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 512 to 561 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    128 TARDBP tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] Rooted 48.0515 39.0445 1.23069
    129 LUC7L luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Measured 4358.13 5811.49 1.33348
    NCBP2L dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Rooted 54.2343 66.7323 1.23044
    PCF11 pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] Squared 178263 118639 1.50257
    VPS24 neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Ranked 94 114 1.21277
    130 no value formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Rooted 55.1026 67.5701 1.22626
    C10orf83 44050 protein. [refseq;acc:nm_178832] Squared 148058 99628.4 1.4861
    CHMP4A protein hspc134 (protein cda04). [swissprot;acc:q9by43] Ranked 94 114 1.21277
    FOXP4 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Measured 2234.68 2978.53 1.33287
    131 no value huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Rooted 55.1113 67.5537 1.22577
    FOXP1 forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Measured 2234.73 2978.57 1.33285
    PPP1R8 nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972] Squared 148058 99628.4 1.4861
    SON son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] Ranked 294.053 242.562 1.21228
    132 ATG5 autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] Squared 36359.2 24466.8 1.48606
    FOXP3 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Measured 2236.61 2980.35 1.33253
    HAT1 histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] Rooted 44.963 55.0576 1.22451
    TOB2 tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Ranked 350 290 1.2069
    133 GABARAP gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Measured 23421.5 17580.4 1.33225
    OSR1 odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Rooted 45.4558 55.5995 1.22316
    TMEM132A gbp protein isoform a. [refseq;acc:nm_017870] Squared 1182.25 1726.55 1.46039
    TOB1 tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Ranked 350 290 1.2069
    134 no value gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Measured 21785.2 16426.1 1.32626
    DAB2IP dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] Ranked 350 290 1.2069
    GATAD2A p66 alpha. [refseq;acc:nm_017660] Squared 81888.8 56306.5 1.45434
    POLE4 dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] Rooted 44.849 54.7964 1.2218
    135 ATG3 apg3p; pc3-96 protein. [refseq;acc:nm_022488] Measured 21785.2 16426.1 1.32626
    CPEB4 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] Ranked 350 290 1.2069
    GATAD2B transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] Squared 81888.8 56306.5 1.45434
    NCBP2 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Rooted 54.935 66.6101 1.21253
    136 no value tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Squared 81888.8 56306.5 1.45434
    ADIPOR2 adiponectin receptor 2. [refseq;acc:nm_024551] Rooted 41.8357 50.6469 1.21061
    CPEB3 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Ranked 350 290 1.2069
    NFYC nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] Measured 3620.77 4763.34 1.31556
    137 CDK3 cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] Squared 81606.8 56215.8 1.45167
    MSI2 musashi 2 isoform a. [refseq;acc:nm_138962] Rooted 54.9787 66.2416 1.20486
    NFYA ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] Measured 3620.77 4763.34 1.31556
    RASAL2 ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Ranked 350 290 1.2069
    138 KCNIP1 kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Measured 2755.15 2094.3 1.31555
    MSI1 musashi 1. [refseq;acc:nm_002442] Rooted 54.9787 66.2416 1.20486
    PPP2CA serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] Ranked 194.372 234.204 1.20493
    UBAC1 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Squared 468498 322755 1.45156
    139 APBA1 amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] Ranked 271.752 225.68 1.20415
    CCNB2 g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] Squared 81592.1 56211.1 1.45153
    KCNIP4 potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Measured 2759.61 2099.49 1.31442
    ZC3H14 nuclear protein ukp68. [refseq;acc:nm_024824] Rooted 54.9787 66.2416 1.20486
    140 CDK2 cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] Squared 81527.6 56190.6 1.45091
    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] Rooted 55.6161 66.7332 1.19989
    KCNIP2 kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] Measured 2760.28 2100.27 1.31425
    RRAGA ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Ranked 59 49 1.20408
    141 CCNB1 g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] Squared 81520.8 56188.5 1.45084

    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/