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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • 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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 708 to 757 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    177 SLC25A43 mitochondrial solute carrier protein. [refseq;acc:nm_145305] Rooted 145.551 168.796 1.1597
    178 no value formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Ranked 226.887 194.72 1.1652
    CPA6 carboxypeptidase b precursor. [refseq;acc:nm_020361] Squared 25326.4 18354.1 1.37988
    MYO5B myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] Measured 21591.5 27904.5 1.29238
    TFDP2 transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Rooted 45.7414 52.932 1.1572
    179 no value huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Ranked 226.884 194.79 1.16476
    CPA3 mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] Squared 25326.3 18354.1 1.37987
    EGFL8 palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] Rooted 50.272 43.4634 1.15665
    MYO5C myosin vc (myosin 5c). [swissprot;acc:q9nqx4] Measured 21591.5 27904.5 1.29238
    180 no value myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]
    CPB2 plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] Squared 25326.2 18354.1 1.37987
    EGFL7 egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] Rooted 50.2801 43.4779 1.15645
    TARDBP tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] Ranked 256.228 298.438 1.16474
    181 B9D1 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] 229.818 267.265 1.16294
    BCAR1 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] Rooted 57.4432 66.3307 1.15472
    EIF4G3 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Measured 4068.56 5252.6 1.29102
    NFU1 hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Squared 55630.4 76083.7 1.36766
    182 no value rna-binding protein. [refseq;acc:nm_019027] Measured 4069.83 5252.17 1.29051
    CCT4 t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Rooted 57.45 66.332 1.1546
    DUT deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] Squared 61733.5 45224.1 1.36506
    HAT1 histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] Ranked 277.546 240.461 1.15422
    183 no value apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Measured 4069.83 5252.17 1.29051
    ACADVL acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] Squared 79779.8 108084 1.35478
    NCBP2 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Ranked 228.306 198.011 1.153
    NEDD9 enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] Rooted 57.4586 66.3336 1.15446
    184 no value small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] Squared 72886.3 98544.5 1.35203
    ATG4A cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Rooted 153.602 133.195 1.15321
    OSR1 odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Ranked 274.027 237.79 1.15239
    SYNCRIP ns1-associated protein 1. [refseq;acc:nm_006372] Measured 4069.83 5252.17 1.29051
    185 ADIPOR2 adiponectin receptor 2. [refseq;acc:nm_024551] Ranked 281.582 246.371 1.14292
    HNRNPR heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Measured 4069.83 5252.17 1.29051
    HS3ST6 c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] Squared 41502.9 30836.8 1.34589
    MAP1LC3B microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Rooted 153.578 133.176 1.1532
    186 EIF4G1 eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Measured 4071.1 5251.75 1.29001
    FLNB filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] Ranked 226.582 198.444 1.14179
    HS3ST3A1 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] Squared 41502.9 30836.8 1.34589
    MAP1LC3A microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Rooted 153.578 133.176 1.1532
    187 ATG4B cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 153.548 133.153 1.15317
    HS3ST3B1 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] Squared 41502.9 30836.8 1.34589
    REV1 rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] Ranked 226.582 198.444 1.14179
    SNRPD3 small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Measured 4569.48 5885.79 1.28807
    188 E2F1 transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] Rooted 46.0352 53.0192 1.15171
    HS3ST2 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] Squared 41502.9 30836.8 1.34589
    PRMT1 protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Ranked 226.582 198.444 1.14179
    STT3B source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Measured 4571.89 5864.86 1.28281
    189 DCPS mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] Squared 41502.9 30836.8 1.34589
    E2F2 transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Rooted 46.0352 53.0192 1.15171
    PRMT8 protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Ranked 226.582 198.444 1.14179
    STT3A oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Measured 4571.89 5864.86 1.28281
    190 AQP4 aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] Squared 71389.9 96037.6 1.34525

    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 HGNC identifier if it exists
    - Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
    - Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
    - Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
    - Filtered specifies whether we only included the high confidence microarry measurements or not.
    - http://analysis.yellowcouch.org/