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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Rank Gene description measured expected final Hugo
Results: HTML CSV LaTeX Showing element 658 to 707 of 3206 in total
Rank
description
measured
expected
final
Hugo
658 U2 SMALL NUCLEAR RIBONUCLEOPROTEIN AUXILIARY FACTOR 35 KDA SUBUNIT RELATED-PROTEIN 1. [SWISSPROT;Acc:Q15695] 0.20255 0.757899 0.267251969 no value
659 SECRETED MODULAR CALCIUM-BINDING PROTEIN 1. [RefSeq;Acc:NM_022137] 0.0285187 0.106766 0.267114063
660 SECRETED MODULAR CALCIUM-BINDING PROTEIN 2; SMOOTH MUSCLE ASSOCIATED PROTEIN 2. [RefSeq;Acc:NM_022138] 0.035822 0.134108 0.267113073 SMOC2
661 PREFOLDIN SUBUNIT 1. [SWISSPROT;Acc:O60925] 0.128438 0.480838 0.267112832 PFDN1
662 CHOLINE DEHYDROGENASE. [RefSeq;Acc:NM_018397] 0.100197 0.375112 0.267112222 CHDH
663 HOMEOBOX PROTEIN SIX2 (SINE OCULIS HOMEOBOX HOMOLOG 2). [SWISSPROT;Acc:Q9NPC8] 0.516908 1.93534 0.267088987 SIX2
664 BRCA1-ASSOCIATED RING DOMAIN PROTEIN 1 (BARD-1). [SWISSPROT;Acc:Q99728] 0.122728 0.45954 0.267067067 BARD1
665 PROLIFERATION-ASSOCIATED PROTEIN 2G4 (CELL CYCLE PROTEIN P38-2G4 HOMOLOG) (HG4-1). [SWISSPROT;Acc:Q9UQ80] 0.083217 0.311645 0.26702498 PA2G4
666 HOMEOBOX PROTEIN SIX1 (SINE OCULIS HOMEOBOX HOMOLOG 1). [SWISSPROT;Acc:Q15475] 0.617064 2.31135 0.266971251 SIX1
667 SQV-7-LIKE PROTEIN (FRAGMENT). [SPTREMBL;Acc:O95454] 0.104453 0.391317 0.266926814 SLC35D2
668 FIDGETIN-LIKE 1. [RefSeq;Acc:NM_022116] 0.431627 1.61735 0.266872971 FIGNL1
669 0.11907 0.44632 0.266781681 RSRC2
670 0.167849 0.629342 0.266705543 USP30
671 INTERLEUKIN ENHANCER-BINDING FACTOR 1 (CELLULAR TRANSCRIPTION FACTOR ILF-1). [SWISSPROT;Acc:Q01167] 0.0872849 0.327271 0.266705269 FOXK2
672 0.0436424 0.163636 0.266704148 no value
673 0.105333 0.394979 0.266680001 SFT2D3
674 KINESIN FAMILY MEMBER C3. [RefSeq;Acc:NM_005550] 0.0861152 0.323402 0.26627912 KIFC3
675 P47 PROTEIN ISOFORM A. [RefSeq;Acc:NM_016143] 0.0978055 0.367477 0.266154072 NSFL1C
676 "TRYPTOPHAN 2,3-DIOXYGENASE (EC 1.13.11.11) (TRYPTOPHAN PYRROLASE) (TRYPTOPHANASE) (TRYPTOPHAN OXYGENASE) (TRYPTAMIN 2,3-DIOXYGENASE) (TRPO). [SWISSPROT;Acc:P48775]" 0.157338 0.591312 0.26608288 TDO2
677 SERINE/THREONINE-PROTEIN KINASE PLK (EC 2.7.1.-) (PLK-1) (SERINE- THREONINE PROTEIN KINASE 13) (STPK13). [SWISSPROT;Acc:P53350] 0.170317 0.640229 0.266025125 PLK1
678 TUBULIN TYROSINE LIGASE-LIKE PROTEIN HOTTL (HQP0207). [SWISSPROT;Acc:Q9Y4R7] 0.544593 2.04792 0.265924938 BRPF1
679 MITOGEN-ACTIVATED PROTEIN KINASE 3 (EC 2.7.1.37) (EXTRACELLULAR SIGNAL-REGULATED KINASE 1) (ERK-1) (INSULIN-STIMULATED MAP2 KINASE) (MAP KINASE 1) (MAPK 1) (P44-ERK1) (ERT2) (P44-MAPK) (MICROTUBULE- ASSOCIATED PROTEIN-2 KINASE). [SWISSPROT;Acc:P273 1.11399 4.19348 0.265648101 MAPK3
680 MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 5 (EC 2.7.1.-) (MAPK/ERK KINASE KINASE 5) (MEK KINASE 5) (MEKK 5) (APOPTOSIS SIGNAL- REGULATING KINASE 1) (ASK-1). [SWISSPROT;Acc:Q99683] 0.166963 0.628521 0.265644266 no value
681 CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II ALPHA CHAIN (EC 2.7.1.123) (CAM-KINASE II ALPHA CHAIN) (CAM KINASE II ALPHA SUBUNIT) (CAMK-II ALPHA SUBUNIT). [SWISSPROT;Acc:Q9UQM7] 0.141368 0.532171 0.265643938 CAMK2A
682 CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II BETA CHAIN (EC 2.7.1.123) (CAM-KINASE II BETA CHAIN) (CAM KINASE II BETA SUBUNIT) (CAMK-II BETA SUBUNIT). [SWISSPROT;Acc:Q13554] 0.159505 0.600447 0.265643762 CAMK2B
683 CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II DELTA CHAIN (EC 2.7.1.123) (CAM-KINASE II DELTA CHAIN) (CAM KINASE II DELTA SUBUNIT) (CAMK-II DELTA SUBUNIT). [SWISSPROT;Acc:Q13557] CAMK2D
684 RIBOSOMAL PROTEIN S6 KINASE ALPHA 3 (EC 2.7.1.37) (S6K-ALPHA 3) (90 KDA RIBOSOMAL PROTEIN S6 KINASE 3) (P90-RSK 3) (RIBOSOMAL S6 KINASE 2) (RSK-2) (PP90RSK2) (INSULIN-STIMULATED PROTEIN KINASE 1) (ISPK-1). [SWISSPROT;Acc:P51812] 0.0708493 0.266708 0.2656437 RPS6KA3
685 HISTIDINE AMMONIA-LYASE (EC 4.3.1.3) (HISTIDASE). [SWISSPROT;Acc:P42357] 0.0814182 0.306494 0.265643699 HAL
686 RIBOSOMAL PROTEIN S6 KINASE ALPHA 1 (EC 2.7.1.37) (S6K-ALPHA 1) (90 KDA RIBOSOMAL PROTEIN S6 KINASE 1) (P90-RSK 1) (RIBOSOMAL S6 KINASE 1) (RSK-1) (PP90RSK1). [SWISSPROT;Acc:Q15418] RPS6KA1
687 SIPA1L2
688 SIGNAL-INDUCED PROLIFERATION-ASSOCIATED 1-LIKE 1. [RefSeq;Acc:NM_015556] 0.0671866 0.25292 0.265643682 no value
689 CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II GAMMA CHAIN (EC 2.7.1.123) (CAM-KINASE II GAMMA CHAIN) (CAM KINASE II GAMMA SUBUNIT) (CAMK-II GAMMA SUBUNIT) (FRAGMENT). [SWISSPROT;Acc:Q13555] 0.139426 0.524861 0.265643666 CAMK2G
690 RIBOSOMAL PROTEIN S6 KINASE ALPHA 6 (EC 2.7.1.37) (S6K-ALPHA 6) (90 KDA RIBOSOMAL PROTEIN S6 KINASE 6) (P90-RSK 6) (RIBOSOMAL S6 KINASE 4) (RSK-4) (PP90RSK4). [SWISSPROT;Acc:Q9UK32] 0.0671204 0.252671 0.265643465 RPS6KA6
691 RIBOSOMAL PROTEIN S6 KINASE ALPHA 2 (EC 2.7.1.37) (S6K-ALPHA 2) (90 KDA RIBOSOMAL PROTEIN S6 KINASE 2) (P90-RSK 2) (RIBOSOMAL S6 KINASE 3) (RSK-3) (PP90RSK3). [SWISSPROT;Acc:Q15349] 0.0698564 0.262971 0.26564298 RPS6KA2
692 0.0644285 0.242538 0.26564291 SIPA1L3
693 "GLUTARYL-COA DEHYDROGENASE, MITOCHONDRIAL PRECURSOR (EC 1.3.99.7) (GCD). [SWISSPROT;Acc:Q92947]" 0.125547 0.472616 0.265642721 GCDH
694 "ATP-BINDING CASSETTE, SUB-FAMILY D, MEMBER 3 (70 KDA PEROXISOMAL MEMBRANE PROTEIN) (PMP70). [SWISSPROT;Acc:P28288]" 0.0441291 0.166122 0.26564272 ABCD3
695 MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 6 (EC 2.7.1.-). [SWISSPROT;Acc:O95382] 0.126275 0.475357 0.265642454 MAP3K6
696 MITOGEN-ACTIVATED PROTEIN KINASE 1 (EC 2.7.1.37) (EXTRACELLULAR SIGNAL-REGULATED KINASE 2) (ERK-2) (MITOGEN-ACTIVATED PROTEIN KINASE 2) (MAP KINASE 2) (MAPK 2) (P42-MAPK) (ERT1). [SWISSPROT;Acc:P28482] 1.33288 5.01763 0.265639356 MAPK1
697 EPIDERMAL GROWTH FACTOR RECEPTOR PATHWAY SUBSTRATE 8-LIKE PROTEIN 2; EPS8-RELATED PROTEIN 2; EPIDERMAL GROWTH FACTOR RECEPTOR PATHWAY SUBSTRATE 8-RELATED PROTEIN 2. [RefSeq;Acc:NM_022772] 0.128497 0.483922 0.265532462 EPS8L2
698 15 KDA SELENOPROTEIN PRECURSOR. [SWISSPROT;Acc:O60613] 0.0424293 0.159817 0.265486775 no value
699 0.160096 0.603029 0.265486403 USP47
700 EPIDERMAL GROWTH FACTOR RECEPTOR KINASE SUBSTRATE EPS8. [SWISSPROT;Acc:Q12929] 0.101882 0.383993 0.265322545 EPS8
701 HRD1 PROTEIN ISOFORM A; SYNOVIOLIN1. [RefSeq;Acc:NM_032431] 0.191556 0.722002 0.265312284 SYVN1
702 EPIDERMAL GROWTH FACTOR RECEPTOR PATHWAY SUBSTRATE 8-LIKE PROTEIN 1 ISOFORM C; EPIDERMAL GROWTH FACTOR RECEPTOR PATHWAY SUBSTRATE 8-RELATED PROTEIN 1; EPS8-RELATED PROTEIN 1. [RefSeq;Acc:NM_139204] 0.0987306 0.372159 0.265291448 EPS8L1
703 WISKOTT-ALDRICH SYNDROME PROTEIN FAMILY MEMBER 2 (WASP-FAMILY PROTEIN MEMBER 2) (VERPROLIN HOMOLOGY DOMAIN-CONTAINING PROTEIN 2). [SWISSPROT;Acc:Q9Y6W5] 0.1433 0.540454 0.26514745 no value
704 WISKOTT-ALDRICH SYNDROME PROTEIN FAMILY MEMBER 3 (WASP-FAMILY PROTEIN MEMBER 3) (VERPROLIN HOMOLOGY DOMAIN-CONTAINING PROTEIN 3). [SWISSPROT;Acc:Q9UPY6] 0.178008 0.671355 0.265147351 WASF3
705 WISKOTT-ALDRICH SYNDROME PROTEIN FAMILY MEMBER 1 (WASP-FAMILY PROTEIN MEMBER 1) (VERPROLIN HOMOLOGY DOMAIN-CONTAINING PROTEIN 1). [SWISSPROT;Acc:Q92558] 0.145472 0.548646 0.26514729 WASF1
706 0.220284 0.830799 0.265147166 AOF2
707 0.0319701 0.120575 0.265147004 RCOR2

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/