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 description Network Comparison Type Hugo Value Type Interaction Map red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 2123 to 2172 of 66312 in total
    Filtered  : 1
    Rank
    		description
    		Network Comparison Type
    		Hugo
    		Value Type
    		Interaction Map
    		red
    		green
    		network_comparison
    133 segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Subtracted DVL2 Measured Low confidence 7034.43 7797.14 762.71
    Ranked 203.007 189.985 13.022
    striated muscle activator of rho-dependent signaling. [refseq;acc:nm_139166] Divided ABRA Rooted 65.2217 69.9574 1.07261
    thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] Subtracted PRSS16 Squared High confidence 71062.2 95488.6 24426.4
    tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Divided TOB1 Ranked 350 290 1.2069
    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] Subtracted E2F1 Rooted Low confidence 64.712 69.8815 5.1695
    134 ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] Divided GSTO2 Measured 6670.21 7286.66 1.09242
    calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] CAPN1 Rooted 64.1512 68.7584 1.07182
    dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] DAB2IP Ranked High confidence 350 290 1.2069
    dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] POLE4 Rooted 44.849 54.7964 1.2218
    g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] Subtracted CCNB2 Measured 12796.8 10886 1910.8
    gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Divided no value 21785.2 16426.1 1.32626
    gk001 protein. [refseq;acc:nm_020198] Subtracted CCDC47 Squared 71062.2 95488.6 24426.4
    helix-loop-helix protein 1 (hen1) (nescient helix loop helix 1) (nscl- 1). [swissprot;acc:q02575] Divided NHLH1 Low confidence 55838.6 49199.4 1.13494
    huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Subtracted no value Ranked High confidence 226.884 194.79 32.094
    multiple pdz domain protein. [refseq;acc:nm_003829] MPDZ Squared Low confidence 67876.4 60909.3 6967.1
    p66 alpha. [refseq;acc:nm_017660] Divided GATAD2A High confidence 81888.8 56306.5 1.45434
    segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Subtracted DVL3 Measured Low confidence 7054.1 7809.38 755.28
    small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] SNRPD1 Rooted High confidence 54.8203 67.934 13.1137
    transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] E2F2 Low confidence 64.712 69.8815 5.1695
    transgelin (smooth muscle protein 22-alpha) (sm22-alpha) (ws3-10) (22 kda actin-binding protein). [swissprot;acc:q01995] Divided TAGLN Ranked 218.561 205.431 1.06391
    transgelin 2 (sm22-alpha homolog). [swissprot;acc:p37802] Subtracted no value 218.36 205.4 12.96
    135 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Divided NCBP2 Rooted High confidence 54.935 66.6101 1.21253
    alpha-aminoadipate aminotransferase; l-kynurenine/alpha-aminoadipate aminotransferase; kynurenine aminotransferase ii. [refseq;acc:nm_016228] Subtracted AADAT Measured Low confidence 9986.51 10741.3 754.79
    apg3p; pc3-96 protein. [refseq;acc:nm_022488] Divided ATG3 High confidence 21785.2 16426.1 1.32626
    calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] CAPN2 Rooted Low confidence 64.1536 68.7605 1.07181
    calsyntenin-2 precursor. [swissprot;acc:q9h4d0] Subtracted CLSTN2 Squared High confidence 71033.4 95440.2 24406.8
    cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] Divided CPEB4 Ranked 350 290 1.2069
    forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Subtracted FOXP4 263.215 231.407 31.808
    high-mobility group 20a. [refseq;acc:nm_018200] Divided HMG20A Measured Low confidence 7248.24 7916.96 1.09226
    methylenetetrahydrofolate reductase (ec 1.5.1.20). [swissprot;acc:p42898] MTHFR Squared 63248.6 71782.7 1.13493
    neuronal protein np25. [swissprot;acc:q9ui15] TAGLN3 Ranked 218.66 205.57 1.06368
    segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Subtracted DVL3 202.96 190.094 12.866
    septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] SEPT7 Rooted 90.452 95.6145 5.1625
    transcription factor jun-b. [swissprot;acc:p17275] JUNB Measured High confidence 5579.18 7488.4 1909.22
    transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] Divided GATAD2B Squared 81888.8 56306.5 1.45434
    voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] Subtracted CACNG8 Rooted 49.2923 62.3969 13.1046
    ww domain binding protein 11; npw38-binding protein npwbp; sh3 domain-binding protein snp70. [refseq;acc:nm_016312] WBP11 Squared Low confidence 67872.2 60906.5 6965.7
    136 adiponectin receptor 2. [refseq;acc:nm_024551] Divided ADIPOR2 Rooted High confidence 41.8357 50.6469 1.21061
    brain protein 44. [swissprot;acc:o95563] BRP44 Squared Low confidence 62640.6 71038.3 1.13406
    calsyntenin-3 precursor. [swissprot;acc:q9bqt9] Subtracted CLSTN3 High confidence 71030.1 95434.8 24404.7
    cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] CDK2 Measured 12787.6 10880.5 1907.1
    cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Divided CPEB3 Ranked 350 290 1.2069
    elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [refseq;acc:nm_018127] Subtracted ELAC2 Squared Low confidence 67872.2 60906.5 6965.7
    forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] FOXP1 Ranked High confidence 263.215 231.407 31.808
    high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] Divided HMG20B Low confidence 202.996 190.854 1.06362
    hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] Subtracted HPRT1 Measured 9896.39 10650.5 754.11
    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] Divided NFYC High confidence 3620.77 4763.34 1.31556
    rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] Subtracted ARHGEF7 Ranked Low confidence 219.344 206.52 12.824
    ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] Divided RPS6KC1 Measured 7020.48 7667.34 1.09214

    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/