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 812 to 861 of 66312 in total
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Network Comparison Type
    		Interaction Map
    		red
    		network_comparison
    		green
    51 MAGEA10 melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Squared Subtracted Low confidence 82347.8 20466.3 61881.5
    NEUROD4 neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Measured Divided High confidence 779.167 1.78438 1390.33
    SPATA6 spermatogenesis associated 6. [refseq;acc:nm_019073] Ranked 133 1.26667 105
    STAMBP associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Squared 28994.2 1.69212 17134.8
    XKR7 dj310o13.4 (novel protein similar to predicted c. elegans and c. intestinalis proteins) (fragment). [sptrembl;acc:q9nug5] Measured Low confidence 7563.09 1.15458 8732.2
    52 no value homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Squared 122475 1.30449 159767
    AMPD2 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] Ranked High confidence 133 1.26667 105
    ATG4B cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Measured Low confidence 13195.9 1.14883 11486.4
    CHD5 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] High confidence 779.167 1.78438 1390.33
    CPSF3 cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Subtracted 23422.4 4042.1 19380.3
    HOXC5 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Squared 173408 69581 242989
    MAGEA6 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Rooted 137.446 16.623 120.823
    MAGEB4 melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Squared Low confidence 82347.8 20466.3 61881.5
    NEURL neuralized-like. [refseq;acc:nm_004210] Rooted Divided High confidence 27.9107 1.58239 44.1656
    NIPSNAP1 nipsnap1 protein. [swissprot;acc:q9bpw8] Ranked Subtracted Low confidence 249.584 22.724 226.86
    Rooted Divided 55.133 1.1265 62.1073
    RASAL2 ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Ranked Subtracted High confidence 350 60 290
    RBM7 putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580] Rooted Low confidence 49.0544 7.7006 56.755
    SMPD2 sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906] Ranked Divided 234.802 1.11149 260.98
    VPS24 neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Squared High confidence 28994.2 1.69212 17134.8
    XKR7 dj310o13.4 (novel protein similar to predicted c. elegans and c. intestinalis proteins) (fragment). [sptrembl;acc:q9nug5] Measured Subtracted Low confidence 7563.09 1169.11 8732.2
    53 no value 60s ribosomal protein l37a. [swissprot;acc:p12751] Ranked 239.692 22.687 217.005
    homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Squared High confidence 173408 69581 242989
    BOK bcl2-related ovarian killer. [refseq;acc:nm_032515] Measured Divided Low confidence 4955.33 1.14207 5659.35
    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] High confidence 779.167 1.78438 1390.33
    CHMP4A protein hspc134 (protein cda04). [swissprot;acc:q9by43] Squared 28994.2 1.69212 17134.8
    GSTO1 glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] Rooted Subtracted Low confidence 63.0631 7.6115 70.6746
    HINT1 histidine triad nucleotide-binding protein 1 (adenosine 5'- monophosphoramidase) (protein kinase c inhibitor 1) (protein kinase c- interacting protein 1) (pkci-1). [swissprot;acc:p49773] Measured 5847.46 1155.5 4691.96
    HOXD4 homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Squared Divided 122475 1.30449 159767
    JUNB transcription factor jun-b. [swissprot;acc:p17275] Ranked High confidence 201.144 1.26611 158.868
    JUND transcription factor jun-d. [swissprot;acc:p17535] Rooted Low confidence 67.1245 1.1257 75.5619
    MAGED2 melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] Squared Subtracted 82347.8 20466.3 61881.5
    NDN necdin. [swissprot;acc:q99608] Rooted High confidence 137.446 16.623 120.823
    NDUFS4 nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Ranked 318.982 59.978 259.004
    Rooted Divided 30.8986 1.50369 46.4619
    PAPOLA poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Measured Subtracted 23326.5 4030.1 19296.4
    TMEM33 db83 protein. [swissprot;acc:p57088] Ranked Divided Low confidence 234.802 1.11149 260.98
    54 no value atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Measured Subtracted 5720.25 1142.75 4577.5
    CPEB3 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Ranked Divided 267.448 1.11056 240.822
    DTX2 deltex 2. [refseq;acc:nm_020892] Measured High confidence 1618.84 1.63814 2651.88
    EXOC2 exocyst complex component sec5. [swissprot;acc:q96kp1] Subtracted 23316 4027.2 19288.8
    GBE1 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Ranked 185.678 59.569 245.247
    HOXB5 homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Squared Divided Low confidence 122475 1.30449 159767
    HOXD4 homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Subtracted High confidence 173408 69581 242989
    JUNB transcription factor jun-b. [swissprot;acc:p17275] Rooted Divided Low confidence 67.118 1.12566 75.5523
    JUND transcription factor jun-d. [swissprot;acc:p17535] Ranked High confidence 200.941 1.26425 158.941
    MAGED1 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Rooted Subtracted 137.446 16.623 120.823
    MAGED4 melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Squared Divided 219048 1.68808 129762
    MAP2K4 dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [swissprot;acc:p45985] Rooted Subtracted Low confidence 63.4164 7.5988 55.8176
    SEPT8 septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Measured Divided 13203.5 1.13859 15033.4

    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/