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 Value Type Hugo Network Comparison Type description Interaction Map Filtered network_comparison red green
    Results: HTML CSV LaTeX Showing element 2625 to 2674 of 66312 in total
    Filtered  : 1
    Rank
    		Value Type
    		Hugo
    		Network Comparison Type
    		description
    		Interaction Map
    		network_comparison
    		red
    		green
    165 Measured MAGEA8 Divided melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] High confidence 1.29736 23693.7 18263
    PLAA Subtracted phospholipase a-2-activating protein (plap) (pla2p). [swissprot;acc:q9y263] Low confidence 635.8 11162 10526.2
    PYGB glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] High confidence 1723.37 4489.19 2765.82
    SLC16A8 Divided monocarboxylate transporter 3 (mct 3). [swissprot;acc:o95907] Low confidence 1.08285 10341.7 11198.5
    Ranked CAPN1 calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] 1.05782 222.508 210.345
    GAD2 glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] High confidence 1.19058 209.299 249.187
    RPL6 Subtracted 60s ribosomal protein l6 (tax-responsive enhancer element binding protein 107) (taxreb107) (neoplasm-related protein c140). [swissprot;acc:q02878] Low confidence 11.653 209.954 221.607
    SPATA6 spermatogenesis associated 6. [refseq;acc:nm_019073] High confidence 28 133 105
    Squared CLEC3B tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] 16470.8 59016.1 75486.9
    HOXB5 Divided homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] 1.40126 173408 242989
    NFE2L2 nuclear factor erythroid 2 related factor 2 (nf-e2 related factor 2) (nfe2-related factor 2) (nuclear factor, erythroid derived 2, like 2) (hebp1). [swissprot;acc:q16236] Low confidence 1.11844 37094.3 41487.9
    PCSK5 Subtracted proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] 5794.8 54208.6 48413.8
    Rooted no value tho complex 3. [refseq;acc:nm_032361] 4.5914 72.7219 77.3133
    MSI1 musashi 1. [refseq;acc:nm_002442] High confidence 11.2629 54.9787 66.2416
    MXI1 Divided max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] 1.1707 55.6486 65.1478
    SEPT6 septin 6. [swissprot;acc:q14141] Low confidence 1.06697 97.7187 104.263
    166 Measured ALG1 Subtracted beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] 635.75 9012.1 8376.35
    MAGEC1 Divided melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] High confidence 1.29736 23693.7 18263
    PYGL Subtracted glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 1723.37 4489.19 2765.82
    SLC16A3 Divided monocarboxylate transporter 4 (mct 4) (mct 3). [swissprot;acc:o15427] Low confidence 1.08263 10325 11178.2
    Ranked CAPN2 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] 1.05781 222.502 210.342
    NAPG gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] High confidence 1.19058 209.299 249.187
    NEUROD4 Subtracted neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] 28 312 284
    TNS3 tumor endothelial marker 6; thyroid specific ptb domain protein; tensin 3. [refseq;acc:nm_022748] Low confidence 11.633 219.336 207.703
    Squared BACH2 Divided transcription regulator protein bach2 (btb and cnc homolog 2). [swissprot;acc:q9byv9] 1.11844 37094.3 41487.9
    CTBP2 Subtracted c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] High confidence 16188.4 69201.8 53013.4
    GABARAP gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Low confidence 5667.7 53479.8 47812.1
    HOXA5 Divided homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] High confidence 1.40126 173408 242989
    Rooted MXD4 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] 1.17064 55.6495 65.1458
    TP53I3 Subtracted tumor protein p53 inducible protein 3; quinone oxidoreductase homolog; p53-induced gene 3 protein. [refseq;acc:nm_004881] Low confidence 4.5874 87.7928 92.3802
    UBE1C Divided ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [refseq;acc:nm_003968] 1.06689 72.46 77.3071
    ZC3H14 Subtracted nuclear protein ukp68. [refseq;acc:nm_024824] High confidence 11.2629 54.9787 66.2416
    167 Measured MAGEA4 Divided melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] 1.29736 23693.7 18263
    MYO15A Subtracted myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] 1723.37 4489.19 2765.82
    PSCD2 Divided cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Low confidence 1.08219 12376.5 11436.5
    VPS41 Subtracted vacuolar assembly protein vps41 homolog (s53). [swissprot;acc:p49754] 634.39 7497.17 8131.56
    Ranked AMPD2 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] High confidence 28 133 105
    GAD1 Divided glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] 1.19058 209.299 249.187
    RHOBTB2 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] Low confidence 1.05749 212.695 201.131
    Subtracted 11.564
    Squared no value Divided homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] High confidence 1.40126 173408 242989
    ATF3 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Low confidence 1.11468 23804.2 26534
    CANT1 Subtracted ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] High confidence 16175.3 64975.9 81151.2
    NKX6-1 homeobox protein nkx-6.1. [swissprot;acc:p78426] Low confidence 5582.8 64485.5 70068.3
    Rooted FLNB filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] High confidence 11.1171 55.6161 66.7332
    RAB24 Divided max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] 1.17062 55.65 65.1448
    RHOBTB2 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] Low confidence 1.06594 68.0417 72.5283
    SLC15A1 Subtracted oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] 4.5831 70.7428 75.3259
    168 Measured no value Divided mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] 1.08218 12376.4 11436.5
    melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] High confidence 1.29736 23693.7 18263

    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/