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 [...,...].
    Network Comparison Type Rank Gene Value Type description Interaction Map Hugo network_comparison Filtered red green
    Results: HTML CSV LaTeX Showing element 501 to 550 of 66312 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Value Type
    		description
    		Interaction Map
    		Hugo
    		network_comparison
    		red
    		green
    63 Squared core1 udp-galactose:n-acetylgalactosamine-alpha-r beta 1,3-galac. [refseq;acc:nm_020156] Low confidence C1GALT1 1.28138 73677.6 57498.7
    melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] High confidence MAGEF1 1.68808 219048 129762
    Rooted kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] KCNIP2 1.36835 43.4554 31.7576
    t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806] Low confidence TBX19 1.10801 61.4851 68.1264
    64 Measured glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] High confidence PYGM 1.6231 4489.19 2765.82
    retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Low confidence HSD17B14 1.13635 15464.1 17572.7
    Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] High confidence GNG11 1.25965 266.868 336.159
    transcription factor jun-d. [swissprot;acc:p17535] Low confidence JUND 1.10552 202.709 183.361
    Squared melanoma antigen, family b, 6. [refseq;acc:nm_173523] High confidence MAGEB6B 1.68808 219048 129762
    neurochondrin. [refseq;acc:nm_014284] Low confidence NCDN 1.28138 73677.6 57498.7
    Rooted 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] High confidence GBE1 1.35128 63.8686 47.2654
    rab11-family interacting protein 4. [refseq;acc:nm_032932] Low confidence RAB11FIP4 1.10693 73.6221 81.4944
    65 Measured neuralized-like. [refseq;acc:nm_004210] High confidence NEURL 1.6229 1657.68 2690.25
    septin 6. [swissprot;acc:q14141] Low confidence SEPT6 1.13593 13005.8 14773.7
    Ranked guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] High confidence GNAQ 1.25807 267.136 336.077
    transcription factor jun-b. [swissprot;acc:p17275] Low confidence JUNB 1.10546 202.728 183.388
    Squared melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] High confidence no value 1.68808 219048 129762
    septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Low confidence SEPT8 1.26497 75490.8 95493.3
    Rooted eferin. [swissprot;acc:o75154] RAB11FIP3 1.10693 73.6221 81.4944
    glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] High confidence PYGB 1.35128 63.8686 47.2654
    66 Measured 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] NDUFA12 1.61795 1991.03 3221.38
    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] Low confidence SON 1.13368 4900.7 5555.81
    Ranked guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] High confidence GNA11 1.25807 267.136 336.077
    mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [refseq;acc:nm_020749] Low confidence MTUS1 1.10518 221.902 200.783
    Squared melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] High confidence MAGEA9 1.68808 219048 129762
    septin 10 isoform 1. [refseq;acc:nm_144710] Low confidence SEPT10 1.26038 74803.9 94281
    Rooted dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] DAB2IP 1.10573 55.8923 61.8016
    glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] High confidence PYGL 1.35128 63.8686 47.2654
    67 Measured beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] ARRB2 1.59177 6475.5 10307.5
    hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Low confidence NFU1 1.1318 12176.9 13781.8
    Ranked guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] High confidence GNAT2 1.25805 267.14 336.075
    retinoblastoma-associated factor 600. [refseq;acc:nm_020765] Low confidence UBR4 1.10505 165.535 149.799
    Squared melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] High confidence MAGEA8 1.68808 219048 129762
    septin 6. [swissprot;acc:q14141] Low confidence SEPT6 1.25751 74378.4 93531.9
    Rooted brachyury protein (t protein). [swissprot;acc:o15178] T 1.10559 61.687 68.2003
    myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] High confidence MYO15A 1.35128 63.8686 47.2654
    68 Measured beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] ARRB1 1.59177 6475.5 10307.5
    putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Low confidence UBAC1 1.12932 19498.1 17265.4
    Ranked 60s ribosomal protein l37a. [swissprot;acc:p12751] no value 1.10455 239.692 217.005
    guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] High confidence GNAZ 1.25805 267.139 336.075
    Squared melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] MAGEC1 1.68808 219048 129762
    retinoblastoma-associated factor 600. [refseq;acc:nm_020765] Low confidence UBR4 1.25653 27909.1 35068.7
    Rooted glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] High confidence PYGM 1.35128 63.8686 47.2654
    ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Low confidence RASAL2 1.10514 55.9786 61.8641
    69 Measured amino acid transporter xat2; likely ortholog of mouse aspartate/glutamate transporter 1 (agt1). [refseq;acc:nm_138817] SLC7A13 1.12253 6991.78 7848.45
    spermatogenesis associated 6. [refseq;acc:nm_019073] High confidence SPATA6 1.59177 6475.5 10307.5
    Ranked guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] GNAT1 1.25805 267.14 336.075
    testis-specific protein tex28. [swissprot;acc:o15482] Low confidence TEX28P2 1.10425 259.517 235.017
    Squared delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial precursor (ec 1.5.1.12) (p5c dehydrogenase). [swissprot;acc:p30038] ALDH4A1 1.25465 80538.1 64191.7
    melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] High confidence MAGEA4 1.68808 219048 129762

    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/