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 network_comparison green
    Results: HTML CSV LaTeX Showing element 1513 to 1562 of 66312 in total
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Network Comparison Type
    		Interaction Map
    		red
    		network_comparison
    		green
    95 RGS19 regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] Rooted Divided High confidence 47.6504 1.29028 36.9304
    RINT1 rad50-interacting protein 1. [refseq;acc:nm_021930] Subtracted Low confidence 64.6594 6.3683 71.0277
    SASH1 sam and sh3 domain containing 1. [refseq;acc:nm_015278] Squared Divided 55150.6 1.18248 46639.9
    SLC7A13 amino acid transporter xat2; likely ortholog of mouse aspartate/glutamate transporter 1 (agt1). [refseq;acc:nm_138817] Ranked 200.497 1.0798 185.679
    Subtracted 14.818
    SON son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] Measured Divided High confidence 2397.19 1.39481 3343.62
    TP53BP2 tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] Squared Subtracted 123324 37046.1 86277.9
    TRAPPC3 bet3 homolog. [swissprot;acc:o43617] Measured 17396.9 3087 20483.9
    96 no value atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Squared Divided 7744.68 1.56161 4959.41
    raptor; p150 target of rapamycin (tor)-scaffold protein containing wd-repeats. [refseq;acc:nm_020761] Subtracted Low confidence 63526.9 9142.6 54384.3
    ATF3 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Ranked High confidence 201.949 48.278 153.671
    CPEB4 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] Measured Divided Low confidence 4630.13 1.10194 5102.14
    DVL1 segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Rooted 68.4921 1.09046 74.6877
    GNAI2 guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] Subtracted High confidence 40.28 15.91 24.37
    LASS2 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Measured Divided 4110.14 1.3856 5694.99
    MAGEA8 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Ranked 88.2482 1.24949 110.265
    PSCD1 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Measured Subtracted Low confidence 12424.3 952 11472.3
    PTPRA vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269] Rooted 69.0723 6.3531 75.4254
    RBM15 putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] Divided High confidence 47.6504 1.29028 36.9304
    SEPT4 septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] Squared Low confidence 63597.2 1.1821 75178.4
    SEPT8 septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Measured Subtracted High confidence 16177.9 3057.5 19235.4
    Squared 90226 36713 126939
    SLC7A7 y+l amino acid transporter 1 (y(+)l-type amino acid transporter 1) (y+lat-1) (y+lat1) (monocyte amino acid permease 2) (mop-2). [swissprot;acc:q9um01] Ranked Divided Low confidence 200.497 1.0798 185.679
    Subtracted 14.818
    97 APBA1 amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] Measured Divided High confidence 2820.51 1.3817 3897.1
    Ranked Subtracted 271.752 46.072 225.68
    Rooted Low confidence 60.7884 6.3252 67.1136
    CPSF4 cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] Squared Divided High confidence 227160 1.55505 146079
    CSTF2 cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] Subtracted 126408 36467.5 89940.5
    DVL2 segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Rooted Divided Low confidence 68.5063 1.09027 74.6906
    GNAI1 guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] Subtracted High confidence 40.2797 15.9092 24.3705
    HAAO 3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [swissprot;acc:p46952] Measured Low confidence 10696.6 942.9 11639.5
    KIF23 kinesin-like protein kif23 (mitotic kinesin-like protein-1) (kinesin- like protein 5). [swissprot;acc:q02241] Squared 57471.1 9007.7 48463.4
    MAGEC1 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Ranked Divided High confidence 88.2482 1.24949 110.265
    NDUFA12 nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] Measured Low confidence 5811.84 1.1011 6399.42
    RAB26 ras-related protein rab-26. [swissprot;acc:q9ulw5] Squared 61365.7 1.17909 52044.8
    RGS20 regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081] Rooted High confidence 47.6504 1.29028 36.9304
    SEPT10 septin 10 isoform 1. [refseq;acc:nm_144710] Measured Subtracted 16067.4 3027 19094.4
    SLC7A11 cystine/glutamate transporter (amino acid transport system xc-) (xct) (calcium channel blocker resistance protein ccbr1). [swissprot;acc:q9upy5] Ranked Divided Low confidence 200.497 1.0798 185.679
    Subtracted 14.818
    98 BRP44 brain protein 44. [swissprot;acc:o95563] Measured High confidence 15999.1 3008 19007.1
    CYLD cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247] Squared Low confidence 57471.1 9007.7 48463.4
    DNASE2B deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Rooted Divided 173.58 1.08981 189.17
    FOS proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Ranked Subtracted High confidence 204.641 43.684 160.957
    GNAI3 guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] Rooted 40.2797 15.9092 24.3705
    GTF3A transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664] Measured Divided Low confidence 7624.8 1.1006 8391.85
    KIAA1012 trs85 homolog. [swissprot;acc:q9y2l5] Squared High confidence 227160 1.55505 146079
    LBX1 transcription factor lbx1. [swissprot;acc:p52954] Rooted 47.6504 1.29028 36.9304
    MAGEA4 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Ranked 88.2482 1.24949 110.265
    MTUS1 mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [refseq;acc:nm_020749] Rooted Subtracted Low confidence 63.1259 6.3046 69.4305

    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/