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 Hugo Interaction Map network_comparison Filtered red green
    Results: HTML CSV LaTeX Showing element 60774 to 60823 of 66312 in total
    Network Comparison Type  : Subtracted
    Interaction Map  : Low confidence
    Filtered  : 1
    Rank
    		Value Type
    		description
    		Hugo
    		network_comparison
    		red
    		green
    3677 Ranked dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [swissprot;acc:p52434] POLR2H 2.768 202.287 199.519
    Squared double-stranded rna-specific adenosine deaminase (ec 3.5.4.-) (drada) (136 kda double-stranded rna binding protein) (p136) (k88dsrbp). [swissprot;acc:p55265] ADAR 1352.3 45809.4 44457.1
    Rooted transcription initiation factor iie, alpha subunit (tfiie-alpha) (general transcription factor iie 56 kda subunit). [swissprot;acc:p29083] GTF2E1 2.1057 72.3561 74.4618
    3678 Measured signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [refseq;acc:nm_005843] STAM2 197.62 8060.37 8257.99
    Ranked nucleoplasmin 3. [swissprot;acc:o75607] NPM3 2.768 203.141 200.373
    Squared highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] NDC80 1352.3 45809.4 44457.1
    Rooted transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084] no value 2.1057 72.3561 74.4618
    3679 Measured 3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110] ACAA1 197.62 8168.73 8366.35
    Ranked topoisomerase (dna) ii binding protein. [refseq;acc:nm_007027] TOPBP1 2.762 202.713 199.951
    Squared double-stranded rna-specific editase 1 (ec 3.5.-.-) (dsrna adenosine deaminase) (rna editing deaminase 1) (rna editing enzyme 1). [swissprot;acc:p78563] no value 1352.3 45809.4 44457.1
    Rooted g1/s-specific cyclin e2. [swissprot;acc:o96020] CCNE2 2.1055 72.2656 74.3711
    3680 Measured ocular development-associated gene. [refseq;acc:nm_021167] GATAD1 197.54 8063.13 8260.67
    Ranked cytochrome b5. [swissprot;acc:p00167] CYB5A 2.761 202.099 199.338
    Squared cullin homolog 1 (cul-1). [swissprot;acc:q13616] CUL1 1352.1 44519.8 43167.7
    Rooted g-rich sequence factor-1 (grsf-1). [swissprot;acc:q12849] GRSF1 2.1051 70.663 72.7681
    3681 Measured prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831] TGS1 197.5 7617.63 7815.13
    Ranked poly(rc)-binding protein 3 (alpha-cp3). [swissprot;acc:p57721] PCBP3 2.759 203.796 201.037
    Squared caax prenyl protease 1 homolog (ec 3.4.24.-) (prenyl protein-specific endoprotease 1) (farnesylated-proteins converting enzyme 1) (face-1) (zinc metalloproteinase ste24 homolog). [swissprot;acc:o75844] ZMPSTE24 1351.9 44141.5 42789.6
    Rooted nadh-ubiquinone oxidoreductase subunit b14.5a (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14.5a) (ci-b14.5a). [swissprot;acc:o95182] NDUFA7 2.1046 70.4686 72.5732
    3682 Measured t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947] TBX6 197.48 7891.57 8089.05
    Ranked dullard homolog. [refseq;acc:nm_015343] DULLARD 2.759 199.556 196.797
    Squared gpi transamidase component pig-s (phosphatidylinositol-glycan biosynthesis, class s protein). [swissprot;acc:q96s52] PIGS 1350.8 45021.6 43670.8
    Rooted glucose-6-phosphate isomerase (ec 5.3.1.9) (gpi) (phosphoglucose isomerase) (pgi) (phosphohexose isomerase) (phi) (neuroleukin) (nlk) (sperm antigen-36) (sa-36). [swissprot;acc:p06744] GPI 2.1044 72.0548 74.1592
    3683 Measured rab geranylgeranyltransferase alpha subunit (ec 2.5.1.-) (rab geranyl- geranyltransferase alpha subunit) (rab gg transferase alpha) (rab ggtase alpha). [swissprot;acc:q92696] RABGGTA 197.44 8184.5 8381.94
    Ranked poly(rc)-binding protein 2 (alpha-cp2) (hnrnp-e2). [swissprot;acc:q15366] no value 2.758 203.797 201.039
    Squared protein p25-beta. [swissprot;acc:p59282] TPPP2 1350.7 43260.5 41909.8
    Rooted hmba-inducible; likely ortholog of mouse cardiac lineage protein 1; menage a quatre 1. [refseq;acc:nm_006460] HEXIM1 2.1038 71.5901 73.6939
    3684 Measured 40s ribosomal protein s9. [swissprot;acc:p46781] RPS9 197.35 7711.01 7908.36
    Ranked poly(rc)-binding protein 4 (alpha-cp4). [swissprot;acc:p57723] PCBP4 2.758 203.797 201.039
    Squared sex comb on midleg-like 2; sex comb on midleg like 2. [refseq;acc:nm_006089] SCML2 1350.7 44747.1 43396.4
    Rooted multifunctional protein ade2 [includes: phosphoribosylaminoimidazole- succinocarboxamide synthase (ec 6.3.2.6) (saicar synthetase); phosphoribosylaminoimidazole carboxylase (ec 4.1.1.21) (air carboxylase) (airc)]. [swissprot;acc:p22234] PAICS 2.1014 72.0081 74.1095
    3685 Measured slingshot 1. [refseq;acc:nm_018984] SSH1 197.27 8256.35 8453.62
    Ranked poly(rc)-binding protein 1 (alpha-cp1) (hnrnp-e1) (nucleic acid binding protein sub2.3). [swissprot;acc:q15365] PCBP1 2.755 203.798 201.043
    Squared 25 kda brain-specific protein (p25-alpha). [swissprot;acc:o94811] TPPP 1350.5 43261.9 41911.4
    Rooted cyclin c. [swissprot;acc:p24863] CCNC 2.1006 72.1495 74.2501
    3686 Measured tubulin gamma-2 chain (gamma-2 tubulin). [swissprot;acc:q9nrh3] TUBG2 197.15 8120.11 8317.26
    Ranked pbk1 protein. [sptrembl;acc:o76021] RSL1D1 2.754 203.023 200.269
    Squared golgi membrane protein sb140; smooth muscle cell associated protein 5. [refseq;acc:nm_030799] YIPF5 1350.3 45637.5 44287.2
    Rooted forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] FOXG1 2.1004 70.5194 72.6198
    3687 Measured zinc finger protein 289, id1 regulated; likely ortholog of mouse zfp289. [refseq;acc:nm_032389] ZNF289 197.12 8154.94 8352.06
    Ranked hyporthetical protein mgc27169. [refseq;acc:nm_176782] C1orf179 2.754 201.842 199.088
    Squared protein cgi-38. [swissprot;acc:q9bw30] TPPP3 1349.2 43269.8 41920.6
    Rooted tumor susceptibility gene 101 protein. [swissprot;acc:q99816] TSG101 2.1 72.4947 74.5947
    3688 Measured calponin homology domain containing protein 1 (fragment). [swissprot;acc:q9y2l9] LRCH1 197.05 8037.49 8234.54
    Ranked ubiquitin carboxyl-terminal hydrolase 16 (ec 3.1.2.15) (ubiquitin thiolesterase 16) (ubiquitin-specific processing protease 16) (deubiquitinating enzyme 16) (ubiquitin processing protease ubp-m). [swissprot;acc:q9y5t5] USP16 2.754 201.832 199.078
    Squared sex comb on midleg homolog 1. [refseq;acc:nm_012236] SCMH1 1348.3 44749.3 43401
    Rooted phosphoenolpyruvate carboxykinase, cytosolic [gtp] (ec 4.1.1.32) (phosphoenolpyruvate carboxylase) (pepck-c). [swissprot;acc:p35558] PCK1 2.0994 70.6598 72.7592
    3689 Measured transcription elongation regulator 1; transcription factor ca150; tata box binding protein (tbp)-associated factor, rna polymerase ii, s, 150kd; tata box-binding protein-associated factor 2s. [refseq;acc:nm_006706] TCERG1 197.05 8037.49 8234.54
    Ranked kh-type splicing regulatory protein (fuse binding protein 2); kh-type splicing regulatory protein (fuse-binding protein 2). [refseq;acc:nm_003685] KHSRP 2.753 203.865 201.112
    Squared serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153] PPP2R1A 1347.3 43850.3 42503

    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/