Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


Navigation/Query Panel:
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expected Gene Rank description measured Hugo final
Results: HTML CSV LaTeX Showing element 601 to 650 of 3206 in total
expected
Rank
description
measured
Hugo
final
0.172653 550 LATS HOMOLOG 1. [RefSeq;Acc:NM_004690] 0.046789 LATS1 0.271000214
551 TBC1 DOMAIN FAMILY PROTEIN C22ORF4. [SWISSPROT;Acc:Q8WUA7] TBC1D22A
552 NUCLEAR RECEPTOR COACTIVATOR 7; ESTROGEN RECEPTOR ASSOCIATED PROTEIN 140 KDA. [RefSeq;Acc:NM_181782] NCOA7
0.173407 1702 ELKS PROTEIN. [RefSeq;Acc:NM_015064] 0.0412444 ERC1 0.237847376
0.173966 1668 MESODERM INDUCTION EARLY RESPONSE 1. [RefSeq;Acc:NM_020948] 0.0415385 no value 0.238773668
1669 DEPDC5
0.174068 1560 "THIOREDOXIN INTERACTING PROTEIN; UPREGULATED BY 1,25-DIHYDROXYVITAMIN D-3. [RefSeq;Acc:NM_006472]" 0.0419848 TXNIP 0.241197693
0.174179 3040 PANTOTHENATE KINASE 3 (EC 2.7.1.33) (PANTOTHENIC ACID KINASE 3) (HPANK3). [SWISSPROT;Acc:Q9H999] 0.0191226 PANK3 0.109787058
0.174446 2655 SECRETORY CARRIER-ASSOCIATED MEMBRANE PROTEIN 2. [SWISSPROT;Acc:O15127] 0.0366237 SCAMP2 0.209942905
0.174809 764 POTENTIAL PHOSPHOLIPID-TRANSPORTING ATPASE IIA (EC 3.6.1.-). [SWISSPROT;Acc:O75110] 0.0460867 ATP9A 0.263640316
765 GAMMA-SNAP-ASSOCIATED FACTOR 1; RAB11-INTERACTING PROTEIN. [RefSeq;Acc:NM_015470] RAB11FIP5
0.17528 444 CYTOCHROME C-TYPE HEME LYASE (EC 4.4.1.17) (CCHL) (HOLOCYTOCHROME C- TYPE SYNTHASE). [SWISSPROT;Acc:P53701] 0.0485005 HCCS 0.27670299
0.17588 2052 SIRTUIN 1; SIR2-LIKE 1; SIRTUIN TYPE 1; SIR2ALPHA; SIRTUIN SILENT MATING TYPE INFORMATION REGULATION 2 HOMOLOG 1 (S. CEREVISIAE). [RefSeq;Acc:NM_012238] 0.0404428 SIRT1 0.229945417
0.175918 2540 SEPRASE (EC 3.4.21.-) (FIBROBLAST ACTIVATION PROTEIN ALPHA) (INTEGRAL MEMBRANE SERINE PROTEASE) (170-KDA MELANOMA MEMBRANE-BOUND GELATINASE). [SWISSPROT;Acc:Q12884] 0.0377549 FAP 0.214616469
0.175939 871 T-CELL LEUKEMIA HOMEOBOX PROTEIN 3 (HOMEOBOX PROTEIN HOX-11L2). [SWISSPROT;Acc:O43711] 0.0457909 TLX3 0.260265774
0.176368 516 0.0480412 METT10D 0.272391817
0.176603 3037 "PANTOTHENATE KINASE 2, MITOCHONDRIAL PRECURSOR (EC 2.7.1.33) (PANTOTHENIC ACID KINASE 2) (HPANK2). [SWISSPROT;Acc:Q9BZ23]" 0.0193888 PANK2 0.109787489
0.176719 28 DOK-LIKE PROTEIN. [RefSeq;Acc:NM_024872] 0.0753031 no value 0.426117735
0.177056 29 DOCKING PROTEIN 1 (P62(DOK)) (DOWNSTREAM OF TYROSINE KINASE 1) (PP62). [SWISSPROT;Acc:Q99704] 0.0754466 DOK1 0.426117161
0.177846 273 0.0542439 TRMT6 0.305004892
0.177917 1147 0.0445191 TMEM132E 0.250223981
0.178036 1769 PEROXISOMAL MEMBRANE PROTEIN 2 (22 KDA PEROXISOMAL MEMBRANE PROTEIN). [SWISSPROT;Acc:Q9NR77] 0.0420153 PXMP2 0.235993282
0.178175 2526 KERATIN ASSOCIATED PROTEIN 4-14; KERATIN ASSOCIATED PROTEIN 4.14. [RefSeq;Acc:NM_033059] 0.0382656 no value 0.214764136
0.178411 561 POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 2; UDP-GALNAC TRANSFERASE 2. [RefSeq;Acc:NM_004481] 0.0483159 GALNT2 0.270812338
0.178458 2525 KERATIN ASSOCIATED PROTEIN 4.9 (FRAGMENT). [SPTREMBL;Acc:Q9BYQ8] 0.0383264 no value 0.214764258
0.178518 2050 ARYL-HYDROCARBON INTERACTING PROTEIN-LIKE 1. [SWISSPROT;Acc:Q9NZN9] 0.0410498 AIPL1 0.22994768
0.178742 2441 MYO-INOSITOL 1-PHOSPHATE SYNTHASE A1. [RefSeq;Acc:NM_016368] 0.0388043 no value 0.217096709
2442 UBIQUITIN-LIKE PROTEIN GDX (UBIQUITIN-LIKE PROTEIN 4). [SWISSPROT;Acc:P11441] UBL4A
0.179636 1379 "SUPPRESSOR OF VAR1, 3-LIKE 1. [RefSeq;Acc:NM_003171]" 0.0439474 SUPV3L1 0.244646953
0.180015 261 APOBEC-1 COMPLEMENTATION FACTOR ISOFORM 1; APOBEC-1 STIMULATING PROTEIN; APO-B RNA EDITING PROTEIN. [RefSeq;Acc:NM_014576] 0.0555455 no value 0.308560398
0.180231 17 0.0856348 0.475139127
0.180308 1734 EAP30 SUBUNIT OF ELL COMPLEX. [RefSeq;Acc:NM_007241] 0.04274 SNF8 0.237038845
0.180355 426 RHO-GTPASE ACTIVATING PROTEIN 10. [RefSeq;Acc:NM_020824] 0.0500251 ARHGAP21 0.277370187
0.180466 262 0.0556846 no value 0.308560061
0.18098 1146 0.0452858 TMEM132B 0.250225439
0.181705 263 RNA-BINDING PROTEIN. [RefSeq;Acc:NM_019027] 0.0560669 no value 0.308560029
0.181906 289 0.054901 C10orf58 0.301809726
0.182179 283 "BETA-CAROTENE 15, 15'-DIOXYGENASE; BETA-CAROTENE 15,15'-MONOOXYGENASE. [RefSeq;Acc:NM_017429]" 0.0549835 BCMO1 0.301810307
284 WD-REPEAT PROTEIN 4. [SWISSPROT;Acc:P57081] WDR4
285 INDOLETHYLAMINE N-METHYLTRANSFERASE (EC 2.1.1.49) (AROMATIC ALKYLAMINE N-METHYLTRANSFERASE) (INDOLAMINE N-METHYLTRANSFERASE) (ARYLAMINE N- METHYLTRANSFERASE) (AMINE N-METHYLTRANSFERASE). [SWISSPROT;Acc:O95050] INMT
0.183485 1561 0.0442559 ARRDC4 0.241196283
0.183589 546 ABHYDROLASE DOMAIN CONTAINING PROTEIN 2 (PROTEIN PHPS1-2). [SWISSPROT;Acc:P08910] 0.0497647 ABHD2 0.271065805
0.183648 1608 KATANIN P80 SUBUNIT B 1; KATANIN (80 KDA); KATANIN P80 (WD40-CONTAINING) SUBUNIT B 1. [RefSeq;Acc:NM_005886] 0.0440508 KATNB1 0.239865395
0.185855 1145 0.0465063 TMEM132D 0.250228942
0.187331 2908 0.0326222 SAP30L 0.174142027
2909 "ATP-BINDING CASSETTE, SUB-FAMILY C, MEMBER 10; MULTIDRUG RESISTANCE-ASSOCIATED PROTEIN 7. [RefSeq;Acc:NM_033450]" ABCC10
0.187896 80 ACTIN-BINDING LIM PROTEIN 1 ISOFORM A; LIM ACTIN-BINDING PROTEIN 1; LIMATIN; ACTIN-BINDING LIM PROTEIN. [RefSeq;Acc:NM_002313] 0.0763094 ABLIM1 0.406125729
0.188319 2657 "SOLUTE CARRIER FAMILY 13, MEMBER 3 (SODIUM-DEPENDENT HIGH-AFFINITY DICARBOXYLATE TRANSPORTER 2) (NA(+)/DICARBOXYLATE COTRANSPORTER 3) (NADC-3) (HNADC3). [SWISSPROT;Acc:Q8WWT9]" 0.0395353 SLC13A3 0.209937924
0.188688 2506 "PLECKSTRIN HOMOLOGY DOMAIN CONTAINING, FAMILY C (WITH FERM DOMAIN) MEMBER 1; MITOGEN INDUCIBLE 2; KINDLIN 2. [RefSeq;Acc:NM_006832]" 0.0405241 PLEKHC1 0.214767765
2507 ALPHA-PARVIN (CALPONIN-LIKE INTEGRIN-LINKED KINASE BINDING PROTEIN) (CH-ILKBP). [SWISSPROT;Acc:Q9NVD7] no value

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Hugo is the bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/