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.


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