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 682 to 731 of 16578 in total
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		Interaction Map
    		red
    		green
    		network_comparison
    171 FOXP3 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Divided Low confidence 219.889 208.064 1.05683
    TIAL1 nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] High confidence 227.202 192.823 1.17829
    TRPC4 short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Subtracted 201.478 228.784 27.306
    172 CAPZA1 f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] Divided Low confidence 213.671 202.205 1.0567
    PPM1B protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] Subtracted 196.714 185.758 10.956
    TBC1D10A ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] High confidence 201.515 228.752 27.237
    TIPRL cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] Divided 174.667 205.556 1.17685
    173 no value guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Subtracted Low confidence 211.679 222.623 10.944
    SNRPD1 small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Divided High confidence 227.032 193.056 1.17599
    TRPC5 short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] Subtracted 201.515 228.752 27.237
    UNC84A sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Divided Low confidence 221.678 209.795 1.05664
    174 DGCR14 dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] High confidence 335 286 1.17133
    FOXP1 forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Low confidence 219.6 207.907 1.05624
    GNG12 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Subtracted 211.679 222.623 10.944
    LUC7L2 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] High confidence 228.1 200.968 27.132
    175 no value f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] Low confidence 212.589 201.755 10.834
    COPS3 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] Divided High confidence 199.949 234.187 1.17123
    FOXP4 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Low confidence 219.593 207.903 1.05623
    LUC7L luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Subtracted High confidence 228.085 201.006 27.079
    176 EIF5 eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] 271.016 244.167 26.849
    POLE4 dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] Divided 275.754 235.908 1.1689
    RC3H2 membrane-associated nucleic acid binding protein. [refseq;acc:nm_018835] Subtracted Low confidence 217.341 206.571 10.77
    TNS3 tumor endothelial marker 6; thyroid specific ptb domain protein; tensin 3. [refseq;acc:nm_022748] Divided 219.336 207.703 1.05601
    177 HBS1L hbs1-like. [refseq;acc:nm_006620] Subtracted 206.166 216.913 10.747
    NCBP2L dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Divided High confidence 229.406 196.695 1.1663
    POP7 ribonuclease p protein subunit p20 (ec 3.1.26.5) (rnasep protein p20) (hpop7). [swissprot;acc:o75817] Low confidence 209.954 221.607 1.0555
    SIN3A transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] Subtracted High confidence 241.07 267.88 26.81
    178 no value formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Divided 226.887 194.72 1.1652
    BPNT1 3'(2'), 5'-bisphosphate nucleotidase 1; bisphosphate 3'-nucleotidase; bpntase; pap-inositol-1,4-phosphatase. [refseq;acc:nm_006085] Low confidence 209.954 221.607 1.0555
    DENR density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] Subtracted High confidence 241.07 267.88 26.81
    GNG4 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Low confidence 211.51 222.252 10.742
    179 no value huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Divided High confidence 226.884 194.79 1.16476
    DNALI1 axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] Subtracted Low confidence 214.779 204.039 10.74
    PAH phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] High confidence 227.357 254.15 26.793
    RPL6 60s ribosomal protein l6 (tax-responsive enhancer element binding protein 107) (taxreb107) (neoplasm-related protein c140). [swissprot;acc:q02878] Divided Low confidence 209.954 221.607 1.0555
    180 DCHS1 protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0] 218.925 207.441 1.05536
    DUS1L pp3111 protein. [refseq;acc:nm_022156] Subtracted High confidence 227.357 254.15 26.793
    GNG3 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Low confidence 211.506 222.243 10.737
    TARDBP tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] Divided High confidence 256.228 298.438 1.16474
    181 B9D1 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] 229.818 267.265 1.16294
    GNG8 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] Subtracted Low confidence 211.484 222.196 10.712
    STAMBPL1 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Divided 196.362 206.979 1.05407
    STX18 syntaxin 18. [swissprot;acc:q9p2w9] Subtracted High confidence 227.357 254.15 26.793
    182 no value rd protein. [swissprot;acc:p18615]
    GNG5 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Low confidence 211.475 222.177 10.702
    HAT1 histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] Divided High confidence 277.546 240.461 1.15422
    PXK px serine/threonine kinase. [refseq;acc:nm_017771] Low confidence 196.372 206.947 1.05385
    183 no value bromodomain adjacent to zinc finger domain protein 1a (atp-utilizing chromatin assembly and remodeling factor 1) (hacf1) (atp-dependent chromatin remodelling protein) (williams syndrome transcription factor-related chromatin remodeling factor 180) (wcrf180) (hwalp1) (chrac subunit acf1) (hspc317). [swissprot;acc:q9nrl2]
    GSTO1 glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] Subtracted High confidence 227.357 254.15 26.793
    HSPB6 heat-shock 20 kda like-protein p20. [swissprot;acc:o14558] Low confidence 219.606 208.904 10.702

    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/