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 [...,...].
    Gene Rank description Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 801 to 850 of 66312 in total
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		Network Comparison Type
    		Interaction Map
    		red
    		green
    		network_comparison
    51 associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] STAMBP Squared Divided High confidence 28994.2 17134.8 1.69212
    ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] GSTO2 Rooted Subtracted Low confidence 62.7951 70.575 7.7799
    cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] CPEB3 Ranked High confidence 350 290 60
    dj310o13.4 (novel protein similar to predicted c. elegans and c. intestinalis proteins) (fragment). [sptrembl;acc:q9nug5] XKR7 Measured Divided Low confidence 7563.09 8732.2 1.15458
    ena/vasodilator stimulated phosphoprotein-like protein (ena/vasp-like protein). [swissprot;acc:q9ui08] no value Subtracted 12768 11571.4 1196.6
    fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] FIP1L1 High confidence 23640.2 19479.8 4160.4
    hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] no value Rooted 137.446 120.823 16.623
    homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] HOXB4 Squared 173408 242989 69581
    homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] HOXC5 Divided Low confidence 122475 159767 1.30449
    junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] JPH2 Ranked 234.802 260.98 1.11149
    kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] KHDRBS2 Rooted High confidence 27.7254 44.0299 1.58807
    melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] MAGEA10 Squared Subtracted Low confidence 82347.8 61881.5 20466.3
    neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] NEUROD4 Measured Divided High confidence 779.167 1390.33 1.78438
    nipsnap2 protein (glioblastoma amplified sequence). [swissprot;acc:o75323] GBAS Ranked Subtracted Low confidence 249.709 226.944 22.765
    Rooted Divided 55.0884 62.0722 1.12677
    spermatogenesis associated 6. [refseq;acc:nm_019073] SPATA6 Ranked High confidence 133 105 1.26667
    52 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] AMPD2
    chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] CHD5 Measured 779.167 1390.33 1.78438
    cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] CPSF3 Subtracted 23422.4 19380.3 4042.1
    cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] ATG4B Divided Low confidence 13195.9 11486.4 1.14883
    dj310o13.4 (novel protein similar to predicted c. elegans and c. intestinalis proteins) (fragment). [sptrembl;acc:q9nug5] XKR7 Subtracted 7563.09 8732.2 1169.11
    homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] HOXC5 Squared High confidence 173408 242989 69581
    homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] no value Divided Low confidence 122475 159767 1.30449
    melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] MAGEA6 Rooted Subtracted High confidence 137.446 120.823 16.623
    melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] MAGEB4 Squared Low confidence 82347.8 61881.5 20466.3
    neuralized-like. [refseq;acc:nm_004210] NEURL Rooted Divided High confidence 27.9107 44.1656 1.58239
    neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] VPS24 Squared 28994.2 17134.8 1.69212
    nipsnap1 protein. [swissprot;acc:q9bpw8] NIPSNAP1 Ranked Subtracted Low confidence 249.584 226.86 22.724
    Rooted Divided 55.133 62.1073 1.1265
    putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580] RBM7 Subtracted 49.0544 56.755 7.7006
    ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] RASAL2 Ranked High confidence 350 290 60
    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] SMPD2 Divided Low confidence 234.802 260.98 1.11149
    53 60s ribosomal protein l37a. [swissprot;acc:p12751] no value Subtracted 239.692 217.005 22.687
    bcl2-related ovarian killer. [refseq;acc:nm_032515] BOK Measured Divided 4955.33 5659.35 1.14207
    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] CDK2AP1 High confidence 779.167 1390.33 1.78438
    db83 protein. [swissprot;acc:p57088] TMEM33 Ranked Low confidence 234.802 260.98 1.11149
    glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] GSTO1 Rooted Subtracted 63.0631 70.6746 7.6115
    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] HINT1 Measured 5847.46 4691.96 1155.5
    homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] no value Squared High confidence 173408 242989 69581
    homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] HOXD4 Divided Low confidence 122475 159767 1.30449
    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] MAGED2 Subtracted 82347.8 61881.5 20466.3
    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] NDUFS4 Ranked High confidence 318.982 259.004 59.978
    Rooted Divided 30.8986 46.4619 1.50369
    necdin. [swissprot;acc:q99608] NDN Subtracted 137.446 120.823 16.623
    poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] PAPOLA Measured 23326.5 19296.4 4030.1
    protein hspc134 (protein cda04). [swissprot;acc:q9by43] CHMP4A Squared Divided 28994.2 17134.8 1.69212
    transcription factor jun-b. [swissprot;acc:p17275] JUNB Ranked 201.144 158.868 1.26611
    transcription factor jun-d. [swissprot;acc:p17535] JUND Rooted Low confidence 67.1245 75.5619 1.1257
    54 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] GBE1 Ranked Subtracted High confidence 185.678 245.247 59.569
    atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] no value Measured Low confidence 5720.25 4577.5 1142.75

    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/