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 description Network Comparison Type Hugo Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 8241 to 8290 of 16578 in total
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		description
    		Network Comparison Type
    		Hugo
    		Interaction Map
    		red
    		green
    		network_comparison
    2061 coronin 2a (wd-repeat protein 2) (ir10). [swissprot;acc:q92828] Subtracted CORO2A Low confidence 202.237 198.427 3.81
    isocitrate dehydrogenase [nad] subunit gamma, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [swissprot;acc:p51553] IDH3G High confidence 222.58 224.32 1.74
    serine/threonine-protein kinase chk1 (ec 2.7.1.-). [swissprot;acc:o14757] Divided CHEK1 Low confidence 196.875 193.141 1.01933
    tbc1 domain family protein c22orf4-like (fragment). [swissprot;acc:q9nu19] TBC1D22B High confidence 218.79 216.981 1.00834
    2062 fibrillin 1 precursor. [swissprot;acc:p35555] Subtracted FBN1 Low confidence 203.261 199.452 3.809
    myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829] Divided no value 200.005 196.213 1.01933
    polymerase (dna directed) sigma; topoisomerase-related function protein 4-1; polymerase (dna-directed) sigma. [refseq;acc:nm_006999] Subtracted POLS High confidence 229.266 227.53 1.736
    tbc1 domain family protein c22orf4. [swissprot;acc:q8wua7] Divided TBC1D22A 218.79 216.981 1.00834
    2063 alpha-fetoprotein enhancer binding protein (at motif-binding factor) (at-binding transcription factor 1). [swissprot;acc:q15911] Subtracted ZFHX3 Low confidence 201.219 197.41 3.809
    glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 2 (ec 2.6.1.16) (hexosephosphate aminotransferase 2) (d-fructose-6- phosphate amidotransferase 2) (gfat 2) (gfat2). [swissprot;acc:o94808] GFPT2 High confidence 222.609 224.344 1.735
    mitochondrial 2-oxodicarboxylate carrier. [swissprot;acc:q9bqt8] Divided SLC25A21 Low confidence 195.333 191.631 1.01932
    ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926] ODC1 High confidence 207.638 205.923 1.00833
    2064 aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763] AASS 207.655 205.939
    coronin 2b (coronin-like protein c) (clipinc) (protein fc96). [swissprot;acc:q9uq03] Subtracted CORO2B Low confidence 202.237 198.428 3.809
    dna polymerase gamma subunit 1 (ec 2.7.7.7) (mitochondrial dna polymerase catalytic subunit) (polg-alpha). [swissprot;acc:p54098] POLG High confidence 216.324 214.599 1.725
    ubiquitin-conjugating enzyme e2 n (ec 6.3.2.19) (ubiquitin-protein ligase n) (ubiquitin carrier protein n) (ubc13) (bendless-like ubiquitin conjugating enzyme). [swissprot;acc:q16781] Divided UBE2N Low confidence 200.396 196.597 1.01932
    2065 heat shock-related 70 kda protein 2 (heat shock 70 kda protein 2). [swissprot;acc:p54652] HSPA2 201.894 198.068
    ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977] Subtracted AZIN1 High confidence 207.667 205.95 1.717
    serine/threonine-protein kinase pak 7 (ec 2.7.1.-) (p21-activated kinase 7) (pak-7) (pak-5). [swissprot;acc:q9p286] PAK7 Low confidence 202.369 198.56 3.809
    ubiquitin-conjugating enzyme e2 n (ec 6.3.2.19) (ubiquitin-protein ligase n) (ubiquitin carrier protein n) (ubc13) (bendless-like ubiquitin conjugating enzyme). [swissprot;acc:q16781] Divided UBE2N High confidence 214.328 212.561 1.00831
    2066 heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] no value Low confidence 201.894 198.068 1.01932
    leukocyte receptor cluster (lrc) member 8. [refseq;acc:nm_052925] Subtracted LENG8 202.349 198.541 3.808
    ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70] ADC High confidence 207.665 205.948 1.717
    proliferating cell nuclear antigen (pcna) (cyclin). [swissprot;acc:p12004] Divided PCNA 229.102 231.001 1.00829
    2067 adenylosuccinate lyase (ec 4.3.2.2) (adenylosuccinase) (asl) (asase). [swissprot;acc:p30566] ADSL 193.226 191.639 1.00828
    aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763] Subtracted AASS 207.655 205.939 1.716
    dehydrodolichyl diphosphate synthase. [refseq;acc:nm_024887] Divided DHDDS Low confidence 199.843 196.055 1.01932
    similar to smhs1 protein. [refseq;acc:nm_145244] Subtracted DDIT4L 200.456 196.648 3.808
    2068 38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [swissprot;acc:q14318] Divided FKBP8 203.696 207.631 1.01932
    eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821] Subtracted EIF3G 199.773 195.965 3.808
    fas apoptotic inhibitory molecule. [refseq;acc:nm_018147] Divided FAIM High confidence 220.8 222.61 1.0082
    ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926] Subtracted ODC1 207.638 205.923 1.715
    2069 dual specificity mitogen-activated protein kinase kinase 1 (ec 2.7.1.-) (map kinase kinase 1) (mapkk 1) (erk activator kinase 1) (mapk/erk kinase 1) (mek1). [swissprot;acc:q02750] Divided MAP2K1 217.555 215.807 1.0081
    fibrillin 3. [refseq;acc:nm_032447] Subtracted FBN3 Low confidence 203.258 199.451 3.807
    fidgetin-like 1. [refseq;acc:nm_022116] FIGNL1 High confidence 215.511 213.814 1.697
    syntaxin 7. [swissprot;acc:o15400] Divided STX7 Low confidence 200.695 196.892 1.01932
    2070 maguk p55 subfamily member 3 (mpp3 protein) (discs, large homolog 3). [swissprot;acc:q13368] Subtracted MPP3 High confidence 218.124 216.433 1.691
    rac gtpase activating protein 1; gtpase activating protein. [refseq;acc:nm_013277] Divided RACGAP1 223.199 225.008 1.0081
    retinal short chain dehydrogenase reductase. [refseq;acc:nm_138969] no value Low confidence 200.105 196.315 1.01931
    syntaxin 12. [refseq;acc:nm_177424] Subtracted STX12 200.566 196.759 3.807
    2071 adapter-related protein complex 3 beta 1 subunit (beta-adaptin 3a) (ap-3 complex beta-3a subunit) (beta-3a-adaptin). [swissprot;acc:o00203] AP3B1 High confidence 199.928 198.24 1.688
    dnaj (hsp40) homolog, subfamily c, member 6; dnaj (hsp40) homolog, subfamily b, member 6. [refseq;acc:nm_014787] DNAJC6 Low confidence 201.84 198.033 3.807
    golgi-associated microtubule-binding protein hook3; hook3 protein. [refseq;acc:nm_032410] Divided HOOK3 199.443 195.665 1.01931
    similar to kinase suppressor of ras (fragment). [sptrembl;acc:q8ivt5] KSR1 High confidence 217.555 215.807 1.0081
    2072 dual specificity mitogen-activated protein kinase kinase 2 (ec 2.7.1.-) (map kinase kinase 2) (mapkk 2) (erk activator kinase 2) (mapk/erk kinase 2) (mek2). [swissprot;acc:p36507] MAP2K2
    ny-ren-24 antigen (fragment). [sptrembl;acc:q9y5a4] Subtracted C19orf29 199.928 198.24 1.688
    putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231] no value Low confidence 203.817 200.011 3.806
    transcription initiation factor iia alpha and beta chains (tfiia p35 and p19 subunits) (tfiia-42) (tfiial). [swissprot;acc:p52655] Divided GTF2A1 202.663 198.824 1.01931
    2073 adapter-related protein complex 3 beta 2 subunit (beta-adaptin 3b) (ap-3 complex beta-3b subunit) (beta-3b-adaptin) (neuron-specific vesicle coat protein beta-nap). [swissprot;acc:q13367] Subtracted no value High confidence 199.928 198.24 1.688
    homeobox protein barh-like 2. [swissprot;acc:q9umq3] BARX2 Low confidence 204.659 200.855 3.804

    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/