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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Gene Rank expected description measured final Hugo
Results: HTML CSV LaTeX Showing element 701 to 750 of 3206 in total
Rank
expected
description
measured
final
Hugo
701 0.722002 HRD1 PROTEIN ISOFORM A; SYNOVIOLIN1. [RefSeq;Acc:NM_032431] 0.191556 0.265312284 SYVN1
702 0.372159 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 0.265291448 EPS8L1
703 0.540454 WISKOTT-ALDRICH SYNDROME PROTEIN FAMILY MEMBER 2 (WASP-FAMILY PROTEIN MEMBER 2) (VERPROLIN HOMOLOGY DOMAIN-CONTAINING PROTEIN 2). [SWISSPROT;Acc:Q9Y6W5] 0.1433 0.26514745 no value
704 0.671355 WISKOTT-ALDRICH SYNDROME PROTEIN FAMILY MEMBER 3 (WASP-FAMILY PROTEIN MEMBER 3) (VERPROLIN HOMOLOGY DOMAIN-CONTAINING PROTEIN 3). [SWISSPROT;Acc:Q9UPY6] 0.178008 0.265147351 WASF3
705 0.548646 WISKOTT-ALDRICH SYNDROME PROTEIN FAMILY MEMBER 1 (WASP-FAMILY PROTEIN MEMBER 1) (VERPROLIN HOMOLOGY DOMAIN-CONTAINING PROTEIN 1). [SWISSPROT;Acc:Q92558] 0.145472 0.26514729 WASF1
706 0.830799 0.220284 0.265147166 AOF2
707 0.120575 0.0319701 0.265147004 RCOR2
708 0.135679 0.0359748 0.265146412 RCOR3
709 0.159487 REST COREPRESSOR. [RefSeq;Acc:NM_015156] 0.0422874 0.265146376 RCOR1
710 0.900943 F-ACTIN CAPPING PROTEIN BETA SUBUNIT (CAPZ BETA). [SWISSPROT;Acc:P47756] 0.238765 0.265016766 CAPZB
711 0.124574 F-ACTIN CAPPING PROTEIN ALPHA-3 SUBUNIT (CAPZ ALPHA-3) (GERM CELL- SPECIFIC PROTEIN 3). [SWISSPROT;Acc:Q96KX2] 0.0330141 0.265015974 CAPZA3
712 1.98825 HISTONE DEACETYLASE 2 (HD2). [SWISSPROT;Acc:Q92769] 0.52666 0.264886206 no value
713 0.263425 DJ153G14.2 (POSSIBLE CA BINDING PROTEIN SIMILAR TO NEFA) (FRAGMENT). [SPTREMBL;Acc:Q9UJN8] 0.0697761 0.264880326
714 0.32416 MULTIPLE COAGULATION FACTOR DEFICIENCY 2; NEURAL STEM CELL DERIVED NEURONAL SURVIVAL PROTEIN; MULTIPLE COAGULATION FACTOR DEFICIENCY PROTEIN 2. [RefSeq;Acc:NM_139279] 0.0858635 0.264879998 MCFD2
715 2.20068 HISTONE DEACETYLASE 1 (HD1). [SWISSPROT;Acc:Q13547] 0.582904 0.264874493 HDAC1
716 0.397328 P28 ING5. [RefSeq;Acc:NM_032329] 0.105213 0.264801373 ING5
717 1.52156 ARP2/3 COMPLEX 16 KDA SUBUNIT (P16-ARC) (ACTIN-RELATED PROTEIN 2/3 COMPLEX SUBUNIT 5). [SWISSPROT;Acc:O15511] 0.402903 0.264795999 ARPC5
718 0.28346 INTERFERON-RELATED DEVELOPMENTAL REGULATOR 2 (SKMC15 PROTEIN). [SWISSPROT;Acc:Q12894] 0.0750554 0.264783038 HYAL3
719 1.60405 0.424703 0.264769178 ARPC5L
720 0.119935 ZINC FINGER PROTEIN 258. [RefSeq;Acc:NM_145310] 0.0317441 0.264677534 ZMYM6
721 1.43987 DJ470L14.3 (NOVEL PROTEIN SIMILAR TO THE ARP2/3 PROTEIN COMPLEX SUBUNIT P21-ARC (ARC21)). [SPTREMBL;Acc:Q9H5B6] 0.381101 0.264677367 no value
722 1.21932 SIMILAR TO ACTIN-RELATED PROTEIN 3-BETA. [SPTREMBL;Acc:Q96BT2] 0.322726 0.264677033 ACTR3B
723 1.99819 ACTIN-LIKE PROTEIN 3 (ACTIN-RELATED PROTEIN 3) (ACTIN-2). [SWISSPROT;Acc:P32391] 0.528875 ACTR3
724 1.3445 ACTIN-RELATED PROTEIN 2/3 COMPLEX SUBUNIT 1A (SOP2-LIKE PROTEIN). [SWISSPROT;Acc:Q92747] 0.355858 0.264676832 ARPC1A
725 1.48471 ARP2/3 COMPLEX 21 KDA SUBUNIT (P21-ARC) (ACTIN-RELATED PROTEIN 2/3 COMPLEX SUBUNIT 3). [SWISSPROT;Acc:O15145] 0.392968 0.264676604 ARPC3
726 0.297409 NARDILYSIN PRECURSOR (EC 3.4.24.61) (N-ARGININE DIBASIC CONVERTASE) (NRD CONVERTASE) (NRD-C). [SWISSPROT;Acc:O43847] 0.0787172 0.26467659 NRD1
727 0.150694 ZINC FINGER PROTEIN 262; CELL DEATH INHIBITING RNA. [RefSeq;Acc:NM_005095] 0.0398851 0.264676099 ZMYM4
728 CONSERVED OLIGOMERIC GOLGI COMPLEX COMPONENT 3 (VESICLE DOCKING PROTEIN SEC34 HOMOLOG) (P94). [SWISSPROT;Acc:Q96JB2] COG3
729 1.47645 ACTIN-LIKE PROTEIN 2 (ACTIN-RELATED PROTEIN 2). [SWISSPROT;Acc:O15142] 0.390781 0.264676081 ACTR2
730 0.116875 ZINC FINGER PROTEIN 261 (DXS6673E PROTEIN). [SWISSPROT;Acc:Q14202] 0.030934 0.264675936 ZMYM3
731 0.117755 ZINC FINGER PROTEIN 198 (FUSED IN MYELOPROLIFERATIVE DISORDERS PROTEIN) (REARRANGED IN ATYPICAL MYELOPROLIFERATIVE DISORDER PROTEIN). [SWISSPROT;Acc:Q9UBW7] 0.0311669 0.26467581 ZMYM2
732 1.20127 ARP2/3 COMPLEX 41 KDA SUBUNIT (P41-ARC) (ACTIN-RELATED PROTEIN 2/3 COMPLEX SUBUNIT 1B). [SWISSPROT;Acc:O15143] 0.317947 0.264675718 ARPC1B
733 1.32007 C-TERMINAL BINDING PROTEIN 1 (CTBP1). [SWISSPROT;Acc:Q13363] 0.349374 0.264663238 CTBP1
734 0.328537 B-CELL LYMPHOMA 6 PROTEIN (BCL-6) (ZINC FINGER PROTEIN 51) (LAZ-3 PROTEIN) (BCL-5). [SWISSPROT;Acc:P41182] 0.0869475 0.264650557 BCL6
735 ZINC FINGER PROTEIN SLUG (NEURAL CREST TRANSCRIPTION FACTOR SLUG) (SNAIL HOMOLOG 2). [SWISSPROT;Acc:O43623] SNAI2
736 PAS DOMAIN CONTAINING SERINE/THREONINE KINASE; PAS-SERINE/THREONINE KINASE. [RefSeq;Acc:NM_015148] PASK
737 0.261825 "B-CELL CLL/LYMPHOMA 6, MEMBER B (ZINC FINGER PROTEIN); ZINC FINGER PROTEIN 62. [RefSeq;Acc:NM_181844]" 0.0692921 0.264650434 BCL6B
738 1.50657 C-TERMINAL BINDING PROTEIN 2 (CTBP2). [SWISSPROT;Acc:P56545] 0.398698 0.264639545 CTBP2
739 0.442554 PEROXISOMAL CARNITINE OCTANOYLTRANSFERASE (EC 2.3.1.-) (COT). [SWISSPROT;Acc:Q9UKG9] 0.117061 0.264512353 CROT
740 0.145821 PROTEIN C20ORF45 (CGI-107). [SWISSPROT;Acc:Q9Y3B1] 0.0385694 0.264498255 SLMO2
741 ZCCHC8
742 BARDET-BIEDL SYNDROME 7 PROTEIN ISOFORM A; BBS2-LIKE 1. [RefSeq;Acc:NM_176824] BBS7
743 HSDL2
744 0.411799 0.10892 0.264497971 INTS10
745 0.1121 BA508N22.1 (HSPC025) (FRAGMENT). [SPTREMBL;Acc:Q9HCW5] 0.0296502 0.26449777 no value
746 0.816964 EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 11 (EIF-3 P25) (EIF3K) (MUSCLE SPECIFIC GENE M9 PROTEIN) (PTD001) (HSPC029) (ARG134). [SWISSPROT;Acc:Q9UBQ5] 0.216085 0.264497579 EIF3K
747 0.729107 0.192847 0.264497529 CLUAP1
748 0.291643 PUTATIVE RNA-BINDING PROTEIN 7 (RNA BINDING MOTIF PROTEIN 7). [SWISSPROT;Acc:Q9Y580] 0.0771388 0.264497348 RBM7
749 0.120157 ERYTHROID DIFFERENTIATION AND DENUCLEATION FACTOR 1. [SWISSPROT;Acc:O60584] 0.0317812 0.264497283 SLMO1
750 0.437464 EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 6 INTERACTING PROTEIN (HSPC021/HSPC025). [SWISSPROT;Acc:Q9Y262] 0.115708 0.264497193 EIF3EIP

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/