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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 518 to 567 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		description
    		red
    		green
    		network_comparison
    130 C10orf83 Squared 44050 protein. [refseq;acc:nm_178832] 148058 99628.4 1.4861
    CHMP4A Ranked protein hspc134 (protein cda04). [swissprot;acc:q9by43] 94 114 1.21277
    FOXP4 Measured forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] 2234.68 2978.53 1.33287
    131 no value Rooted huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] 55.1113 67.5537 1.22577
    FOXP1 Measured forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] 2234.73 2978.57 1.33285
    PPP1R8 Squared 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] 148058 99628.4 1.4861
    SON Ranked 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] 294.053 242.562 1.21228
    132 ATG5 Squared autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] 36359.2 24466.8 1.48606
    FOXP3 Measured forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] 2236.61 2980.35 1.33253
    HAT1 Rooted histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] 44.963 55.0576 1.22451
    TOB2 Ranked tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 350 290 1.2069
    133 GABARAP Measured gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] 23421.5 17580.4 1.33225
    OSR1 Rooted odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] 45.4558 55.5995 1.22316
    TMEM132A Squared gbp protein isoform a. [refseq;acc:nm_017870] 1182.25 1726.55 1.46039
    TOB1 Ranked tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] 350 290 1.2069
    134 no value Measured gaba-a receptor-associated protein. [sptrembl;acc:q9by60] 21785.2 16426.1 1.32626
    DAB2IP Ranked dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] 350 290 1.2069
    GATAD2A Squared p66 alpha. [refseq;acc:nm_017660] 81888.8 56306.5 1.45434
    POLE4 Rooted dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] 44.849 54.7964 1.2218
    135 ATG3 Measured apg3p; pc3-96 protein. [refseq;acc:nm_022488] 21785.2 16426.1 1.32626
    CPEB4 Ranked cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] 350 290 1.2069
    GATAD2B Squared transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] 81888.8 56306.5 1.45434
    NCBP2 Rooted 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] 54.935 66.6101 1.21253
    136 no value Squared tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] 81888.8 56306.5 1.45434
    ADIPOR2 Rooted adiponectin receptor 2. [refseq;acc:nm_024551] 41.8357 50.6469 1.21061
    CPEB3 Ranked cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] 350 290 1.2069
    NFYC Measured 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] 3620.77 4763.34 1.31556
    137 CDK3 Squared cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] 81606.8 56215.8 1.45167
    MSI2 Rooted musashi 2 isoform a. [refseq;acc:nm_138962] 54.9787 66.2416 1.20486
    NFYA Measured 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] 3620.77 4763.34 1.31556
    RASAL2 Ranked ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] 350 290 1.2069
    138 KCNIP1 Measured kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] 2755.15 2094.3 1.31555
    MSI1 Rooted musashi 1. [refseq;acc:nm_002442] 54.9787 66.2416 1.20486
    PPP2CA Ranked serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] 194.372 234.204 1.20493
    UBAC1 Squared putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 468498 322755 1.45156
    139 APBA1 Ranked 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] 271.752 225.68 1.20415
    CCNB2 Squared g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] 81592.1 56211.1 1.45153
    KCNIP4 Measured potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] 2759.61 2099.49 1.31442
    ZC3H14 Rooted nuclear protein ukp68. [refseq;acc:nm_024824] 54.9787 66.2416 1.20486
    140 CDK2 Squared cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] 81527.6 56190.6 1.45091
    FLNB Rooted 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] 55.6161 66.7332 1.19989
    KCNIP2 Measured 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] 2760.28 2100.27 1.31425
    RRAGA Ranked ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] 59 49 1.20408
    141 CCNB1 Squared g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] 81520.8 56188.5 1.45084
    REV1 Rooted rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] 55.6161 66.7332 1.19989
    RRAGC Ranked ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] 59 49 1.20408
    SNRPD2 Measured small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] 4405.4 5782.08 1.3125
    142 CDC2 Squared cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] 81478.9 56175.2 1.45044
    PITRM1 Measured metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] 9276.47 7090.37 1.30832
    PRMT1 Rooted protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] 55.6161 66.7332 1.19989

    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/