E-4 5.34E-2 3.85 (17621,118,388,10)
GO:0031326 regulation of cellular biosynthetic process 2.93E-4 5.5E-2 1.34 (17621,3980,388,117)
GO:0006355 regulation of transcription, DNA-templated 3.03E-4 5.62E-2 1.38 (17621,3332,388,101)
GO:1903506 regulation of nucleic acid-templated transcription 3.07E-4 5.62E-2 1.38 (17621,3333,388,101)
GO:0019219 regulation of nucleobase-containing compound metabolic process 3.23E-4 5.84E-2 1.34 (17621,3907,388,115)
GO:1903706 regulation of hemopoiesis 3.83E-4 6.85E-2 2.19 (17621,476,388,23)
GO:0002385 mucosal immune response 3.87E-4 6.85E-2 7.83 (17621,29,388,5)
GO:0051253 negative regulation of RNA metabolic process 4.09E-4 7.14E-2 1.65 (17621,1320,388,48)
GO:0055082 cellular chemical homeostasis 4.1E-4 7.08E-2 1.95 (17621,700,388,30)
GO:1902871 positive regulation of amacrine cell differentiation 4.84E-4 8.26E-2 45.41 (17621,2,388,2)
GO:1902868 positive regulation of retina development in camera-type eye 4.84E-4 8.17E-2 45.41 (17621,2,388,2)
GO:0061075 positive regulation of neural retina development 4.84E-4 8.08E-2 45.41 (17621,2,388,2)
GO:0021893 cerebral cortex GABAergic interneuron fate commitment 4.84E-4 7.99E-2 45.41 (17621,2,388,2)
GO:0009439 cyanate metabolic process 4.84E-4 7.91E-2 45.41 (17621,2,388,2)
GO:0009440 cyanate catabolic process 4.84E-4 7.83E-2 45.41 (17621,2,388,2)
GO:0046712 GDP catabolic process 4.84E-4 7.74E-2 45.41 (17621,2,388,2)
GO:0010556 regulation of macromolecule biosynthetic process 5.18E-4 8.21E-2 1.33 (17621,3789,388,111)
GO:0071281 cellular response to iron ion 5.46E-4 8.57E-2 17.03 (17621,8,388,3)
GO:0006323 DNA packaging 5.49E-4 8.53E-2 5.80 (17621,47,388,6)
GO:0043044 ATP-dependent chromatin remodeling 5.65E-4 8.68E-2 4.27 (17621,85,388,8)
GO:0009064 glutamine family amino acid metabolic process 6.64E-4 1.01E-1 4.74 (17621,67,388,7)
GO:0010558 negative regulation of macromolecule biosynthetic process 7.14E-4 1.08E-1 1.59 (17621,1427,388,50)
GO:0002251 organ or tissue specific immune response 7.2E-4 1.08E-1 6.88 (17621,33,388,5)
GO:0045638 negative regulation of myeloid cell differentiation 7.68E-4 1.14E-1 4.08 (17621,89,388,8)
GO:0031935 regulation of chromatin silencing 8.29E-4 1.21E-1 6.68 (17621,34,388,5)
GO:0002042 cell migration involved in sprouting angiogenesis 8.48E-4 1.23E-1 9.08 (17621,20,388,4)
GO:0009890 negative regulation of biosynthetic process 9.54E-4 1.37E-1 1.55 (17621,1520,388,52)

Notably, for the 57 first GO terms of the above table, we have a (true) FDR < 1%.

13 initial genes only

Method

We provided GOrilla with two lists:

  • the list of background genes: their 23,221 RefSeq ids, just as before

The system has recognized 21304 genes out of 23545 gene terms entered by the user. 21304 genes were recognised by gene symbol and 0 genes by other gene IDs. 314 duplicate genes were removed (keeping the highest ranking instance of each gene) leaving a total of 20990 genes. Only 17621 of these genes are associated with a GO term.

  • the list of the 13 initial genes involved in hemochromatosis and iron metabolism regulation we chose to work with. Namely:

HFE TFR2 HFE2 HAMP SLC40A1 BMP6 TMPRSS6 TFRC SLC11A2 CYBRD1 NEO1 CIAPIN1 SLC39A14

The system has recognized 13 genes out of 13 gene terms entered by the user. 13 genes were recognized by gene symbol and 0 genes by other gene IDs.

Note that we set the p-value threshold to the largest possible value in GOrilla, which is 10^-3. The FDR q-value given by GOrilla are obtained by performing the Benjamini and Hochberg correction.

Results

GO term Description P-value FDR q-value Enrichment (N, B, n, b)
GO:0055072 iron ion homeostasis 1.53E-28 2.35E-24 219.80 (17621,74,13,12)
GO:0006879 cellular iron ion homeostasis 2.09E-26 1.61E-22 248.50 (17621,60,13,11)
GO:0055076 transition metal ion homeostasis 9E-26 4.61E-22 133.32 (17621,122,13,12)
GO:0046916 cellular transition metal ion homeostasis 1.08E-23 4.17E-20 146.18 (17621,102,13,11)
GO:0055065 metal ion homeostasis 2.11E-17 6.49E-14 27.71 (17621,587,13,12)
GO:0055080 cation homeostasis 1.02E-16 2.62E-13 24.31 (17621,669,13,12)
GO:0098771 inorganic ion homeostasis 1.22E-16 2.69E-13 23.96 (17621,679,13,12)
GO:0050801 ion homeostasis 4.33E-16 8.32E-13 21.57 (17621,754,13,12)
GO:0006875 cellular metal ion homeostasis 1.12E-15 1.91E-12 28.35 (17621,526,13,11)
GO:0030003 cellular cation homeostasis 5.24E-15 8.06E-12 24.64 (17621,605,13,11)
GO:0006873 cellular ion homeostasis 6.63E-15 9.26E-12 24.13 (17621,618,13,11)
GO:0010039 response to iron ion 1.21E-14 1.56E-11 301.21 (17621,27,13,6)
GO:0048878 chemical homeostasis 2.38E-14 2.81E-11 15.46 (17621,1052,13,12)
GO:0055082 cellular chemical homeostasis 2.61E-14 2.87E-11 21.30 (17621,700,13,11)
GO:0019725 cellular homeostasis 1.39E-13 1.43E-10 18.29 (17621,815,13,11)
GO:0042592 homeostatic process 1.01E-12 9.67E-10 11.31 (17621,1438,13,12)
GO:0006826 iron ion transport 1.18E-12 1.06E-9 147.87 (17621,55,13,6)
GO:0060586 multicellular organismal iron ion homeostasis 6.22E-12 5.32E-9 774.55 (17621,7,13,4)
GO:0000041 transition metal ion transport 6.06E-11 4.9E-8 78.20 (17621,104,13,6)
GO:0034755 iron ion transmembrane transport 8.78E-11 6.75E-8 451.82 (17621,12,13,4)
GO:0071281 cellular response to iron ion 1.75E-8 1.28E-5 508.30 (17621,8,13,3)
GO:0065008 regulation of biological quality 5.5E-8 3.84E-5 4.52 (17621,3600,13,12)
GO:0010038 response to metal ion 7.56E-8 5.05E-5 23.92 (17621,340,13,6)
GO:0010035 response to inorganic substance 6.14E-7 3.93E-4 16.77 (17621,485,13,6)
GO:1990641 response to iron ion starvation 1.51E-6 9.27E-4 903.64 (17621,3,13,2)
GO:0048871 multicellular organismal homeostasis 2.17E-6 1.28E-3 40.46 (17621,134,13,4)
GO:0015682 ferric iron transport 2.21E-6 1.26E-3 112.96 (17621,36,13,3)
GO:0033572 transferrin transport 2.21E-6 1.21E-3 112.96 (17621,36,13,3)
GO:0072512 trivalent inorganic cation transport 2.21E-6 1.17E-3 112.96 (17621,36,13,3)
GO:0030001 metal ion transport 2.21E-6 1.13E-3 13.46 (17621,604,13,6)
GO:0006953 acute-phase response 2.61E-6 1.29E-3 107.01 (17621,38,13,3)
GO:0033212 iron assimilation 3.01E-6 1.45E-3 677.73 (17621,4,13,2)
GO:0015691 cadmium ion transport 5.02E-6 2.34E-3 542.18 (17621,5,13,2)
GO:0070574 cadmium ion transmembrane transport 5.02E-6 2.27E-3 542.18 (17621,5,13,2)
GO:0006812 cation transport 9.62E-6 4.23E-3 10.44 (17621,779,13,6)
GO:0042221 response to chemical 1.01E-5 4.3E-3 4.85 (17621,2516,13,9)
GO:0002526 acute inflammatory response 1.1E-5 4.58E-3 66.66 (17621,61,13,3)
GO:0034756 regulation of iron ion transport 1.4E-5 5.68E-3 338.87 (17621,8,13,2)
GO:0071421 manganese ion transmembrane transport 1.8E-5 7.11E-3 301.21 (17621,9,13,2)
GO:0090092 regulation of transmembrane receptor protein serine/threonine kinase signaling pathway 2.29E-5 8.79E-3 22.31 (17621,243,13,4)
GO:0030509 BMP signaling pathway 2.89E-5 1.08E-2 48.41 (17621,84,13,3)
GO:0006828 manganese ion transport 5.25E-5 1.92E-2 180.73 (17621,15,13,2)
GO:0090100 positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway 5.32E-5 1.9E-2 39.48 (17621,103,13,3)
GO:0070887 cellular response to chemical stimulus 5.4E-5 1.89E-2 5.91 (17621,1606,13,7)
GO:0046887 positive regulation of hormone secretion 9.69E-5 3.31E-2 32.27 (17621,126,13,3)
GO:0006811 ion transport 1.41E-4 4.72E-2 6.50 (17621,1252,13,6)
GO:0002793 positive regulation of peptide secretion 1.62E-4 5.31E-2 27.11 (17621,150,13,3)
GO:0007178 transmembrane receptor protein serine/threonine kinase signaling pathway 2.19E-4 7.02E-2 24.50 (17621,166,13,3)
GO:0097421 liver regeneration 2.31E-4 7.24E-2 87.45 (17621,31,13,2)
GO:0010628 positive regulation of gene expression 2.34E-4 7.18E-2 4.70 (17621,2017,13,7)
GO:0006954 inflammatory response 2.46E-4 7.4E-2 12.10 (17621,448,13,4)
GO:0071773 cellular response to BMP stimulus 2.62E-4 7.74E-2 82.15 (17621,33,13,2)
GO:0071772 response to BMP 2.62E-4 7.6E-2 82.15 (17621,33,13,2)
GO:0071248 cellular response to metal ion 2.92E-4 8.31E-2 22.22 (17621,183,13,3)
GO:0071241 cellular response to inorganic substance 4.37E-4 1.22E-1 19.36 (17621,210,13,3)
GO:0010817 regulation of hormone levels 4.59E-4 1.26E-1 10.27 (17621,528,13,4)
GO:0045124 regulation of bone resorption 4.67E-4 1.26E-1 61.61 (17621,44,13,2)
GO:0098662 inorganic cation transmembrane transport 4.93E-4 1.31E-1 10.08 (17621,538,13,4)
GO:0010862 positive regulation of pathway-restricted SMAD protein phosphorylation 5.56E-4 1.45E-1 56.48 (17621,48,13,2)
GO:0046850 regulation of bone remodeling 6.28E-4 1.61E-1 53.16 (17621,51,13,2)
GO:0098657 import into cell 6.64E-4 1.67E-1 9.32 (17621,582,13,4)
GO:0010106 cellular response to iron ion starvation 7.38E-4 1.83E-1 1,355.46 (17621,1,13,1)
GO:0002626 negative regulation of T cell antigen processing and presentation 7.38E-4 1.8E-1 1,355.46 (17621,1,13,1)
GO:1904283 negative regulation of antigen processing and presentation of endogenous peptide antigen via MHC class I 7.38E-4 1.77E-1 1,355.46 (17621,1,13,1)
GO:1904282 regulation of antigen processing and presentation of endogenous peptide antigen via MHC class I 7.38E-4 1.74E-1 1,355.46 (17621,1,13,1)
GO:0015684 ferrous iron transport 7.38E-4 1.72E-1 1,355.46 (17621,1,13,1)
GO:0015675 nickel cation transport 7.38E-4 1.69E-1 1,355.46 (17621,1,13,1)
GO:0015692 lead ion transport 7.38E-4 1.67E-1 1,355.46 (17621,1,13,1)
GO:1903988 ferrous iron export across plasma membrane 7.38E-4 1.64E-1 1,355.46 (17621,1,13,1)
GO:1903874 ferrous iron transmembrane transport 7.38E-4 1.62E-1 1,355.46 (17621,1,13,1)
GO:0035444 nickel cation transmembrane transport 7.38E-4 1.6E-1 1,355.46 (17621,1,13,1)
GO:1903414 iron cation export 7.38E-4 1.58E-1 1,355.46 (17621,1,13,1)
GO:0098655 cation transmembrane transport 7.54E-4 1.59E-1 9.01 (17621,602,13,4)
GO:0010647 positive regulation of cell communication 8.03E-4 1.67E-1 4.73 (17621,1720,13,6)
GO:0023056 positive regulation of signaling 8.21E-4 1.68E-1 4.71 (17621,1727,13,6)
GO:0046883 regulation of hormone secretion 8.23E-4 1.66E-1 15.58 (17621,261,13,3)
GO:1903532 positive regulation of secretion by cell 8.32E-4 1.66E-1 15.52 (17621,262,13,3)
GO:0006355 regulation of transcription, DNA-templated 8.38E-4 1.65E-1 3.25 (17621,3332,13,8)
GO:1903506 regulation of nucleic acid-templated transcription 8.4E-4 1.64E-1 3.25 (17621,3333,13,8)
GO:2001141 regulation of RNA biosynthetic process 8.56E-4 1.65E-1 3.24 (17621,3342,13,8)
GO:0098660 inorganic ion transmembrane transport 8.89E-4 1.69E-1 8.62 (17621,629,13,4)
GO:0060393 regulation of pathway-restricted SMAD protein phosphorylation 8.97E-4 1.68E-1 44.44 (17621,61,13,2)
GO:0006357 regulation of transcription by RNA polymerase II 9.57E-4 1.77E-1 3.75 (17621,2527,13,7)
GO:0070838 divalent metal ion transport 9.68E-4 1.77E-1 14.73 (17621,276,13,3)

Notably, for the 40 first GO terms of the above table, we have a (true) FDR < 1%.

All 444 genes (inferred only ; w/o original genes)

Method

We provided GOrilla with two lists:

  • the list of background genes: their 23,221 RefSeq ids, just as before

  • the list of the 410 inferred genes, which we denoted new_genes_v7_wo_orig.list (note that GOrilla only found 430 of them, yet our custom script only found 324, so GOrilla did better than us. In other for GOrilla to give us this information, we had to run a separate analysis with this list as single list, ie without background)

The system has recognized 430 genes out of 457 gene terms entered by the user. 430 genes were recognized by gene symbol and 0 genes by other gene IDs . Only 388 of these genes are associated with a GO term.

Results

GO term Description P-value FDR q-value Enrichment (N, B, n, b)
GO:0006334 nucleosome assembly 2.44E-18 3.74E-14 9.45 (17621,125,388,26)
GO:0034728 nucleosome organization 2.05E-16 1.57E-12 7.57 (17621,162,388,27)
GO:0034723 DNA replication-dependent nucleosome organization 5.27E-16 2.7E-12 21.19 (17621,30,388,14)
GO:0006335 DNA replication-dependent nucleosome assembly 5.27E-16 2.03E-12 21.19 (17621,30,388,14)
GO:0055076 transition metal ion homeostasis 2.24E-15 6.88E-12 8.56 (17621,122,388,23)
GO:0065004 protein-DNA complex assembly 2.28E-15 5.85E-12 6.59 (17621,193,388,28)
GO:0046916 cellular transition metal ion homeostasis 5.87E-15 1.29E-11 9.35 (17621,102,388,21)
GO:0071824 protein-DNA complex subunit organization 3.83E-14 7.35E-11 5.68 (17621,232,388,29)
GO:0010273 detoxification of copper ion 6.5E-14 1.11E-10 30.28 (17621,15,388,10)
GO:0000183 chromatin silencing at rDNA 9.01E-14 1.39E-10 17.89 (17621,33,388,13)
GO:0061687 detoxification of inorganic compound 1.7E-13 2.38E-10 28.38 (17621,16,388,10)
GO:0060968 regulation of gene silencing 3.52E-13 4.51E-10 6.83 (17621,153,388,23)
GO:0006333 chromatin assembly or disassembly 4.51E-13 5.33E-10 8.72 (17621,99,388,19)
GO:0006342 chromatin silencing 1.09E-12 1.2E-9 8.98 (17621,91,388,18)
GO:0071280 cellular response to copper ion 7.87E-12 8.06E-9 17.84 (17621,28,388,11)
GO:0071294 cellular response to zinc ion 2.12E-11 2.03E-8 19.75 (17621,23,388,10)
GO:0046688 response to copper ion 2.51E-11 2.27E-8 13.97 (17621,39,388,12)
GO:0045814 negative regulation of gene expression, epigenetic 2.68E-11 2.29E-8 7.50 (17621,109,388,18)
GO:0006882 cellular zinc ion homeostasis 2.92E-11 2.36E-8 16.11 (17621,31,388,11)
GO:0060964 regulation of gene silencing by miRNA 7.84E-11 6.03E-8 7.05 (17621,116,388,18)
GO:0055069 zinc ion homeostasis 9.31E-11 6.81E-8 14.69 (17621,34,388,11)
GO:0060966 regulation of gene silencing by RNA 1.05E-10 7.34E-8 6.93 (17621,118,388,18)
GO:0060147 regulation of posttranscriptional gene silencing 1.05E-10 7.02E-8 6.93 (17621,118,388,18)
GO:0045652 regulation of megakaryocyte differentiation 1.08E-10 6.92E-8 8.85 (17621,77,388,15)
GO:0040029 regulation of gene expression, epigenetic 2.61E-10 1.6E-7 4.58 (17621,248,388,25)
GO:0016458 gene silencing 6.61E-10 3.91E-7 5.50 (17621,165,388,20)
GO:0071276 cellular response to cadmium ion 4.89E-9 2.79E-6 12.27 (17621,37,388,10)
GO:0006325 chromatin organization 6.28E-9 3.45E-6 2.72 (17621,684,388,41)
GO:0055072 iron ion homeostasis 7.27E-9 3.85E-6 7.98 (17621,74,388,13)
GO:0010043 response to zinc ion 2.1E-8 1.07E-5 9.25 (17621,54,388,11)
GO:0045653 negative regulation of megakaryocyte differentiation 2.29E-8 1.14E-5 19.87 (17621,16,388,7)
GO:0006879 cellular iron ion homeostasis 6.67E-8 3.2E-5 8.33 (17621,60,388,11)
GO:0046686 response to cadmium ion 4.86E-7 2.26E-4 7.83 (17621,58,388,10)
GO:0010038 response to metal ion 5.77E-7 2.61E-4 3.21 (17621,340,388,24)
GO:0016233 telomere capping 5.96E-7 2.62E-4 13.25 (17621,24,388,7)
GO:0045637 regulation of myeloid cell differentiation 6.11E-7 2.61E-4 3.68 (17621,247,388,20)
GO:0071248 cellular response to metal ion 6.41E-7 2.66E-4 4.22 (17621,183,388,17)
GO:0010039 response to iron ion 1.44E-6 5.84E-4 11.77 (17621,27,388,7)
GO:0032200 telomere organization 1.5E-6 5.92E-4 5.13 (17621,115,388,13)
GO:0034622 cellular protein-containing complex assembly 1.71E-6 6.57E-4 2.24 (17621,812,388,40)
GO:0065003 protein-containing complex assembly 1.92E-6 7.19E-4 1.94 (17621,1262,388,54)
GO:0022607 cellular component assembly 3.32E-6 1.22E-3 1.66 (17621,2162,388,79)
GO:0034755 iron ion transmembrane transport 3.52E-6 1.26E-3 18.92 (17621,12,388,5)
GO:0071241 cellular response to inorganic substance 4.29E-6 1.5E-3 3.68 (17621,210,388,17)
GO:0043933 protein-containing complex subunit organization 5.12E-6 1.75E-3 1.79 (17621,1544,388,61)
GO:0060586 multicellular organismal iron ion homeostasis 7.69E-6 2.57E-3 25.95 (17621,7,388,4)
GO:0010035 response to inorganic substance 1.06E-5 3.47E-3 2.53 (17621,485,388,27)
GO:0006336 DNA replication-independent nucleosome assembly 1.43E-5 4.58E-3 7.12 (17621,51,388,8)
GO:0045934 negative regulation of nucleobase-containing compound metabolic process 1.46E-5 4.58E-3 1.78 (17621,1457,388,57)
GO:0034724 DNA replication-independent nucleosome organization 1.66E-5 5.1E-3 6.99 (17621,52,388,8)
GO:0055065 metal ion homeostasis 1.8E-5 5.41E-3 2.32 (17621,587,388,30)
GO:0016584 nucleosome positioning 1.8E-5 5.33E-3 14.19 (17621,16,388,5)
GO:0045926 negative regulation of growth 2.23E-5 6.46E-3 3.24 (17621,238,388,17)
GO:0038111 interleukin-7-mediated signaling pathway 2.74E-5 7.8E-3 9.73 (17621,28,388,6)
GO:0034080 CENP-A containing nucleosome assembly 2.8E-5 7.83E-3 7.75 (17621,41,388,7)
GO:0055080 cation homeostasis 3.47E-5 9.52E-3 2.17 (17621,669,388,32)
GO:0006536 glutamate metabolic process 4.16E-5 1.12E-2 9.08 (17621,30,388,6)
GO:0006875 cellular metal ion homeostasis 4.4E-5 1.17E-2 2.33 (17621,526,388,27)
GO:0031936 negative regulation of chromatin silencing 4.55E-5 1.18E-2 11.95 (17621,19,388,5)
GO:0098771 inorganic ion homeostasis 4.61E-5 1.18E-2 2.14 (17621,679,388,32)
GO:0031055 chromatin remodeling at centromere 5.24E-5 1.32E-2 7.06 (17621,45,388,7)
GO:0007166 cell surface receptor signaling pathway 5.33E-5 1.32E-2 1.57 (17621,2109,388,73)
GO:0051276 chromosome organization 6.2E-5 1.51E-2 2.55 (17621,392,388,22)
GO:0030003 cellular cation homeostasis 7.83E-5 1.88E-2 2.18 (17621,605,388,29)
GO:0036017 response to erythropoietin 1.03E-4 2.42E-2 27.25 (17621,5,388,3)
GO:0006873 cellular ion homeostasis 1.13E-4 2.64E-2 2.13 (17621,618,388,29)
GO:0045892 negative regulation of transcription, DNA-templated 1.38E-4 3.16E-2 1.74 (17621,1224,388,47)
GO:0042592 homeostatic process 1.43E-4 3.23E-2 1.67 (17621,1438,388,53)
GO:1903507 negative regulation of nucleic acid-templated transcription 1.43E-4 3.19E-2 1.74 (17621,1226,388,47)
GO:0050801 ion homeostasis 1.44E-4 3.16E-2 1.99 (17621,754,388,33)
GO:1902679 negative regulation of RNA biosynthetic process 1.49E-4 3.22E-2 1.74 (17621,1228,388,47)
GO:0051252 regulation of RNA metabolic process 1.56E-4 3.32E-2 1.38 (17621,3595,388,109)
GO:0006303 double-strand break repair via nonhomologous end joining 1.8E-4 3.79E-2 5.05 (17621,72,388,8)
GO:0043486 histone exchange 1.94E-4 4.03E-2 5.78 (17621,55,388,7)
GO:0006826 iron ion transport 1.94E-4 3.98E-2 5.78 (17621,55,388,7)
GO:2001141 regulation of RNA biosynthetic process 2.16E-4 4.37E-2 1.39 (17621,3342,388,102)
GO:0000726 non-recombinational repair 2.18E-4 4.35E-2 4.91 (17621,74,388,8)
GO:0009889 regulation of biosynthetic process 2.69E-4 5.31E-2 1.33 (17621,4054,388,119)
GO:0048878 chemical homeostasis 2.78E-4 5.41E-2 1.77 (17621,1052,388,41)
GO:0019725 cellular homeostasis 2.79E-4 5.37E-2 1.89 (17621,815,388,34)
GO:0098754 detoxification 2.82E-4 5.34E-2 3.85 (17621,118,388,10)
GO:0031326 regulation of cellular biosynthetic process 2.93E-4 5.5E-2 1.34 (17621,3980,388,117)
GO:0006355 regulation of transcription, DNA-templated 3.03E-4 5.62E-2 1.38 (17621,3332,388,101)
GO:1903506 regulation of nucleic acid-templated transcription 3.07E-4 5.62E-2 1.38 (17621,3333,388,101)
GO:0019219 regulation of nucleobase-containing compound metabolic process 3.23E-4 5.84E-2 1.34 (17621,3907,388,115)
GO:1903706 regulation of hemopoiesis 3.83E-4 6.85E-2 2.19 (17621,476,388,23)
GO:0002385 mucosal immune response 3.87E-4 6.85E-2 7.83 (17621,29,388,5)
GO:0051253 negative regulation of RNA metabolic process 4.09E-4 7.14E-2 1.65 (17621,1320,388,48)
GO:0055082 cellular chemical homeostasis 4.1E-4 7.08E-2 1.95 (17621,700,388,30)
GO:1902871 positive regulation of amacrine cell differentiation 4.84E-4 8.26E-2 45.41 (17621,2,388,2)
GO:1902868 positive regulation of retina development in camera-type eye 4.84E-4 8.17E-2 45.41 (17621,2,388,2)
GO:0061075 positive regulation of neural retina development 4.84E-4 8.08E-2 45.41 (17621,2,388,2)
GO:0021893 cerebral cortex GABAergic interneuron fate commitment 4.84E-4 7.99E-2 45.41 (17621,2,388,2)
GO:0009439 cyanate metabolic process 4.84E-4 7.91E-2 45.41 (17621,2,388,2)
GO:0009440 cyanate catabolic process 4.84E-4 7.83E-2 45.41 (17621,2,388,2)
GO:0046712 GDP catabolic process 4.84E-4 7.74E-2 45.41 (17621,2,388,2)
GO:0010556 regulation of macromolecule biosynthetic process 5.18E-4 8.21E-2 1.33 (17621,3789,388,111)
GO:0071281 cellular response to iron ion 5.46E-4 8.57E-2 17.03 (17621,8,388,3)
GO:0006323 DNA packaging 5.49E-4 8.53E-2 5.80 (17621,47,388,6)
GO:0043044 ATP-dependent chromatin remodeling 5.65E-4 8.68E-2 4.27 (17621,85,388,8)
GO:0009064 glutamine family amino acid metabolic process 6.64E-4 1.01E-1 4.74 (17621,67,388,7)
GO:0010558 negative regulation of macromolecule biosynthetic process 7.14E-4 1.08E-1 1.59 (17621,1427,388,50)
GO:0002251 organ or tissue specific immune response 7.2E-4 1.08E-1 6.88 (17621,33,388,5)
GO:0045638 negative regulation of myeloid cell differentiation 7.68E-4 1.14E-1 4.08 (17621,89,388,8)
GO:0031935 regulation of chromatin silencing 8.29E-4 1.21E-1 6.68 (17621,34,388,5)
GO:0002042 cell migration involved in sprouting angiogenesis 8.48E-4 1.23E-1 9.08 (17621,20,388,4)
GO:0009890 negative regulation of biosynthetic process 9.54E-4 1.37E-1 1.55 (17621,1520,388,52)

Notably, for the 56 first GO terms of the above table, we have a (true) FDR < 1%.