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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1958 to 2007 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		Value Type
    		red
    		green
    		network_comparison
    245 MYO5C myosin vc (myosin 5c). [swissprot;acc:q9nqx4] Divided Rooted 146.94 167.046 1.13683
    RPL19 60s ribosomal protein l19. [swissprot;acc:p14118] Subtracted Ranked 240.73 264.729 23.999
    SNRPD3 small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Divided 226.109 202.333 1.11751
    246 no value 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] Subtracted 243.583 267.528 23.945
    myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Divided Rooted 146.94 167.046 1.13683
    CDK2AP2 doc-1 related protein (doc-1r). [swissprot;acc:o75956] Subtracted 27.9136 37.2872 9.3736
    DYNLT1 cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] Measured 13241.4 11864 1377.4
    EIF4G3 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Divided Ranked 237.312 212.363 1.11748
    HHEX homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [swissprot;acc:q03014] Subtracted Squared 54726.7 45358.5 9368.2
    HOMER3 homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] Divided Measured 4252.66 5213.05 1.22583
    PYGB glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Squared 8875.01 6768.05 1.31131
    247 no value 60s ribosomal protein l12. [swissprot;acc:p30050] Subtracted Ranked 243.583 267.527 23.944
    rna-binding protein. [refseq;acc:nm_019027] Divided 237.302 212.41 1.11719
    DDX56 probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] Rooted 47.3621 53.8355 1.13668
    FZR1 fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] Subtracted Measured 13241.4 11864 1377.4
    NEUROD6 neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Rooted 27.9136 37.2872 9.3736
    NME3 nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] Squared 33982.3 43159.1 9176.8
    PYGL glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Divided 8875.01 6768.05 1.31131
    WAS wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Measured 6416.68 7865.15 1.22574
    248 no value apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Ranked 237.302 212.41 1.11719
    dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] Subtracted 243.583 267.527 23.944
    CRK proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Divided Measured 6417.18 7859.6 1.22477
    IDH2 isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [swissprot;acc:p48735] Subtracted Squared 37226.9 46400.1 9173.2
    LSM5 u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Divided Rooted 56.0466 63.4808 1.13264
    MYO15A myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Squared 8875.01 6768.05 1.31131
    NEUROD1 neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Subtracted Rooted 27.9136 37.2872 9.3736
    PCSK5 proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] Measured 13241.4 11864 1377.4
    249 ABL2 tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Divided 6417.18 7859.59 1.22477
    BRF1 transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] Rooted 55.5965 62.9349 1.13199
    CDC23 cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661] Subtracted Squared 51616.7 42588.9 9027.8
    NEUROD4 neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Rooted 27.9136 37.2872 9.3736
    PYGM glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Divided Squared 8875.01 6768.05 1.31131
    SNRPD2 small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Subtracted Measured 4405.4 5782.08 1376.68
    SNRPD3 small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Ranked 226.109 202.333 23.776
    SYNCRIP ns1-associated protein 1. [refseq;acc:nm_006372] Divided 237.302 212.41 1.11719
    250 no value proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Measured 6417.18 7859.6 1.22477
    CHD5 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Subtracted Rooted 27.9136 37.2872 9.3736
    CTBP2 c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] Divided Squared 69201.8 53013.4 1.30536
    HARS2 histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590] Subtracted 34527.9 43507.9 8980
    HNRNPR heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Divided Ranked 237.302 212.41 1.11719
    NOLA1 nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Rooted 55.5965 62.9349 1.13199
    PLDN pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] Subtracted Ranked 210.693 186.95 23.743
    SH2D3C sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] Measured 4578.09 5939.91 1361.82
    251 BCAR3 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 4579.34 5940.64 1361.3
    BCL6B b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] Divided Squared 69165.6 52992.1 1.30521
    CDK2AP1 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] Subtracted Rooted 27.9136 37.2872 9.3736
    HARS histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081] Squared 34506.3 43476 8969.7
    HCK tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Divided Measured 6417.18 7859.6 1.22477
    MAX max protein. [swissprot;acc:p25912] Rooted 56.3054 63.7148 1.13159
    RPS20 40s ribosomal protein s20. [swissprot;acc:p17075] Subtracted Ranked 243.5 267.21 23.71

    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/