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 Hugo Network Comparison Type Value Type Interaction Map red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 3964 to 4013 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Network Comparison Type
    		Value Type
    		red
    		green
    		network_comparison
    496 inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566] INPP4A Subtracted Measured 6167.93 7007.7 839.77
    nostrin. [refseq;acc:nm_052946] NOSTRIN Divided 4682.87 4093.05 1.1441
    pescadillo homolog 1. [swissprot;acc:o00541] PES1 Subtracted Rooted 49.2488 54.4603 5.2115
    suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] PPAN-P2RY11 Divided Ranked 250.938 234.134 1.07177
    tubby protein homolog. [swissprot;acc:p50607] TUB Squared 30286.5 36362 1.2006
    497 chromodomain y-like protein 2. [refseq;acc:nm_152342] CDYL2 Subtracted 29016.1 34169.2 5153.1
    eap30 subunit of ell complex. [refseq;acc:nm_007241] SNF8 Divided Measured 4682.87 4093.05 1.1441
    probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] EBNA1BP2 Ranked 251.344 234.514 1.07177
    protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743] PRKCI Squared 30286.5 36362 1.2006
    putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] DHX15 Subtracted Measured 4714.85 5554.38 839.53
    pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] HDGFL1 Divided Rooted 55.1759 60.2621 1.09218
    squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] SART1 Subtracted Ranked 225.026 209.798 15.228
    transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] SIN3A Rooted 50.4687 45.2733 5.1954
    498 density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] DENR
    liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] SLC39A6 Divided Measured 4682.87 4093.05 1.1441
    numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757] NUMB Squared 30286.5 36362 1.2006
    probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] DDX6 Rooted 55.1759 60.2621 1.09218
    rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] ARHGEF6 Ranked 220.161 235.95 1.07172
    t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711] TLX3 Subtracted 237.28 252.492 15.212
    testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] CDY1B Squared 29012.2 34163.9 5151.7
    transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] BTF3 Measured 6933.17 7766.54 833.37
    499 chromodomain protein, y chromosome-like isoform a; cdy-like, autosomal; testis-specific chromodomain y-like protein. [refseq;acc:nm_004824] CDYL Squared 29012.2 34163.9 5151.7
    glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] GAD2 Divided Measured 4682.87 4093.05 1.1441
    homeobox protein barh-like 1. [swissprot;acc:q9hbu1] BARX1 Subtracted Ranked 237.28 252.492 15.212
    proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] NOL1 Rooted 49.7541 54.9425 5.1884
    rw1 protein (fragment). [swissprot;acc:q92545] TMEM131 Divided 55.1759 60.2621 1.09218
    tbc1 domain family member 5. [swissprot;acc:q92609] TBC1D5 Squared 30286.5 36362 1.2006
    transcription factor btf3 homolog 3. [swissprot;acc:q13892] no value Subtracted Measured 6938.22 7770.65 832.43
    triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938] TPI1 Divided Ranked 231.496 248.048 1.0715
    500 60s ribosomal protein l7. [swissprot;acc:p18124] no value Rooted 52.6483 48.2135 1.09198
    block of proliferation 1. [swissprot;acc:q14137] BOP1 Subtracted 49.4884 54.6735 5.1851
    gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] NAPG Divided Measured 4682.87 4093.05 1.1441
    huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291] HIP1 Subtracted 10733.4 9902.6 830.8
    inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564] ING2 Divided Ranked 224.662 240.673 1.07127
    opsin 4 (melanopsin). [swissprot;acc:q9uhm6] OPN4 Subtracted 237.28 252.492 15.212
    testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7] CDY2B Squared 29012.4 34164 5151.6
    tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294] TULP1 Divided 30286.5 36362 1.2006
    501 cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] CDK3 Subtracted Rooted 93.6481 88.4638 5.1843
    cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] CYC1 Divided Ranked 238.704 255.68 1.07112
    dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602] POLR1A Rooted 50.4253 46.1792 1.09195
    glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] GAD1 Measured 4682.87 4093.05 1.1441
    glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [swissprot;acc:p57057] SLC37A1 Subtracted Squared 29224 34362.1 5138.1
    goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4] COL4A3BP Measured 10725.6 9896.32 829.28
    t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [swissprot;acc:o43763] TLX2 Ranked 237.28 252.492 15.212
    vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0] VPS29 Divided Squared 30286.5 36362 1.2006
    502 60s ribosomal protein l30. [swissprot;acc:p04645] RPL30 Rooted 50.4616 46.2257 1.09164
    huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146] HIP1R Subtracted Measured 10719 9891.08 827.92
    mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778] MAPK11 Rooted 84.6378 89.8201 5.1823
    numb-like protein (numb-r). [swissprot;acc:q9y6r0] NUMBL Divided Squared 30286.5 36362 1.2006
    oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1] ARHGAP26 Ranked 238.704 255.68 1.07112

    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/