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 Hugo description Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1308 to 1357 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Network Comparison Type
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    164 Divided SLC39A6 liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] Ranked 209.299 249.187 1.19058
    Subtracted ARRB1 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 133 105 28
    DUT deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] Squared 61733.5 45224.1 16509.4
    GBE1 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Measured 4489.19 2765.82 1723.37
    MSI2 musashi 2 isoform a. [refseq;acc:nm_138962] Rooted 54.9787 66.2416 11.2629
    165 Divided GAD2 glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] Ranked 209.299 249.187 1.19058
    HOXB5 homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Squared 173408 242989 1.40126
    MAGEA8 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Measured 23693.7 18263 1.29736
    MXI1 max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Rooted 55.6486 65.1478 1.1707
    Subtracted CLEC3B tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] Squared 59016.1 75486.9 16470.8
    MSI1 musashi 1. [refseq;acc:nm_002442] Rooted 54.9787 66.2416 11.2629
    PYGB glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Measured 4489.19 2765.82 1723.37
    SPATA6 spermatogenesis associated 6. [refseq;acc:nm_019073] Ranked 133 105 28
    166 Divided HOXA5 homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Squared 173408 242989 1.40126
    MAGEC1 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Measured 23693.7 18263 1.29736
    MXD4 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Rooted 55.6495 65.1458 1.17064
    NAPG gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] Ranked 209.299 249.187 1.19058
    Subtracted CTBP2 c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] Squared 69201.8 53013.4 16188.4
    NEUROD4 neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Ranked 312 284 28
    PYGL glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Measured 4489.19 2765.82 1723.37
    ZC3H14 nuclear protein ukp68. [refseq;acc:nm_024824] Rooted 54.9787 66.2416 11.2629
    167 Divided no value homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Squared 173408 242989 1.40126
    GAD1 glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] Ranked 209.299 249.187 1.19058
    MAGEA4 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Measured 23693.7 18263 1.29736
    RAB24 max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Rooted 55.65 65.1448 1.17062
    Subtracted AMPD2 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] Ranked 133 105 28
    CANT1 ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] Squared 64975.9 81151.2 16175.3
    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] Rooted 55.6161 66.7332 11.1171
    MYO15A myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Measured 4489.19 2765.82 1723.37
    168 Divided no value gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Ranked 82.5916 98.0548 1.18722
    melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Measured 23693.7 18263 1.29736
    HSD17B14 retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Squared 173408 242989 1.40126
    SNRPD3 small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Rooted 56.3709 65.8949 1.16895
    Subtracted BCL6B b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] Squared 69165.6 52992.1 16173.5
    CHD5 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Ranked 312 284 28
    PYGM glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Measured 4489.19 2765.82 1723.37
    REV1 rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] Rooted 55.6161 66.7332 11.1171
    169 Divided ATG3 apg3p; pc3-96 protein. [refseq;acc:nm_022488] Ranked 82.5916 98.0548 1.18722
    COPS3 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] Rooted 62.762 53.7761 1.1671
    MAGEA10 melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Measured 23693.7 18263 1.29736
    SYMPK symplekin. [swissprot;acc:q92797] Squared 124118 88668.8 1.39979
    Subtracted no value formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Measured 4245.52 5942.75 1697.23
    CDK2AP1 cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] Ranked 312 284 28
    PASK pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148] Squared 69165 52991.7 16173.3
    PRMT1 protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Rooted 55.6161 66.7332 11.1171
    170 Divided B9D1 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] 53.4993 45.9227 1.16499
    CTPS2 cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] Squared 96730.5 69286.7 1.39609
    MAGEB4 melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Measured 23693.7 18263 1.29736
    TIA1 nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Ranked 227.199 192.715 1.17894
    Subtracted no value huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Measured 4247.86 5941.88 1694.02

    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/