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 green network_comparison
    Results: HTML CSV LaTeX Showing element 1377 to 1426 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		description
    		red
    		green
    		network_comparison
    345 CMPK Ranked ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] 242.14 265.697 1.09729
    DHX15 Rooted putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] 56.2615 62.2958 1.10725
    HSD17B14 Measured retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] 20446.1 24136.4 1.18049
    SH3GL1 Squared sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] 35793 44595.3 1.24592
    346 CSE1L importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] 34018.3 42373 1.24559
    GRAP Rooted grb2-related adaptor protein. [swissprot;acc:q13588] 61.4282 68.0107 1.10716
    RPS3 Ranked 40s ribosomal protein s3. [swissprot;acc:p23396] 241.612 265.119 1.09729
    SEPT1 Measured septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] 14229.2 16780.7 1.17931
    347 AK3 Ranked gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7] 242.14 265.697 1.09729
    PRSS7 Measured enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] 4991.02 5885.09 1.17914
    SNRPD2 Squared small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] 16573.6 20637.8 1.24522
    TIPRL Rooted cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] 66.4284 60.0004 1.10713
    348 no value Ranked adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] 242.14 265.696 1.09728
    GORASP2 Squared golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] 42566.2 52985.3 1.24477
    NOC3L Rooted ad24 protein. [refseq;acc:nm_022451] 49.2558 54.5235 1.10695
    SF3B2 Measured splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] 4991.02 5885.09 1.17914
    349 DHX15 putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] 4714.85 5554.38 1.17806
    LSM4 Rooted u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] 56.0061 61.9704 1.10649
    MED22 Ranked surfeit locus protein 5. [swissprot;acc:q15528] 242.14 265.696 1.09728
    SH3GL2 Squared sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962] 35533.9 44227 1.24464
    350 ARMET armet protein precursor (arginine-rich protein). [swissprot;acc:p55145] 35508.7 44191.4 1.24452
    NAV2 Rooted neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117] 61.3383 67.8668 1.10643
    SCAPER Ranked zinc finger protein 291. [swissprot;acc:q9by12] 242.14 265.696 1.09728
    ZNF547 Measured sedlin. [swissprot;acc:o14582] 17396.9 20483.9 1.17745
    351 no value synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]
    ANKS1B Rooted e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] 61.3352 67.8618 1.10641
    HDC Squared histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113] 35508.6 44191.3 1.24452
    PEX1 Ranked peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] 242.14 265.696 1.09728
    352 no value Squared 40s ribosomal protein s28. [swissprot;acc:p25112] 30682.9 38183.6 1.24446
    NAV1 Rooted neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] 61.3354 67.8621 1.10641
    TRAPPC3 Measured bet3 homolog. [swissprot;acc:o43617] 17396.9 20483.9 1.17745
    TXNDC9 Ranked protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530] 242.14 265.696 1.09728
    353 GATAD2A Measured p66 alpha. [refseq;acc:nm_017660] 12839 10911.1 1.17669
    GIPC1 Ranked rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] 231.73 211.252 1.09694
    NAV3 Rooted neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] 61.3354 67.8623 1.10641
    NONO Squared 54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [swissprot;acc:q15233] 71383 57399.3 1.24362
    354 GATAD2B Measured transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] 12839 10911.1 1.17669
    PSPC1 Squared paraspeckle protein 1. [refseq;acc:nm_018282] 71360.3 57385.8 1.24352
    STX10 Ranked syntaxin 10 (syn10). [swissprot;acc:o60499] 234.691 257.442 1.09694
    WDR12 Rooted wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] 49.2848 54.5246 1.10632
    355 no value Measured tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] 12839 10911.1 1.17669
    PRSS7 Rooted enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] 58.0752 64.23 1.10598
    STX6 Ranked syntaxin 6. [swissprot;acc:o43752] 234.673 257.414 1.09691
    UNC84A Squared sad1/unc-84 protein-like 1. [swissprot;acc:o94901] 15588.1 19381.8 1.24337
    356 no value Ranked 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] 243.24 266.796 1.09684
    SF3B2 Rooted splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] 58.0752 64.23 1.10598
    SH3GL3 Squared sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963] 35247.5 43820.5 1.24322
    TCP1 Measured t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] 11004.2 12944.2 1.1763
    357 no value Ranked 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] 243.12 266.661 1.09683
    GRB2 Rooted growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354] 61.2684 67.755 1.10587

    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/