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 Hugo Network Comparison Type Value Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 2275 to 2324 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Network Comparison Type
    		Value Type
    		red
    		network_comparison
    		green
    285 dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602] POLR1A Subtracted Ranked 242.691 22.79 265.481
    eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] EIF4G3 Measured 4068.56 1184.04 5252.6
    poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] PAPOLA Divided 23326.5 1.20885 19296.4
    ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] RRM2B Subtracted Squared 32117 7937 40054
    t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] CCT4 Divided Ranked 224.647 1.10532 203.242
    transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] HRAS Subtracted Rooted 108.653 8.301 100.352
    286 60s ribosomal protein l30. [swissprot;acc:p04645] RPL30 Ranked 242.593 22.772 265.365
    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] NEDD9 Divided 224.633 1.1052 203.251
    exocyst complex component sec5. [swissprot;acc:q96kp1] EXOC2 Measured 23316 1.20878 19288.8
    ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] RRM1 Subtracted Squared 32056.4 7909.4 39965.8
    rna-binding protein. [refseq;acc:nm_019027] no value Measured 4069.83 1182.34 5252.17
    smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] CSRP2 Divided Rooted 51.8717 1.11965 46.3287
    t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] PBK Squared 6693.64 1.27956 8564.94
    transforming protein n-ras. [swissprot;acc:p01111] no value Subtracted Rooted 108.65 8.3 100.35
    287 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] RPS4Y2 Divided Ranked 240.758 1.10517 266.079
    apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] no value Subtracted Measured 4069.83 1182.34 5252.17
    kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] KHDRBS3 Divided Squared 6693.64 1.27956 8564.94
    likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] SHCBP1 Rooted 51.8714 1.11965 46.3281
    poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] PAPOLG Measured 23303.1 1.2087 19279.5
    splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] SF3B1 Subtracted Ranked 225.217 22.758 202.459
    t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] TCP1 Rooted 97.1967 8.1053 105.302
    wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] WAS Squared 28878.8 7904.7 36783.5
    288 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] no value Divided Ranked 240.758 1.10517 266.078
    cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] CPSF3 Measured 23422.4 1.20857 19380.3
    kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] KHDRBS1 Squared 6693.64 1.27956 8564.94
    lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] CSRP3 Rooted 51.8789 1.11949 46.3416
    ns1-associated protein 1. [refseq;acc:nm_006372] SYNCRIP Subtracted Measured 4069.83 1182.34 5252.17
    proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] CRK Squared 28896.2 7870.8 36767
    small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] no value Rooted 55.8956 8.068 63.9636
    syntaxin 10 (syn10). [swissprot;acc:o60499] STX10 Ranked 234.691 22.751 257.442
    289 heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] HNRNPR Measured 4069.83 1182.34 5252.17
    hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] no value Divided Ranked 272.781 1.10486 246.892
    kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] KHDRBS2 Squared 6693.64 1.27956 8564.94
    pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] PRPF31 Rooted 57.4274 1.11899 64.2609
    small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] SNRPF Subtracted 55.8956 8.068 63.9636
    syntaxin 6. [swissprot;acc:o43752] STX6 Ranked 234.673 22.741 257.414
    tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] ABL2 Squared 28896.2 7870.8 36767
    u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] LSM6 Divided Measured 4682.88 1.20571 5646.19
    290 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] NCBP2 Squared 15734.4 1.27916 20126.8
    atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] no value Rooted 75.6323 1.11788 67.6572
    eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] EIF4G1 Subtracted Measured 4071.1 1180.65 5251.75
    proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] no value Squared 28896.2 7870.8 36767
    ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] RRM2 Divided Ranked 231.969 1.10428 210.064
    suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] no value Subtracted 242.109 22.681 264.79
    tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] TFIP11 Divided Measured 4991.48 1.20487 6014.08
    wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] WAS Subtracted Rooted 66.1122 8.0316 74.1438
    291 adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819] AK2 Ranked 241.509 22.654 264.163
    nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] NFYB Divided 251.679 1.10368 228.037
    pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] PLDN Subtracted Measured 5894.75 1178.9 7073.65
    proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] CRK Rooted 66.1064 8.001 74.1074

    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/