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 Network Comparison Type description Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1575 to 1624 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Interaction Map
    		red
    		green
    		network_comparison
    197 RPL27 60s ribosomal protein l27. [swissprot;acc:p08526] Ranked Low confidence 211.912 201.556 1.05138
    TIMM23 mitochondrial import inner membrane translocase subunit tim23. [swissprot;acc:o14925] Rooted 65.3912 69.4 1.0613
    198 ATP1B3 sodium/potassium-transporting atpase beta-3 chain (sodium/potassium- dependent atpase beta-3 subunit) (atpb-3). [swissprot;acc:p54709] Squared 52520.9 47400.8 1.10802
    BRAF b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] Measured High confidence 17710.9 13977.7 1.26708
    COG5 conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] Rooted Low confidence 67.1873 71.2973 1.06117
    DGKD diacylglycerol kinase, delta (ec 2.7.1.107) (diglyceride kinase) (dgk-delta) (dag kinase delta) (130 kda diacylglycerol kinase) (fragment). [swissprot;acc:q16760] Measured 6519.03 6997.26 1.07336
    FOXP3 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Ranked High confidence 263.191 231.394 1.13741
    GAD1 glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] Rooted 59.6399 51.9242 1.1486
    HSPB6 heat-shock 20 kda like-protein p20. [swissprot;acc:o14558] Ranked Low confidence 219.606 208.904 1.05123
    PTPRB protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] Squared High confidence 71062.2 95488.6 1.34373
    199 CRYAA alpha crystallin a chain. [swissprot;acc:p02489] Ranked Low confidence 219.589 208.895 1.05119
    EGFL8 palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] High confidence 242.735 276.059 1.13729
    HEYL hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571] Squared Low confidence 52187.1 47109.7 1.10778
    PHB prohibitin. [swissprot;acc:p35232] Measured 10642 11422.5 1.07334
    PPP2CA serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] High confidence 4916.8 3888.18 1.26455
    PRSS16 thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] Squared 71062.2 95488.6 1.34373
    STT3B source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Rooted 61.2893 70.3856 1.14842
    TPM4 tropomyosin alpha 4 chain (tropomyosin 4) (tm30p1). [swissprot;acc:p07226] Low confidence 70.8512 75.1709 1.06097
    200 BCAR1 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] Measured High confidence 4808.79 6074.21 1.26315
    BRD3 bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059] Squared Low confidence 54179.7 48910.9 1.10772
    CCDC47 gk001 protein. [refseq;acc:nm_020198] High confidence 71062.2 95488.6 1.34373
    CRYAB alpha crystallin b chain (alpha(b)-crystallin) (rosenthal fiber component). [swissprot;acc:p02511] Ranked Low confidence 219.543 208.868 1.05111
    EGFL7 egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] High confidence 242.718 276.018 1.1372
    RINT1 rad50-interacting protein 1. [refseq;acc:nm_021930] Measured Low confidence 6926.74 7434.04 1.07324
    RPL27 60s ribosomal protein l27. [swissprot;acc:p08526] Rooted 69.691 73.939 1.06095
    STT3A oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] High confidence 61.2893 70.3856 1.14842
    201 ARAF a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] Measured Low confidence 10392.7 9683.56 1.07323
    CCT4 t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] High confidence 4810.22 6075.04 1.26294
    CLSTN2 calsyntenin-2 precursor. [swissprot;acc:q9h4d0] Squared 71033.4 95440.2 1.3436
    CYC1 cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] Ranked Low confidence 208.591 219.23 1.051
    DDOST dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] Rooted High confidence 61.2893 70.3856 1.14842
    HEY1 hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [swissprot;acc:q9y5j3] Squared Low confidence 52176.8 47103.2 1.10771
    NCBP2L dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Rooted 71.1262 75.4476 1.06076
    SF4 splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Ranked High confidence 240.133 211.382 1.13601
    202 no value splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] Rooted 57.3527 65.7973 1.14724
    CLSTN3 calsyntenin-3 precursor. [swissprot;acc:q9bqt9] Squared 71030.1 95434.8 1.34358
    GNG4 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Ranked Low confidence 211.51 222.252 1.05079
    NCBP2 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Rooted 71.0652 75.377 1.06067
    NEDD9 enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] Measured High confidence 4812.01 6076.09 1.26269
    PGM3 phosphoacetylglucosamine mutase (ec 5.4.2.3) (pagm) (acetylglucosamine phosphomutase) (n-acetylglucosamine-phosphate mutase) (phosphoglucomutase 3). [swissprot;acc:o95394] Squared Low confidence 55537.3 50139.7 1.10765
    RAF1 raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Measured 10391.8 9682.99 1.0732
    TRPC4 short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Ranked High confidence 201.478 228.784 1.13553
    203 no value hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] Squared 20988.2 15632.1 1.34263
    sodium/hydrogen exchanger 6 (na(+)/h(+) exchanger 6) (nhe-6). [swissprot;acc:q92581] Rooted Low confidence 66.3503 70.3749 1.06066
    transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] High confidence 46.3291 53.1063 1.14628
    ATG12 autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] Measured 11757.8 9352.11 1.25723
    GNG3 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Ranked Low confidence 211.506 222.243 1.05076
    SLU7 step ii splicing factor slu7. [refseq;acc:nm_006425] Measured 9870.83 10591.9 1.07305
    TBC1D10A ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] Ranked High confidence 201.515 228.752 1.13516
    TNXB tenascin-x precursor (tn-x) (hexabrachion-like). [swissprot;acc:p22105] Squared Low confidence 52164 47095.1 1.10763

    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/