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 network_comparison green
    Results: HTML CSV LaTeX Showing element 514 to 563 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		description
    		red
    		network_comparison
    		green
    129 NCBP2L Rooted dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] 54.2343 1.23044 66.7323
    PCF11 Squared pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] 178263 1.50257 118639
    VPS24 Ranked neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] 94 1.21277 114
    130 no value Rooted formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] 55.1026 1.22626 67.5701
    C10orf83 Squared 44050 protein. [refseq;acc:nm_178832] 148058 1.4861 99628.4
    CHMP4A Ranked protein hspc134 (protein cda04). [swissprot;acc:q9by43] 94 1.21277 114
    FOXP4 Measured forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] 2234.68 1.33287 2978.53
    131 no value Rooted huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] 55.1113 1.22577 67.5537
    FOXP1 Measured forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] 2234.73 1.33285 2978.57
    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 1.4861 99628.4
    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 1.21228 242.562
    132 ATG5 Squared autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] 36359.2 1.48606 24466.8
    FOXP3 Measured forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] 2236.61 1.33253 2980.35
    HAT1 Rooted histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] 44.963 1.22451 55.0576
    TOB2 Ranked tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 350 1.2069 290
    133 GABARAP Measured gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] 23421.5 1.33225 17580.4
    OSR1 Rooted odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] 45.4558 1.22316 55.5995
    TMEM132A Squared gbp protein isoform a. [refseq;acc:nm_017870] 1182.25 1.46039 1726.55
    TOB1 Ranked tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] 350 1.2069 290
    134 no value Measured gaba-a receptor-associated protein. [sptrembl;acc:q9by60] 21785.2 1.32626 16426.1
    DAB2IP Ranked dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] 350 1.2069 290
    GATAD2A Squared p66 alpha. [refseq;acc:nm_017660] 81888.8 1.45434 56306.5
    POLE4 Rooted dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] 44.849 1.2218 54.7964
    135 ATG3 Measured apg3p; pc3-96 protein. [refseq;acc:nm_022488] 21785.2 1.32626 16426.1
    CPEB4 Ranked cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] 350 1.2069 290
    GATAD2B Squared transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] 81888.8 1.45434 56306.5
    NCBP2 Rooted 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] 54.935 1.21253 66.6101
    136 no value Squared tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] 81888.8 1.45434 56306.5
    ADIPOR2 Rooted adiponectin receptor 2. [refseq;acc:nm_024551] 41.8357 1.21061 50.6469
    CPEB3 Ranked cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] 350 1.2069 290
    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 1.31556 4763.34
    137 CDK3 Squared cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] 81606.8 1.45167 56215.8
    MSI2 Rooted musashi 2 isoform a. [refseq;acc:nm_138962] 54.9787 1.20486 66.2416
    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 1.31556 4763.34
    RASAL2 Ranked ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] 350 1.2069 290
    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 1.31555 2094.3
    MSI1 Rooted musashi 1. [refseq;acc:nm_002442] 54.9787 1.20486 66.2416
    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 1.20493 234.204
    UBAC1 Squared putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 468498 1.45156 322755
    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 1.20415 225.68
    CCNB2 Squared g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] 81592.1 1.45153 56211.1
    KCNIP4 Measured potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] 2759.61 1.31442 2099.49
    ZC3H14 Rooted nuclear protein ukp68. [refseq;acc:nm_024824] 54.9787 1.20486 66.2416
    140 CDK2 Squared cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] 81527.6 1.45091 56190.6
    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 1.19989 66.7332
    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 1.31425 2100.27
    RRAGA Ranked ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] 59 1.20408 49
    141 CCNB1 Squared g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] 81520.8 1.45084 56188.5
    REV1 Rooted rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] 55.6161 1.19989 66.7332
    RRAGC Ranked ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] 59 1.20408 49

    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/