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 Value Type Gene Hugo description Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1113 to 1162 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Value Type
    		Hugo
    		description
    		red
    		green
    		network_comparison
    279 Measured GPSM2 mosaic protein lgn. [swissprot;acc:p81274] 3119.98 2579.49 1.20953
    Ranked RBBP7 histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] 252.644 228.42 1.10605
    Squared MSI2 musashi 2 isoform a. [refseq;acc:nm_138962] 15569.5 19953.6 1.28158
    Rooted WASL neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] 66.0989 74.0609 1.12046
    280 Measured RGS17 regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] 3119.98 2579.49 1.20953
    Ranked MTA1 metastasis-associated protein mta1. [swissprot;acc:q13330] 252.512 228.356 1.10578
    Squared MSI1 musashi 1. [refseq;acc:nm_002442] 15569.5 19953.6 1.28158
    Rooted no value ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] 57.9068 64.8562 1.12001
    281 Measured GNAO1 guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] 3119.98 2579.49 1.20953
    Ranked no value 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 241.808 267.335 1.10557
    Squared ZC3H14 nuclear protein ukp68. [refseq;acc:nm_024824] 15569.5 19953.6 1.28158
    Rooted SNRPA1 u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] 57.9068 64.8562 1.12001
    282 Measured RAP1GAP rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] 3119.98 2579.49 1.20953
    Ranked RBBP4 chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028] 252.39 228.297 1.10553
    Squared CLEC11A stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] 59704 76460.4 1.28066
    Rooted SF3A2 splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] 57.9819 64.9302 1.11984
    283 Measured POLI polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] 5221.28 6314.35 1.20935
    Ranked RPL11 60s ribosomal protein l11. [swissprot;acc:p39026] 241.828 267.346 1.10552
    Squared DTX2 deltex 2. [refseq;acc:nm_020892] 6627.24 8484.19 1.2802
    Rooted KLF5 krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887] 57.9819 64.9302 1.11984
    284 Measured PXN paxillin. [swissprot;acc:p49023] 5221.28 6314.35 1.20935
    Ranked BCAR1 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] 224.657 203.235 1.10541
    Squared CLEC3A c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] 59464 76120.8 1.28012
    Rooted CSRP1 cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] 51.8647 46.3161 1.1198
    285 Measured PAPOLA poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] 23326.5 19296.4 1.20885
    Ranked CCT4 t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] 224.647 203.242 1.10532
    Squared DTX1 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] 6680.89 8549.44 1.27969
    Rooted DDX54 atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] 48.4278 54.2262 1.11973
    286 Measured EXOC2 exocyst complex component sec5. [swissprot;acc:q96kp1] 23316 19288.8 1.20878
    Ranked 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] 224.633 203.251 1.1052
    Squared PBK 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] 6693.64 8564.94 1.27956
    Rooted CSRP2 smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] 51.8717 46.3287 1.11965
    287 Measured PAPOLG poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] 23303.1 19279.5 1.2087
    Ranked RPS4Y2 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] 240.758 266.079 1.10517
    Squared KHDRBS3 kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] 6693.64 8564.94 1.27956
    Rooted SHCBP1 likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] 51.8714 46.3281 1.11965
    288 Measured CPSF3 cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] 23422.4 19380.3 1.20857
    Ranked no value 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 240.758 266.078 1.10517
    Squared KHDRBS1 kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] 6693.64 8564.94 1.27956
    Rooted CSRP3 lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] 51.8789 46.3416 1.11949
    289 Measured LSM6 u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] 4682.88 5646.19 1.20571
    Ranked no value hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] 272.781 246.892 1.10486
    Squared KHDRBS2 kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] 6693.64 8564.94 1.27956
    Rooted PRPF31 pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] 57.4274 64.2609 1.11899
    290 Measured TFIP11 tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] 4991.48 6014.08 1.20487
    Ranked RRM2 ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] 231.969 210.064 1.10428
    Squared NCBP2 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] 15734.4 20126.8 1.27916
    Rooted no value atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 75.6323 67.6572 1.11788
    291 Measured UBAC1 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 44490.5 36927.5 1.20481
    Ranked NFYB 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] 251.679 228.037 1.10368

    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/