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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measured Rank Gene description Hugo expected final
Results: HTML CSV LaTeX Showing element 601 to 650 of 3206 in total
measured
Rank
description
Hugo
expected
final
0.0401322 1349 HUMAN IMMUNODEFICIENCY VIRUS TYPE I ENHANCER-BINDING PROTEIN 2 (HIV-EP2). [SWISSPROT;Acc:P31629] HIVEP2 0.163681 0.245185452
0.0401445 502 CDV3 0.146476 0.274068789
0.0401827 2660 "SOLUTE CARRIER FAMILY 13, MEMBER 2 (RENAL SODIUM/DICARBOXYLATE COTRANSPORTER) (NA(+)/DICARBOXYLATE COTRANSPORTER 1) (NADC-1). [SWISSPROT;Acc:Q13183]" SLC13A2 0.191403 0.209937671
0.0403386 1176 "COP9 SUBUNIT 6 (MOV34 HOMOLOG, 34 KD). [RefSeq;Acc:NM_006833]" COPS6 0.161745 0.249396272
0.0403612 900 TEX9 0.155595 0.259399081
0.0404428 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] SIRT1 0.17588 0.229945417
0.0404532 657 STEP II SPLICING FACTOR SLU7. [RefSeq;Acc:NM_006425] SLU7 0.151367 0.267252439
0.0404812 200 POLYADENYLATE-BINDING PROTEIN 3 (POLY(A)-BINDING PROTEIN 3) (PABP 3) (TESTIS-SPECIFIC POLY(A)-BINDING PROTEIN). [SWISSPROT;Acc:Q9H361] PABPC3 0.125733 0.321961617
0.0405241 2506 "PLECKSTRIN HOMOLOGY DOMAIN CONTAINING, FAMILY C (WITH FERM DOMAIN) MEMBER 1; MITOGEN INDUCIBLE 2; KINDLIN 2. [RefSeq;Acc:NM_006832]" PLEKHC1 0.188688 0.214767765
2507 ALPHA-PARVIN (CALPONIN-LIKE INTEGRIN-LINKED KINASE BINDING PROTEIN) (CH-ILKBP). [SWISSPROT;Acc:Q9NVD7] no value
0.0406169 813 DEAD-BOX PROTEIN ABSTRAKT HOMOLOG. [SWISSPROT;Acc:Q9UJV9] 0.155406 0.261359922
0.0406567 1166 HISTONE DEACETYLASE 11 (HD11). [SWISSPROT;Acc:Q96DB2] HDAC11 0.16302 0.249397007
0.0410035 847 no value 0.157329 0.260622644
0.0410294 2696 "ENDONUCLEASE G, MITOCHONDRIAL PRECURSOR (EC 3.1.30.-) (ENDO G). [SWISSPROT;Acc:Q14249]" ENDOG 0.19727 0.207986009
0.0410498 2050 ARYL-HYDROCARBON INTERACTING PROTEIN-LIKE 1. [SWISSPROT;Acc:Q9NZN9] AIPL1 0.178518 0.22994768
0.0410645 2916 38 KDA FK-506 BINDING PROTEIN HOMOLOG (FKBPR38) (FK506-BINDING PROTEIN 8). [SWISSPROT;Acc:Q14318] FKBP8 0.239274 0.171621238
0.0411277 1091 3-OXO-5-ALPHA-STEROID 4-DEHYDROGENASE 1 (EC 1.3.99.5) (STEROID 5-ALPHA-REDUCTASE 1) (SR TYPE 1) (S5AR). [SWISSPROT;Acc:P18405] SRD5A1 0.163477 0.251580956
0.0411817 1156 CYB5D2 0.164951 0.249660202
0.0412444 1702 ELKS PROTEIN. [RefSeq;Acc:NM_015064] ERC1 0.173407 0.237847376
0.0413389 178 FILAMIN A (ALPHA-FILAMIN) (FILAMIN 1) (ENDOTHELIAL ACTIN-BINDING PROTEIN) (ABP-280) (NONMUSCLE FILAMIN). [SWISSPROT;Acc:P21333] no value 0.122543 0.337341994
0.0413585 1009 C20orf72 0.162467 0.254565543
0.0413596 176 PROTEIN ARGININE N-METHYLTRANSFERASE 1 (EC 2.1.1.-) (INTERFERON RECEPTOR 1-BOUND PROTEIN 4). [SWISSPROT;Acc:Q99873] PRMT1 0.122604 0.33734299
0.0415188 644 no value 0.154846 0.268129626
0.0415296 1270 HYPOXIA-INDUCIBLE FACTOR-3 ALPHA ISOFORM A; INHIBITORY PAS DOMAIN PROTEIN. [RefSeq;Acc:NM_152794] HIF3A 0.168345 0.246693397
0.0415385 1668 MESODERM INDUCTION EARLY RESPONSE 1. [RefSeq;Acc:NM_020948] no value 0.173966 0.238773668
1669 DEPDC5
0.0416456 165 MUSASHI 1. [RefSeq;Acc:NM_002442] MSI1 0.120995 0.344192735
0.0416551 299 KRUEPPEL-LIKE FACTOR 5 (INTESTINAL-ENRICHED KRUEPPEL-LIKE FACTOR) (COLON KRUEPPEL-LIKE FACTOR) (TRANSCRIPTION FACTOR BTEB2) (BASIC TRANSCRIPTION ELEMENT BINDING PROTEIN 2) (BTE-BINDING PROTEIN 2) (GC BOX BINDING PROTEIN 2). [SWISSPROT;Acc:Q13887] KLF5 0.138666 0.3003988
0.0416917 2882 ADAPTER-RELATED PROTEIN COMPLEX 3 BETA 1 SUBUNIT (BETA-ADAPTIN 3A) (AP-3 COMPLEX BETA-3A SUBUNIT) (BETA-3A-ADAPTIN). [SWISSPROT;Acc:O00203] AP3B1 0.225994 0.184481446
0.0417611 1340 SFRS PROTEIN KINASE 1; SR PROTEIN KINASE 1. [RefSeq;Acc:NM_003137] SRPK1 0.170257 0.24528272
1341 XAP-5 PROTEIN (HXC-26 PROTEIN). [SWISSPROT;Acc:Q14320] FAM50A
1342 SERINE/THREONINE PROTEIN KINASE 23 (EC 2.7.1.37) (MUSCLE-SPECIFIC SERINE KINASE 1) (MSSK-1). [SWISSPROT;Acc:Q9UPE1] SRPK3
1343 CYCLIC-AMP-DEPENDENT TRANSCRIPTION FACTOR ATF-6 ALPHA (ACTIVATING TRANSCRIPTION FACTOR 6 ALPHA) (ATF6-ALPHA). [SWISSPROT;Acc:P18850] ATF6
0.0417836 1311 SERBP1 0.170042 0.245725174
0.0418316 1131 PYRIDOXINE 5'-PHOSPHATE OXIDASE. [RefSeq;Acc:NM_018129] PNPO 0.166987 0.250508123
0.0418885 1312 "3-HYDROXYANTHRANILATE 3,4-DIOXYGENASE (EC 1.13.11.6) (3-HAO) (3-HYDROXYANTHRANILIC ACID DIOXYGENASE) (3-HYDROXYANTHRANILATE OXYGENASE). [SWISSPROT;Acc:P46952]" HAAO 0.170469 0.245725029
1313 ZINC FINGER PROTEIN-LIKE 1; ZINC-FINGER PROTEIN IN MEN1 REGION. [RefSeq;Acc:NM_006782] ZFPL1
0.0419409 1309 HOMEOBOX PROSPERO-LIKE PROTEIN PROX1 (PROX 1). [SWISSPROT;Acc:Q92786] PROX1 0.170682 0.245725384
0.0419848 1560 "THIOREDOXIN INTERACTING PROTEIN; UPREGULATED BY 1,25-DIHYDROXYVITAMIN D-3. [RefSeq;Acc:NM_006472]" TXNIP 0.174068 0.241197693
0.0420153 1769 PEROXISOMAL MEMBRANE PROTEIN 2 (22 KDA PEROXISOMAL MEMBRANE PROTEIN). [SWISSPROT;Acc:Q9NR77] PXMP2 0.178036 0.235993282
0.0420473 340 SPLICING FACTOR 3A SUBUNIT 3 (SPLICEOSOME ASSOCIATED PROTEIN 61) (SAP 61) (SF3A60). [SWISSPROT;Acc:Q12874] SF3A3 0.147618 0.28483857
0.0420495 2911 ANKS6 0.241467 0.174141808
0.0421286 459 COLLAGEN ALPHA 3(IV) CHAIN PRECURSOR (GOODPASTURE ANTIGEN). [SWISSPROT;Acc:Q01955] COL4A3 0.15287 0.275584484
0.0421586 2980 HOMEOBOX PROTEIN HOX-A5 (HOX-1C). [SWISSPROT;Acc:P20719] HOXA5 0.302084 0.139559195
0.0422874 709 REST COREPRESSOR. [RefSeq;Acc:NM_015156] RCOR1 0.159487 0.265146376
0.0422886 203 POLYADENYLATE-BINDING PROTEIN 1 (POLY(A)-BINDING PROTEIN 1) (PABP 1). [SWISSPROT;Acc:P11940] PABPC1 0.131347 0.321960913
0.0423362 2308 DJ718P11.1.2 (NOVEL CLASS II AMINOTRANSFERASE SIMILAR TO SERINE PALMOTYLTRANSFERASE (ISOFORM 2)) (FRAGMENT). [SPTREMBL;Acc:Q9UGB5] no value 0.19065 0.222062418
0.0423484 1279 EPSIN 1; EH DOMAIN-BINDING MITOTIC PHOSPHOPROTEIN. [RefSeq;Acc:NM_013333] EPN1 0.171872 0.246394992
0.042399 2521 KERATIN ASSOCIATED PROTEIN 4-12; KERATIN ASSOCIATED PROTEIN 4.12. [RefSeq;Acc:NM_031854] no value 0.19742 0.214765475
0.0424091 3018 PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E (EC 5.2.1.8) (PPIASE E) (ROTAMASE E) (CYCLOPHILIN E) (CYCLOPHILIN 33). [SWISSPROT;Acc:Q9UNP9] PPIE 0.349357 0.121391871

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/