Worg Enrichment pipeline
Table of Contents
Current Inputs
| input | background |
| /home/nceglia/codebase/projects/breast-cancer/website/onco.txt | background |
The gene IDs converted to UNIPROT_ACCESSION are:
| CAMK1D | Q8BW96 |
| CBLN4 | Q8BME9 |
| CDH26 | P59862 |
| CNOT4 | Q8BT14 |
| CREB3L1 | Q9Z125 |
| DAPK1 | Q80YE7 |
| FOXN3 | Q499D0 |
| GPNMB | Q99P91 |
| HEATR5A | Q5PRF0 |
| KALRN | A2CG49 |
| LRP12 | Q8BUJ9 |
| NFIX | P70257 |
| RNF144A | Q925F3 |
| SDK2 | Q6V4S5 |
| SMCR8 | Q3UMB5 |
| SNAP25 | P60879 |
| TPK1 | Q9R0M5 |
| TYMS | P07607 |
The background gene IDs converted to UNIPROT_ACCESSION are:
N/A
Number of genes submitted:
35
Number of genes matched to UNIPROT_ACCESSION:
18
Number of background genes submited:
N/A
Number of background genes matched to UNIPROT_ACCESSION:
N/A
The gene ID type is
OFFICIAL_GENE_SYMBOL
The genome build is
mm9
The TFBS build is
3kb_up_1kb_down_promoter_hits_BBLS_1_0_FDR_0_2_detailed.tsv
The TF enrichment cutoff is
0.1
Enrichment analysis
GO enrichment
Genes with GO terms
| CAMK1D | Q8BW96 | Q8BW96 | ['GO:0004683', 'GO:0005516', 'GO:0005524', 'GO:0005634', 'GO:0005737', 'GO:0006954', 'GO:0010976', 'GO:0032793', 'GO:0042981', 'GO:0050766', 'GO:0050773', 'GO:0060267', 'GO:0071622', 'GO:0090023'] | ['Allosteric enzyme', 'Alternative splicing', 'ATP-binding', 'Calcium', 'Calmodulin-binding', 'Complete proteome', 'Cytoplasm', 'Inflammatory response', 'Kinase', 'Neurogenesis', 'Nucleotide-binding', 'Nucleus', 'Phosphoprotein', 'Reference proteome', 'Serine/threonine-protein kinase', 'Transferase'] |
| CBLN4 | Q8BME9 | Q8BME9 | ['GO:0005515', 'GO:0005615', 'GO:0009306', 'GO:0030054', 'GO:0045202'] | ['Cell junction', 'Complete proteome', 'Disulfide bond', 'Glycoprotein', 'Reference proteome', 'Secreted', 'Signal', 'Synapse'] |
| CDH26 | P59862 | P59862 | ['GO:0005509', 'GO:0005886', 'GO:0007156', 'GO:0016021'] | ['Calcium', 'Cell adhesion', 'Cell membrane', 'Complete proteome', 'Glycoprotein', 'Membrane', 'Reference proteome', 'Repeat', 'Signal', 'Transmembrane', 'Transmembrane helix'] |
| CNOT4 | Q8BT14 | Q8BT14 | ['GO:0000166', 'GO:0003723', 'GO:0004842', 'GO:0005634', 'GO:0005737', 'GO:0006351', 'GO:0006355', 'GO:0008270', 'GO:0051865'] | ['3D-structure', 'Alternative splicing', 'Coiled coil', 'Complete proteome', 'Cytoplasm', 'Ligase', 'Metal-binding', 'Nucleus', 'Phosphoprotein', 'Reference proteome', 'RNA-binding', 'Transcription', 'Transcription regulation', 'Ubl conjugation', 'Ubl conjugation pathway', 'Zinc', 'Zinc-finger'] |
| CREB3L1 | Q9Z125 | Q9Z125 | ['GO:0001077', 'GO:0003682', 'GO:0005634', 'GO:0005789', 'GO:0006986', 'GO:0016021', 'GO:0030500', 'GO:0043565', 'GO:0046983'] | ['Activator', 'Alternative splicing', 'Complete proteome', 'DNA-binding', 'Endoplasmic reticulum', 'Glycoprotein', 'Membrane', 'Nucleus', 'Reference proteome', 'Signal-anchor', 'Transcription', 'Transcription regulation', 'Transmembrane', 'Transmembrane helix', 'Unfolded protein response'] |
| DAPK1 | Q80YE7 | Q80YE7 | ['GO:0004674', 'GO:0005516', 'GO:0005524', 'GO:0005829', 'GO:0006915', 'GO:0006916', 'GO:0007243', 'GO:0008624', 'GO:2000310'] | ['Alternative splicing', 'ANK repeat', 'Apoptosis', 'ATP-binding', 'Calmodulin-binding', 'Complete proteome', 'Kinase', 'Nucleotide-binding', 'Phosphoprotein', 'Reference proteome', 'Repeat', 'Serine/threonine-protein kinase', 'Transferase', 'Ubl conjugation'] |
| FOXN3 | Q499D0 | Q499D0 | ['GO:0000122', 'GO:0003690', 'GO:0003705', 'GO:0005667', 'GO:0007049', 'GO:0007389', 'GO:0008134', 'GO:0008301', 'GO:0009790', 'GO:0009888', 'GO:0043565', 'GO:0051090'] | ['Cell cycle', 'Complete proteome', 'DNA-binding', 'Nucleus', 'Phosphoprotein', 'Reference proteome', 'Repressor', 'Transcription', 'Transcription regulation'] |
| GPNMB | Q99P91 | Q99P91 | ['GO:0005178', 'GO:0005887', 'GO:0007155', 'GO:0008201', 'GO:0030659', 'GO:0042470'] | ['Complete proteome', 'Cytoplasmic vesicle', 'Glycoprotein', 'Membrane', 'Phosphoprotein', 'Reference proteome', 'Signal', 'Transmembrane', 'Transmembrane helix'] |
| HEATR5A | Q5PRF0 | Q5PRF0 | ['GO:0005488'] | ['Alternative splicing', 'Complete proteome', 'Phosphoprotein', 'Reference proteome', 'Repeat'] |
| KALRN | A2CG49 | A2CG49 | ['GO:0004674', 'GO:0005089', 'GO:0005524', 'GO:0005543', 'GO:0005856', 'GO:0035023', 'GO:0046872'] | ['3D-structure', 'Alternative initiation', 'Alternative splicing', 'ATP-binding', 'Complete proteome', 'Cytoplasm', 'Cytoskeleton', 'Direct protein sequencing', 'Disulfide bond', 'Guanine-nucleotide releasing factor', 'Immunoglobulin domain', 'Kinase', 'Magnesium', 'Metal-binding', 'Nucleotide-binding', 'Phosphoprotein', 'Reference proteome', 'Repeat', 'Serine/threonine-protein kinase', 'SH3 domain', 'Transferase'] |
| LRP12 | Q8BUJ9 | Q8BUJ9 | ['GO:0004872', 'GO:0005905', 'GO:0006897'] | ['Alternative splicing', 'Coated pit', 'Complete proteome', 'Disulfide bond', 'Endocytosis', 'Glycoprotein', 'Membrane', 'Receptor', 'Reference proteome', 'Repeat', 'Signal', 'Transmembrane', 'Transmembrane helix'] |
| NFIX | P70257 | P70257 | ['GO:0000122', 'GO:0003677', 'GO:0003700', 'GO:0005515', 'GO:0005634', 'GO:0006260', 'GO:0006351', 'GO:0045944'] | ['Activator', 'Alternative splicing', 'Complete proteome', 'DNA replication', 'DNA-binding', 'Nucleus', 'Phosphoprotein', 'Reference proteome', 'Repressor', 'Transcription', 'Transcription regulation'] |
| RNF144A | Q925F3 | Q925F3 | ['GO:0008270', 'GO:0016021', 'GO:0016874'] | ['Complete proteome', 'Ligase', 'Membrane', 'Metal-binding', 'Reference proteome', 'Repeat', 'Transmembrane', 'Transmembrane helix', 'Ubl conjugation pathway', 'Zinc', 'Zinc-finger'] |
| SDK2 | Q6V4S5 | Q6V4S5 | ['GO:0007155', 'GO:0016021'] | ['Alternative splicing', 'Cell adhesion', 'Complete proteome', 'Disulfide bond', 'Glycoprotein', 'Immunoglobulin domain', 'Membrane', 'Phosphoprotein', 'Reference proteome', 'Repeat', 'Signal', 'Transmembrane', 'Transmembrane helix'] |
| SMCR8 | Q3UMB5 | Q3UMB5 | [] | ['Alternative splicing', 'Complete proteome', 'Phosphoprotein', 'Reference proteome'] |
| SNAP25 | P60879 | P60879 | ['GO:0005802', 'GO:0019717', 'GO:0030054', 'GO:0045202', 'GO:0048471', 'GO:0070032'] | ['3D-structure', 'Alternative splicing', 'Cell junction', 'Cell membrane', 'Coiled coil', 'Complete proteome', 'Cytoplasm', 'Direct protein sequencing', 'Lipoprotein', 'Membrane', 'Palmitate', 'Phosphoprotein', 'Reference proteome', 'Repeat', 'Synapse', 'Synaptosome'] |
| TPK1 | Q9R0M5 | Q9R0M5 | ['GO:0004788', 'GO:0005524', 'GO:0006772', 'GO:0009229', 'GO:0016301'] | ['3D-structure', 'Alternative splicing', 'ATP-binding', 'Complete proteome', 'Kinase', 'Nucleotide-binding', 'Reference proteome', 'Transferase'] |
| TYMS | P07607 | P07607 | ['GO:0004799', 'GO:0005634', 'GO:0005743', 'GO:0005759'] | ['3D-structure', 'Complete proteome', 'Cytoplasm', 'Membrane', 'Methyltransferase', 'Mitochondrion', 'Mitochondrion inner membrane', 'Nucleotide biosynthesis', 'Nucleus', 'Phosphoprotein', 'Reference proteome', 'Transferase'] |
Genes with TF GO terms
GO keywords = ['Transcription factor']
DAVID Enrichment
| id | categoryName | termName | percent | benjamini |
| 790000053 | SP_PIR_KEYWORDS | alternative splicing | 66.66666666666666 | 0.036057383639032214 |
| 790001162 | SP_PIR_KEYWORDS | phosphoprotein | 66.66666666666666 | 0.31145830685304166 |
| 790000825 | SP_PIR_KEYWORDS | kinase | 22.22222222222222 | 0.41447494762370984 |
| 790001547 | SP_PIR_KEYWORDS | transferase | 27.77777777777778 | 0.4238989003313529 |
| 790001388 | SP_PIR_KEYWORDS | serine/threonine-protein kinase | 16.666666666666664 | 0.4475657665295336 |
| 860002569 | UP_TISSUE | Salivary gland | 16.666666666666664 | 0.9630031396279259 |
| 790000218 | SP_PIR_KEYWORDS | calmodulin-binding | 11.11111111111111 | 0.6073411063126959 |
TFs upstream of genes
| V1 | V2 | V3 | names.targets.motifs.full. | |
|---|---|---|---|---|
| 13 | P60879 | SNAP25 | ['uc008mop.1'] | [('HNF4', -1462), ('AP-2rep', 182), ('HNF4', 234), ('PUR1', 234), ('ETS2', 654), ('HNF4', 694)] |
| 14 | Q6V4S5 | SDK2 | ['uc007mfd.1', 'uc007mfg.1'] | [('HNF4', -354), ('CLOCK:BMAL', -184), ('CLOCK:BMAL', -184), ('USF', -185), ('HNF4', -127), ('NRF-1', 1), ('NRF-1', 3), ('HNF4', 724), ('HNF4', 734)] |
| 3 | Q8BME9 | CBLN4 | [] | [('ETS2', -2851), ('HNF4', -2840), ('PPARG', -2840), ('MAFA', -2829), ('PPARG', -2826), ('HNF4', -2825), ('PPARG', -2675), ('HNF4', -2674), ('HNF4', -2419), ('HNF4', -2400), ('SOX5', -274), ('HNF4', -234), ('AP-2rep', -191), ('HNF4', -106)] |
| 16 | Q9Z125 | CREB3L1 | ['uc008kxf.1'] | [('HNF4', -1673), ('hbp1', -1557), ('MAFA', -1456), ('MAFA', -1008), ('PUR1', -275), ('HNF4', -122), ('PUR1', -125), ('STAT6', -115), ('ETS2', 565)] |
| 7 | A2CG49 | KALRN | ['uc007zar.2', 'uc007zas.1', 'uc007zat.1', 'uc007zav.1', 'uc007zax.2', 'uc012aew.1'] | [] |
| 2 | Q8BT14 | CNOT4 | ['uc009bid.2', 'uc009big.2'] | [] |
| 4 | Q8BUJ9 | LRP12 | ['uc007vom.1', 'uc007von.1'] | [('SOX5', -2831), ('STAT6', -2098), ('HNF4, COUP', -2047), ('myogenin', -1498), ('AP-2rep', -1307), ('HNF4', -1263), ('STAT6', -933), ('ETS2', -348), ('AML1', 781), ('HNF4', 811), ('PPARG', 810)] |
| 12 | P70257 | NFIX | ['uc009mne.1', 'uc009mnf.1'] | [('HNF4', -2458), ('HNF4', -242), ('MAFA', 390), ('HNF4', 669), ('ETS2', 949)] |
| 1 | Q80YE7 | DAPK1 | ['uc007qvm.1', 'uc007qvn.1'] | [('myogenin', 350), ('HNF4', 401), ('HNF4', 701), ('PPARG', 701)] |
| 8 | Q499D0 | FOXN3 | ['uc007ors.1'] | [('ETS2', -11)] |
| 17 | Q8BW96 | CAMK1D | [] | [('ETS2', 247)] |
| 18 | Q99P91 | GPNMB | [] | [('HNF4', -1543), ('HNF4', -1319), ('IRF', -21), ('YY1', 771), ('HNF4', 798), ('PUR1', 798), ('HNF4', 959)] |
| 9 | Q5PRF0 | HEATR5A | ['uc007nna.1', 'uc007nnc.1'] | [('HNF4', -2675), ('HNF4', -2532), ('SOX5', -2399), ('SOX5', -2390), ('NF-kappaB', -2019), ('NF-kappaB', -2019), ('NF-kappaB', -2018), ('NF-kappaB (p65)', -2018), ('HNF4', -2008), ('PUR1', -2011), ('Oct-1', -1120), ('AML1', -1043), ('CREB, ATF', -16), ('CREB', -18), ('CREB, ATF', -15), ('YY1', 1), ('HNF4', 654), ('HNF4', 713), ('HNF4', 740), ('NRSF', 839), ('REST', 841), ('PPARG', 881), ('HNF4', 882), ('NRSF', 889), ('NRSE', 888), ('REST', 891)] |
| 15 | Q3UMB5 | SMCR8 | ['uc007jgn.1', 'uc011xvr.1'] | [('AML1', -2983), ('myogenin', -2289), ('E2A', -2289), ('STAT6', -1758), ('Stat3', -1572), ('HNF4', -1517), ('PPARG', -1518), ('HNF4', -1093), ('myogenin', -990), ('CLOCK:BMAL', 170), ('CLOCK:BMAL', 170), ('HNF4', 310), ('HNF4', 330), ('PPARG', 329), ('AP-2rep', 856)] |
| 10 | P07607 | TYMS | [] | [('AP-2rep', -143), ('GABPA', -25)] |
| 11 | Q9R0M5 | TPK1 | ['uc009bsq.1', 'uc009bsr.1'] | [('HNF4', -2810), ('HNF4', -2660), ('HNF4', -2586), ('SOX5', -2122), ('HNF4', -1871), ('ETS2', -1764), ('Stat3', -1758), ('HEB', -384), ('HEB', -181), ('HNF4', -43), ('HNF4', 314), ('STAT6', 780), ('AML1', 891)] |
| 5 | P59862 | CDH26 | [] | [('HNF4', -907), ('NFAT3', -874), ('STAT6', -809), ('HNF4', -434), ('Nkx2-5', -36)] |
| 6 | Q925F3 | RNF144A | ['uc007nff.1'] | [('HNF4', -1512), ('GR', -258), ('AML1', -176), ('HNF4', 0), ('ETS2', 526)] |
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TFBS enrichment
| TFBS.in.list | TFBS.in.genome | List.size..bp. | Genome.size..bp. | Motif.uniprot | Motif.accession | Odd.ratio | Positive.enriched | Negative.enriched | pVal | Pos..significant | Neg..significant | Target.uniprots | Target.distances | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| NRSF | 2 | 152 | 72018 | 113648405 | NA | M01028 | 20.7672317774941 | TRUE | FALSE | 0.00443240927450349 | TRUE | FALSE | P60879, P60879 | 839, 889 |
| REST | 2 | 168 | 72018 | 113648405 | NA | M01256 | 18.7851751249139 | TRUE | FALSE | 0.0053685100753714 | TRUE | FALSE | P60879, P60879 | 841, 891 |
| CLOCK:BMAL | 4 | 1446 | 72018 | 113648405 | NA | M01116 | 4.36567156975379 | TRUE | FALSE | 0.0143479487702934 | TRUE | FALSE | Q8BT14, Q8BT14, Q6V4S5, Q6V4S5 | -184, -184, 170, 170 |
| NF-kappaB | 3 | 847 | 72018 | 113648405 | P25799 | M00774 | 5.58920386149944 | TRUE | FALSE | 0.0174205256819664 | TRUE | FALSE | P60879, P60879, P60879 | -2019, -2019, -2018 |
| STAT6 | 6 | 3335 | 72018 | 113648405 | P52633 | M00494 | 2.83900611208739 | TRUE | FALSE | 0.0210798598028063 | TRUE | FALSE | Q8BUJ9, A2CG49, A2CG49, Q6V4S5, Q9Z125, Q8BW96 | -115, -2098, -933, -1758, 780, -809 |
| HNF4 | 48 | 54822 | 72018 | 113648405 | P49698 | M01033 | 1.38165262542814 | TRUE | FALSE | 0.0331213656083842 | TRUE | FALSE | Q80YE7, Q80YE7, Q80YE7, Q8BT14, Q8BT14, Q8BT14, Q8BT14, Q8BME9, Q8BME9, Q8BME9, Q8BME9, Q8BME9, Q8BME9, Q8BME9, Q8BUJ9, Q8BUJ9, A2CG49, A2CG49, Q499D0, Q499D0, Q499D0, Q5PRF0, Q5PRF0, P70257, P70257, P70257, P70257, P60879, P60879, P60879, P60879, P60879, P60879, P60879, Q6V4S5, Q6V4S5, Q6V4S5, Q6V4S5, Q9Z125, Q9Z125, Q9Z125, Q9Z125, Q9Z125, Q9Z125, Q8BW96, Q8BW96, Q99P91, Q99P91 | -1462, 234, 694, -354, -127, 724, 734, -2840, -2825, -2674, -2419, -2400, -234, -106, -1673, -122, -1263, 811, -2458, -242, 669, 401, 701, -1543, -1319, 798, 959, -2675, -2532, -2008, 654, 713, 740, 882, -1517, -1093, 310, 330, -2810, -2660, -2586, -1871, -43, 314, -907, -434, -1512, 0 |
| IRF | 1 | 53 | 72018 | 113648405 | P15314 | M00772 | 29.7756509550843 | TRUE | FALSE | 0.0336304459428852 | TRUE | FALSE | P70257 | -21 |
| NF-kappaB (p65) | 1 | 115 | 72018 | 113648405 | Q04207 | M00052 | 13.7254276728468 | TRUE | FALSE | 0.07085074135113 | TRUE | FALSE | P60879 | -2018 |
| NRSE | 1 | 117 | 72018 | 113648405 | NA | M00325 | 13.4918480737812 | TRUE | FALSE | 0.0720272255843307 | TRUE | FALSE | P60879 | 888 |
| PUR1 | 5 | 3713 | 72018 | 113648405 | P42669 | M01721 | 2.12507978432767 | TRUE | FALSE | 0.0902021496096343 | TRUE | FALSE | Q80YE7, Q8BUJ9, Q8BUJ9, P70257, P60879 | 234, -275, -125, 798, -2011 |
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TFBS enrichment for TFs in list
| TFBS.in.list | TFBS.in.genome | List.size..bp. | Genome.size..bp. | Motif.uniprot | Motif.accession | Odd.ratio | Positive.enriched | Negative.enriched | pVal | Pos..significant | Neg..significant | Target.uniprots | Target.distances |
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Output Networks
Initial network
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TFs in network
TF connected network
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TF edges in network
Enriched TF connected network
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