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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Hugo measured expected Gene final description Rank
Results: HTML CSV LaTeX Showing element 51 to 100 of 3206 in total
Hugo  : no value
measured
expected
final
description
Rank
0.0331615 0.142049 0.233451133 PRESENILIN-LIKE PROTEIN 1 (EC 3.4.99.-) (SPPL2B PROTEIN). [SWISSPROT;Acc:Q8TCT7] 1852
0.0333153 0.155451 0.214313835 METABOTROPIC GLUTAMATE RECEPTOR 3 PRECURSOR (MGLUR3). [SWISSPROT;Acc:Q14832] 2555
0.0334849 0.110947 0.301809873 "FATTY ACID-BINDING PROTEIN, EPIDERMAL (E-FABP) (PSORIASIS-ASSOCIATED FATTY ACID-BINDING PROTEIN HOMOLOG) (PA-FABP). [SWISSPROT;Acc:Q01469]" 287
0.034272 0.122748 0.279206179 373
0.0344618 0.125634 0.274303135 492
0.0364961 0.150941 0.241790501 ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 7 (ADP-RIBOSYLATION FACTOR-LIKE PROTEIN LAK). [SWISSPROT;Acc:P56559] 1550
0.0367538 0.139602 0.263275598 "SIRTUIN 7; SIR2-RELATED PROTEIN TYPE 7; SIRTUIN TYPE 7; SIRTUIN (SILENT MATING TYPE INFORMATION REGULATION 2, S.CEREVISIAE, HOMOLOG) 7; SILENT MATING TYPE INFORMATION REGULATION 2, S.CEREVISIAE, HOMOLOG 7; SIRTUIN SILENT MATING TYPE INFORMATION REGULATION" 773
0.036822 0.15167 0.242777082 IMPORTIN 7; RAN-BINDING PROTEIN 7. [RefSeq;Acc:NM_006391] 1495
0.0368814 0.136094 0.270999456 SH3 DOMAIN-BINDING GLUTAMIC ACID-RICH-LIKE PROTEIN 2 (FOVEA-ASSOCIATED SH3 DOMAIN BINDING PROTEIN). [SWISSPROT;Acc:Q9UJC5] 554
0.0371369 0.196598 0.188897649 2872
0.0372023 0.196899 0.188941031 CGI-142; HEPATOMA-DERIVED GROWTH FACTOR 2. [RefSeq;Acc:NM_016073] 2862
0.0373117 0.130845 0.28515954 GA BINDING PROTEIN BETA-2 CHAIN (GABP-BETA-2 SUBUNIT) (TRANSCRIPTION FACTOR E4TF1-47) (GAPBP-2) (NUCLEAR RESPIRATORY FACTOR-2 SUBUNIT GAMMA). [SWISSPROT;Acc:Q06545] 333
0.037776 0.154523 0.244468461 BA271B5.1 (SIMILAR TO RIBOSOMAL PROTEIN S7). [SPTREMBL;Acc:Q9H1S9] 1386
0.0378274 0.1468 0.257679837 FATTY ACID DESATURASE 1; LINOLEOYL-COA DESATURASE (DELTA-6-DESATURASE)-LIKE 1; DELTA-5 DESATURASE; DELTA-5 FATTY ACID DESATURASE. [RefSeq;Acc:NM_013402] 924
0.0378601 0.144194 0.26256363 784
0.0382656 0.178175 0.214764136 KERATIN ASSOCIATED PROTEIN 4-14; KERATIN ASSOCIATED PROTEIN 4.14. [RefSeq;Acc:NM_033059] 2526
0.0383264 0.178458 0.214764258 KERATIN ASSOCIATED PROTEIN 4.9 (FRAGMENT). [SPTREMBL;Acc:Q9BYQ8] 2525
0.038359 0.163741 0.234266311 1823
0.0384625 0.155989 0.246571874 KAPPA B-RAS 1. [RefSeq;Acc:NM_020345] 1273
0.038631 0.158546 0.243657992 RNA HELICASE-RELATED PROTEIN; RNA HELICASE-LIKE PROTEIN; SF3B125 DEAD-BOX PROTEIN. [RefSeq;Acc:NM_007372] 1433
0.0388043 0.178742 0.217096709 MYO-INOSITOL 1-PHOSPHATE SYNTHASE A1. [RefSeq;Acc:NM_016368] 2441
0.038917 0.619812 0.062788394 RIBOSOMAL PROTEIN S6 KINASE-LIKE 1. [RefSeq;Acc:NM_031464] 3169
0.0391008 0.366305 0.106743834 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-7 SUBUNIT. [SWISSPROT;Acc:O60262] 3042
0.0394801 0.163824 0.240990941 NEFA-INTERACTING NUCLEAR PROTEIN NIP30. [RefSeq;Acc:NM_024946] 1567
0.0397033 0.156754 0.253284127 "ATP-DEPENDENT DNA HELICASE II, 70 KDA SUBUNIT (LUPUS KU AUTOANTIGEN PROTEIN P70) (KU70) (70 KDA SUBUNIT OF KU ANTIGEN) (THYROID-LUPUS AUTOANTIGEN) (TLAA) (CTC BOX BINDING FACTOR 75 KDA SUBUNIT) (CTCBF) (CTC75). [SWISSPROT;Acc:P12956]" 1040
0.039713 0.15268 0.260106104 PUTATIVE PRE-MRNA SPLICING FACTOR RNA HELICASE (ATP-DEPENDENT RNA HELICASE #3) (DEAH-BOX PROTEIN 16). [SWISSPROT;Acc:O60231] 878
0.0399967 0.14739 0.271366443 SMALL NUCLEAR RIBONUCLEOPROTEIN E (SNRNP-E) (SM PROTEIN E) (SM-E) (SME). [SWISSPROT;Acc:P08578] 534
0.0405241 0.188688 0.214767765 ALPHA-PARVIN (CALPONIN-LIKE INTEGRIN-LINKED KINASE BINDING PROTEIN) (CH-ILKBP). [SWISSPROT;Acc:Q9NVD7] 2507
0.0406169 0.155406 0.261359922 DEAD-BOX PROTEIN ABSTRAKT HOMOLOG. [SWISSPROT;Acc:Q9UJV9] 813
0.0410035 0.157329 0.260622644 847
0.0413389 0.122543 0.337341994 FILAMIN A (ALPHA-FILAMIN) (FILAMIN 1) (ENDOTHELIAL ACTIN-BINDING PROTEIN) (ABP-280) (NONMUSCLE FILAMIN). [SWISSPROT;Acc:P21333] 178
0.0415188 0.154846 0.268129626 644
0.0415385 0.173966 0.238773668 MESODERM INDUCTION EARLY RESPONSE 1. [RefSeq;Acc:NM_020948] 1668
0.0423362 0.19065 0.222062418 DJ718P11.1.2 (NOVEL CLASS II AMINOTRANSFERASE SIMILAR TO SERINE PALMOTYLTRANSFERASE (ISOFORM 2)) (FRAGMENT). [SPTREMBL;Acc:Q9UGB5] 2308
0.042399 0.19742 0.214765475 KERATIN ASSOCIATED PROTEIN 4-12; KERATIN ASSOCIATED PROTEIN 4.12. [RefSeq;Acc:NM_031854] 2521
0.0424293 0.159817 0.265486775 15 KDA SELENOPROTEIN PRECURSOR. [SWISSPROT;Acc:O60613] 698
0.042516 0.151058 0.281454805 357
0.0429558 0.142328 0.301808499 "BETA-CAROTENE DIOXYGENASE 2; PUTATIVE B,B-CAROTENE-9',10'-DIOXYGENASE. [RefSeq;Acc:NM_031938]" 294
0.0431276 0.223379 0.193069178 "SUCCINATE DEHYDROGENASE [UBIQUINONE] CYTOCHROME B SMALL SUBUNIT, MITOCHONDRIAL PRECURSOR (CYBS) (SUCCINATE-UBIQUINONE REDUCTASE MEMBRANE ANCHOR SUBUNIT) (QPS2) (CII-4) (SUCCINATE DEHYDROGENASE COMPLEX SUBUNIT D) (SUCCINATE-UBIQUINONE OXIDOREDUCTASE CYTOCH" 2835
0.0436424 0.163636 0.266704148 672
0.0436957 0.203458 0.21476521 2522
0.0444453 0.352603 0.126049126 ENDO-BETA-N-ACETYLGLUCOSAMINIDASE. [RefSeq;Acc:NM_022759] 3004
0.044904 0.188793 0.237847802 1700
0.0454701 0.217847 0.208724931 GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE (EC 2.7.7.12) (GAL-1-P URIDYLYLTRANSFERASE) (UDP-GLUCOSE--HEXOSE-1-PHOSPHATE URIDYLYLTRANSFERASE). [SWISSPROT;Acc:P07902] 2677
0.0483186 0.171674 0.281455549 356
0.048624 0.498014 0.097635809 METHYLTRANSFERASE LIKE 2. [RefSeq;Acc:NM_018396] 3090
0.0486609 0.241353 0.201617133 SIMILAR TO ZINC FINGER PROTEIN 277. [SPTREMBL;Acc:Q8WWA6] 2769
0.0488461 0.204356 0.239024545 1642
0.050323 0.210535 0.23902439 MYOSIN VI. [SWISSPROT;Acc:Q9UM54] 1646
0.0503334 0.170278 0.295595438 MITOCHONDRIAL 28S RIBOSOMAL PROTEIN S32 (S32MT) (MRP-S32) (PTD007) (HSPC204). [SWISSPROT;Acc:Q9Y6G3] 308

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/