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 7641 to 7690 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Interaction Map
    		red
    		network_comparison
    		green
    956 CCNB1 g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] Rooted High confidence 93.5901 1.05846 88.4209
    DHX15 putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] Ranked Low confidence 203.365 1.02476 198.452
    FMO3 dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513] Measured High confidence 5364.77 1.09695 5884.89
    HMHA1 myeloblast kiaa0223 (fragment). [sptrembl;acc:q92619] Low confidence 8628.43 1.03884 8963.59
    MORF4L2 transcription factor-like protein mrgx (morf-related gene x protein) (mortality factor 4-like 2) (msl3-2 protein). [swissprot;acc:q15014] Squared 43043.2 1.04865 41046.3
    SORBS3 vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] Ranked High confidence 211.812 1.03458 204.732
    SPTLC2 serine palmitoyltransferase 2 (ec 2.3.1.50) (long chain base biosynthesis protein 2) (lcb 2) (serine-palmitoyl-coa transferase 2) (spt 2). [swissprot;acc:o15270] Squared 24804.6 1.15283 28595.4
    TSC1 hamartin (tuberous sclerosis 1 protein). [swissprot;acc:q92574] Rooted Low confidence 71.7776 1.03958 74.6184
    957 ARAF a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] Ranked High confidence 129.913 1.03453 134.399
    CDC2 cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] Rooted 93.5619 1.05839 88.4001
    EIF3D eukaryotic translation initiation factor 3 subunit 7 (eif-3 zeta) (eif3 p66) (eif3d). [swissprot;acc:o15371] Low confidence 70.3503 1.03958 73.1347
    GGNBP2 c3hc4-type zinc finger protein; likely ortholog of mouse dioxin inducible factor 3. [refseq;acc:nm_024835] Squared 37515.5 1.04865 35775
    NARS asparaginyl-trna synthetase, cytoplasmic (ec 6.1.1.22) (asparagine-- trna ligase) (asnrs). [swissprot;acc:o43776] High confidence 26822.8 1.15243 30911.4
    QPRT nicotinate-nucleotide pyrophosphorylase [carboxylating] (ec 2.4.2.19) (quinolinate phosphoribosyltransferase [decarboxylating]) (qaprtase) (qprtase). [swissprot;acc:q15274] Measured Low confidence 7895.83 1.0388 8202.18
    SSRP1 structure-specific recognition protein 1 (ssrp1) (recombination signal sequence recognition protein) (t160) (chromatin-specific transcription elongation factor 80 kda subunit) (fact 80 kda subunit). [swissprot;acc:q08945] High confidence 4483.26 1.09692 4917.77
    TAF6 transcription initiation factor tfiid 70 kda subunit (tafii-70) (tafii-80) (tafii80). [swissprot;acc:p49848] Ranked Low confidence 201.82 1.02476 196.944
    958 C21orf66 gc-rich sequence dna-binding factor homolog. [swissprot;acc:q9y5b6] Squared 44222 1.04864 42170.8
    DHX15 putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] Rooted 71.3594 1.03955 74.1815
    ESRRA steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474] High confidence 82.1645 1.05832 86.9566
    PCYT1B cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] Measured Low confidence 8059.35 1.03878 8371.9
    RAF1 raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Ranked High confidence 129.921 1.03452 134.406
    SEPHS2 selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] Squared 29830.2 1.15239 34375.9
    SNF1LK probable serine/threonine protein kinase snf1lk (ec 2.7.1.-). [swissprot;acc:p57059] Ranked Low confidence 194.842 1.02475 190.136
    SUPT16H chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192] Measured High confidence 4483.26 1.09692 4917.77
    959 no value guanine nucleotide-binding protein beta subunit-like protein 12.3 (p205) (receptor of activated protein kinase c 1) (rack1) (receptor for activated c kinase). [swissprot;acc:p25388] Ranked 237.558 1.03431 229.677
    sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] Measured 4379.28 1.09689 4803.59
    AP1S3 adapter-related protein complex 1 sigma 1c subunit (sigma-adaptin 1c) (adaptor protein complex ap-1 sigma-1c subunit) (golgi adaptor ha1/ap1 adaptin sigma-1c subunit) (clathrin assembly protein complex 1 sigma- 1c small chain) (sigma 1c subunit of ap-1 clathrin). [swissprot;acc:q96pc3] Rooted Low confidence 70.9125 1.03954 73.7163
    CAMKK2 calcium/calmodulin-dependent protein kinase kinase 2 beta isoform 1; camkk beta protein; calcium/calmodulin-dependent protein kinase beta. [refseq;acc:nm_006549] Squared 46830.4 1.04861 44659.4
    MICAL2 flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] High confidence 29830.2 1.15239 34375.9
    PCYT1A cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] Measured Low confidence 8059.5 1.03875 8371.83
    SSBP1 single-stranded dna-binding protein, mitochondrial precursor (mt-ssb) (mtssb) (pwp1-interacting protein 17). [swissprot;acc:q04837] Ranked 194.842 1.02475 190.136
    WBP2 ww domain binding protein 2 (wbp-2). [swissprot;acc:q969t9] Rooted High confidence 62.1275 1.05828 65.7481
    960 CAMKK1 calcium/calmodulin-dependent protein kinase 1 alpha isoform a; camkk alpha protein. [refseq;acc:nm_032294] Squared Low confidence 46830.4 1.04861 44659.4
    INPP4B inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] High confidence 29830.2 1.15239 34375.9
    NDUFB9 nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] Rooted 66.4035 1.05813 70.2633
    PRKCE protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156] Measured 11773 1.09688 10733.2
    RTN2 reticulon protein 2 (neuroendocrine-specific protein-like 1) (nsp-like protein 1) (nspli). [swissprot;acc:o75298] Low confidence 8206.42 1.03873 8524.26
    SHROOM2 apical-like protein (apxl protein). [swissprot;acc:q13796] Rooted 71.1712 1.03954 73.9852
    SLC5A5 sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911] Ranked 200.05 1.02473 195.223
    ZRF1 zuotin related factor-1 (m-phase phosphoprotein 11). [swissprot;acc:q99543] High confidence 237.558 1.03431 229.677
    961 BDH1 d-beta-hydroxybutyrate dehydrogenase, mitochondrial precursor (ec 1.1.1.30) (bdh) (3-hydroxybutyrate dehydrogenase). [swissprot;acc:q02338] Rooted Low confidence 69.7681 1.03952 72.5256
    CREB5 camp response element-binding protein cre-bpa. [refseq;acc:nm_004904] Measured 8484.77 1.03872 8813.34
    LIG4 dna ligase iv (ec 6.5.1.1) (polydeoxyribonucleotide synthase [atp]). [swissprot;acc:p49917] Squared 46606.6 1.0486 44446.5
    PICALM phosphatidylinositol-binding clathrin assembly protein (clathrin assembly lymphoid myeloid leukemia protein). [swissprot;acc:q13492] Ranked 203.548 1.02472 198.638
    PPIB peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [swissprot;acc:p23284] Measured High confidence 11773 1.09688 10733.2
    PPP2R5E serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537] Ranked 130.066 1.0343 134.527
    RALGDS ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] Rooted 98.7609 1.05785 93.3602
    SEPHS1 selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] Squared 29830.2 1.15239 34375.9
    962 CCNG2 cyclin g2. [swissprot;acc:q16589] Ranked 130.066 1.0343 134.527
    DFFA dna fragmentation factor alpha subunit (dna fragmentation factor 45 kda subunit) (dff-45) (inhibitor of cad) (icad). [swissprot;acc:o00273] Rooted Low confidence 69.7681 1.03952 72.5256

    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/