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:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description measured expected final Hugo
Results: HTML CSV LaTeX Showing element 708 to 757 of 3206 in total
Rank
description
measured
expected
final
Hugo
708 0.0359748 0.135679 0.265146412 RCOR3
709 REST COREPRESSOR. [RefSeq;Acc:NM_015156] 0.0422874 0.159487 0.265146376 RCOR1
710 F-ACTIN CAPPING PROTEIN BETA SUBUNIT (CAPZ BETA). [SWISSPROT;Acc:P47756] 0.238765 0.900943 0.265016766 CAPZB
711 F-ACTIN CAPPING PROTEIN ALPHA-3 SUBUNIT (CAPZ ALPHA-3) (GERM CELL- SPECIFIC PROTEIN 3). [SWISSPROT;Acc:Q96KX2] 0.0330141 0.124574 0.265015974 CAPZA3
712 HISTONE DEACETYLASE 2 (HD2). [SWISSPROT;Acc:Q92769] 0.52666 1.98825 0.264886206 no value
713 DJ153G14.2 (POSSIBLE CA BINDING PROTEIN SIMILAR TO NEFA) (FRAGMENT). [SPTREMBL;Acc:Q9UJN8] 0.0697761 0.263425 0.264880326
714 MULTIPLE COAGULATION FACTOR DEFICIENCY 2; NEURAL STEM CELL DERIVED NEURONAL SURVIVAL PROTEIN; MULTIPLE COAGULATION FACTOR DEFICIENCY PROTEIN 2. [RefSeq;Acc:NM_139279] 0.0858635 0.32416 0.264879998 MCFD2
715 HISTONE DEACETYLASE 1 (HD1). [SWISSPROT;Acc:Q13547] 0.582904 2.20068 0.264874493 HDAC1
716 P28 ING5. [RefSeq;Acc:NM_032329] 0.105213 0.397328 0.264801373 ING5
717 ARP2/3 COMPLEX 16 KDA SUBUNIT (P16-ARC) (ACTIN-RELATED PROTEIN 2/3 COMPLEX SUBUNIT 5). [SWISSPROT;Acc:O15511] 0.402903 1.52156 0.264795999 ARPC5
718 INTERFERON-RELATED DEVELOPMENTAL REGULATOR 2 (SKMC15 PROTEIN). [SWISSPROT;Acc:Q12894] 0.0750554 0.28346 0.264783038 HYAL3
719 0.424703 1.60405 0.264769178 ARPC5L
720 ZINC FINGER PROTEIN 258. [RefSeq;Acc:NM_145310] 0.0317441 0.119935 0.264677534 ZMYM6
721 DJ470L14.3 (NOVEL PROTEIN SIMILAR TO THE ARP2/3 PROTEIN COMPLEX SUBUNIT P21-ARC (ARC21)). [SPTREMBL;Acc:Q9H5B6] 0.381101 1.43987 0.264677367 no value
722 SIMILAR TO ACTIN-RELATED PROTEIN 3-BETA. [SPTREMBL;Acc:Q96BT2] 0.322726 1.21932 0.264677033 ACTR3B
723 ACTIN-LIKE PROTEIN 3 (ACTIN-RELATED PROTEIN 3) (ACTIN-2). [SWISSPROT;Acc:P32391] 0.528875 1.99819 ACTR3
724 ACTIN-RELATED PROTEIN 2/3 COMPLEX SUBUNIT 1A (SOP2-LIKE PROTEIN). [SWISSPROT;Acc:Q92747] 0.355858 1.3445 0.264676832 ARPC1A
725 ARP2/3 COMPLEX 21 KDA SUBUNIT (P21-ARC) (ACTIN-RELATED PROTEIN 2/3 COMPLEX SUBUNIT 3). [SWISSPROT;Acc:O15145] 0.392968 1.48471 0.264676604 ARPC3
726 NARDILYSIN PRECURSOR (EC 3.4.24.61) (N-ARGININE DIBASIC CONVERTASE) (NRD CONVERTASE) (NRD-C). [SWISSPROT;Acc:O43847] 0.0787172 0.297409 0.26467659 NRD1
727 ZINC FINGER PROTEIN 262; CELL DEATH INHIBITING RNA. [RefSeq;Acc:NM_005095] 0.0398851 0.150694 0.264676099 ZMYM4
728 CONSERVED OLIGOMERIC GOLGI COMPLEX COMPONENT 3 (VESICLE DOCKING PROTEIN SEC34 HOMOLOG) (P94). [SWISSPROT;Acc:Q96JB2] COG3
729 ACTIN-LIKE PROTEIN 2 (ACTIN-RELATED PROTEIN 2). [SWISSPROT;Acc:O15142] 0.390781 1.47645 0.264676081 ACTR2
730 ZINC FINGER PROTEIN 261 (DXS6673E PROTEIN). [SWISSPROT;Acc:Q14202] 0.030934 0.116875 0.264675936 ZMYM3
731 ZINC FINGER PROTEIN 198 (FUSED IN MYELOPROLIFERATIVE DISORDERS PROTEIN) (REARRANGED IN ATYPICAL MYELOPROLIFERATIVE DISORDER PROTEIN). [SWISSPROT;Acc:Q9UBW7] 0.0311669 0.117755 0.26467581 ZMYM2
732 ARP2/3 COMPLEX 41 KDA SUBUNIT (P41-ARC) (ACTIN-RELATED PROTEIN 2/3 COMPLEX SUBUNIT 1B). [SWISSPROT;Acc:O15143] 0.317947 1.20127 0.264675718 ARPC1B
733 C-TERMINAL BINDING PROTEIN 1 (CTBP1). [SWISSPROT;Acc:Q13363] 0.349374 1.32007 0.264663238 CTBP1
734 B-CELL LYMPHOMA 6 PROTEIN (BCL-6) (ZINC FINGER PROTEIN 51) (LAZ-3 PROTEIN) (BCL-5). [SWISSPROT;Acc:P41182] 0.0869475 0.328537 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 "B-CELL CLL/LYMPHOMA 6, MEMBER B (ZINC FINGER PROTEIN); ZINC FINGER PROTEIN 62. [RefSeq;Acc:NM_181844]" 0.0692921 0.261825 0.264650434 BCL6B
738 C-TERMINAL BINDING PROTEIN 2 (CTBP2). [SWISSPROT;Acc:P56545] 0.398698 1.50657 0.264639545 CTBP2
739 PEROXISOMAL CARNITINE OCTANOYLTRANSFERASE (EC 2.3.1.-) (COT). [SWISSPROT;Acc:Q9UKG9] 0.117061 0.442554 0.264512353 CROT
740 PROTEIN C20ORF45 (CGI-107). [SWISSPROT;Acc:Q9Y3B1] 0.0385694 0.145821 0.264498255 SLMO2
741 ZCCHC8
742 BARDET-BIEDL SYNDROME 7 PROTEIN ISOFORM A; BBS2-LIKE 1. [RefSeq;Acc:NM_176824] BBS7
743 HSDL2
744 0.10892 0.411799 0.264497971 INTS10
745 BA508N22.1 (HSPC025) (FRAGMENT). [SPTREMBL;Acc:Q9HCW5] 0.0296502 0.1121 0.26449777 no value
746 EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 11 (EIF-3 P25) (EIF3K) (MUSCLE SPECIFIC GENE M9 PROTEIN) (PTD001) (HSPC029) (ARG134). [SWISSPROT;Acc:Q9UBQ5] 0.216085 0.816964 0.264497579 EIF3K
747 0.192847 0.729107 0.264497529 CLUAP1
748 PUTATIVE RNA-BINDING PROTEIN 7 (RNA BINDING MOTIF PROTEIN 7). [SWISSPROT;Acc:Q9Y580] 0.0771388 0.291643 0.264497348 RBM7
749 ERYTHROID DIFFERENTIATION AND DENUCLEATION FACTOR 1. [SWISSPROT;Acc:O60584] 0.0317812 0.120157 0.264497283 SLMO1
750 EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 6 INTERACTING PROTEIN (HSPC021/HSPC025). [SWISSPROT;Acc:Q9Y262] 0.115708 0.437464 0.264497193 EIF3EIP
751 0.0771387 0.291643 0.264497005 C15orf44
752 LIPOPOLYSACCHARIDE-RESPONSIVE AND BEIGE-LIKE ANCHOR PROTEIN (CDC4-LIKE PROTEIN) (BEIGE-LIKE PROTEIN). [SWISSPROT;Acc:P50851] 0.0321572 0.121579 0.264496336 no value
753 LUPUS LA PROTEIN (SJOGREN SYNDROME TYPE B ANTIGEN) (SS-B) (LA RIBONUCLEOPROTEIN) (LA AUTOANTIGEN). [SWISSPROT;Acc:P05455] 0.302351 1.14316 0.264487036 SSB
754 U4/U6-ASSOCIATED RNA SPLICING FACTOR. [RefSeq;Acc:NM_004698] 0.351386 1.32896 0.264406754 PRPF3
755 0.0328701 0.124442 0.264139921 CCDC93
756 BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 5 (APOPTOSIS INHIBITOR SURVIVIN) (APOPTOSIS INHIBITOR 4). [SWISSPROT;Acc:O15392] 0.168097 0.636394 0.264139825 BIRC5
757 FAS APOPTOTIC INHIBITORY MOLECULE. [RefSeq;Acc:NM_018147] 0.118199 0.447876 0.2639101 FAIM

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/