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 Network Comparison Type description 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
    		Network Comparison Type
    		description
    		Hugo
    		Value Type
    		Interaction Map
    		red
    		green
    		network_comparison
    133 Subtracted formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] no value Ranked High confidence 226.887 194.72 32.167
    inad-like protein isoform 3; pdz domain protein (drosophila inad-like); protein associated to tight junctions; pals1-associated tight junction protein; inactivation no after-potential d-like protein. [refseq;acc:nm_005799] INADL Squared Low confidence 67882.7 60913.7 6969
    segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] DVL2 Measured 7034.43 7797.14 762.71
    Ranked 203.007 189.985 13.022
    thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] PRSS16 Squared High confidence 71062.2 95488.6 24426.4
    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] E2F1 Rooted Low confidence 64.712 69.8815 5.1695
    134 Divided ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] 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
    gaba-a receptor-associated protein. [sptrembl;acc:q9by60] no value Measured 21785.2 16426.1 1.32626
    helix-loop-helix protein 1 (hen1) (nescient helix loop helix 1) (nscl- 1). [swissprot;acc:q02575] NHLH1 Squared Low confidence 55838.6 49199.4 1.13494
    p66 alpha. [refseq;acc:nm_017660] GATAD2A High confidence 81888.8 56306.5 1.45434
    transgelin (smooth muscle protein 22-alpha) (sm22-alpha) (ws3-10) (22 kda actin-binding protein). [swissprot;acc:q01995] TAGLN Ranked Low confidence 218.561 205.431 1.06391
    Subtracted g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] CCNB2 Measured High confidence 12796.8 10886 1910.8
    gk001 protein. [refseq;acc:nm_020198] CCDC47 Squared 71062.2 95488.6 24426.4
    huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] no value Ranked 226.884 194.79 32.094
    multiple pdz domain protein. [refseq;acc:nm_003829] MPDZ Squared Low confidence 67876.4 60909.3 6967.1
    segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] DVL3 Measured 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 2 (sm22-alpha homolog). [swissprot;acc:p37802] no value Ranked 218.36 205.4 12.96
    135 Divided 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] NCBP2 Rooted High confidence 54.935 66.6101 1.21253
    apg3p; pc3-96 protein. [refseq;acc:nm_022488] ATG3 Measured 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
    cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] CPEB4 Ranked High confidence 350 290 1.2069
    high-mobility group 20a. [refseq;acc:nm_018200] 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
    transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] GATAD2B Squared High confidence 81888.8 56306.5 1.45434
    Subtracted alpha-aminoadipate aminotransferase; l-kynurenine/alpha-aminoadipate aminotransferase; kynurenine aminotransferase ii. [refseq;acc:nm_016228] AADAT Measured Low confidence 9986.51 10741.3 754.79
    calsyntenin-2 precursor. [swissprot;acc:q9h4d0] CLSTN2 Squared High confidence 71033.4 95440.2 24406.8
    forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] FOXP4 Ranked 263.215 231.407 31.808
    segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] DVL3 Low confidence 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
    voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] 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 Divided adiponectin receptor 2. [refseq;acc:nm_024551] 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
    cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] CPEB3 Ranked High confidence 350 290 1.2069
    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] HMG20B Low confidence 202.996 190.854 1.06362
    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] NFYC Measured High confidence 3620.77 4763.34 1.31556
    ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] RPS6KC1 Low confidence 7020.48 7667.34 1.09214
    transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664] GTF3A Rooted 72.3705 77.5037 1.07093
    tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] no value Squared High confidence 81888.8 56306.5 1.45434
    Subtracted calsyntenin-3 precursor. [swissprot;acc:q9bqt9] CLSTN3 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
    elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [refseq;acc:nm_018127] 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

    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/