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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 708 to 757 of 7460 in total
    Value Type  : Ranked
    Interaction Map  : High confidence
    Rank
    description
    Network Comparison Type
    Filtered
    red
    green
    network_comparison
    177 transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] Subtracted 1 241.07 267.88 26.81
    178 density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583]
    formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Divided 226.887 194.72 1.1652
    integral membrane protein cii-3b. [sptrembl;acc:o75609] 0 14951.6 13204.2 1.13234
    transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664] Subtracted 10899.5 12217.4 1317.9
    179 estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] 12190.3 13497.2 1306.9
    huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Divided 1 226.884 194.79 1.16476
    mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] 0 9473.01 10723.7 1.13203
    phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] Subtracted 1 227.357 254.15 26.793
    180 pp3111 protein. [refseq;acc:nm_022156]
    probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] 0 7690.02 8991.19 1301.17
    rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513] Divided 8407.67 9516.92 1.13193
    tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] 1 256.228 298.438 1.16474
    181 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] 229.818 267.265 1.16294
    importin 7; ran-binding protein 7. [refseq;acc:nm_006391] 0 14864.7 16820.7 1.13159
    putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] Subtracted 4119 5397 1278
    syntaxin 18. [swissprot;acc:q9p2w9] 1 227.357 254.15 26.793
    182 histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] Divided 277.546 240.461 1.15422
    phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669] Subtracted 0 4119 5397 1278
    putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544] Divided 11573.8 10231.3 1.13121
    rd protein. [swissprot;acc:p18615] Subtracted 1 227.357 254.15 26.793
    183 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Divided 228.306 198.011 1.153
    dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] Subtracted 0 3859 2582 1277
    glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] 1 227.357 254.15 26.793
    ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Divided 0 11613 13133.5 1.13093
    184 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] Subtracted 1 227.357 254.15 26.793
    ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376] 0 3284 4554.5 1270.5
    odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Divided 1 274.027 237.79 1.15239
    similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] 0 6279.56 5569.42 1.12751
    185 adiponectin receptor 2. [refseq;acc:nm_024551] 1 281.582 246.371 1.14292
    atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] Subtracted 227.357 254.15 26.793
    ubiquitin-conjugating enzyme e2-18 kda ubch7 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (ubcm4) (e2-f1) (l-ubc). [swissprot;acc:p51966] 0 3284 4554.5 1270.5
    zinc finger protein 277. [swissprot;acc:q9nrm2] Divided 6279.56 5569.42 1.12751
    186 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] 11935.1 10592.8 1.12672
    cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] Subtracted 12677.7 13941.7 1264
    filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] Divided 1 226.582 198.444 1.14179
    j domain containing protein 1. [swissprot;acc:q9ukb3] Subtracted 227.357 254.15 26.793
    187 adenylosuccinate synthase-like 1. [refseq;acc:nm_152328] Divided 0 9955.22 11213.7 1.12641
    rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] 1 226.582 198.444 1.14179
    secreted modular calcium-binding protein 1. [refseq;acc:nm_022137] Subtracted 0 14003.7 12743.3 1260.4
    sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] 1 227.357 254.15 26.793
    188 60s ribosomal protein l15. [swissprot;acc:p39030] Divided 0 11745.2 13203.1 1.12413
    ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] Subtracted 1 227.357 254.15 26.793
    protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Divided 226.582 198.444 1.14179
    transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] Subtracted 0 8409.21 9668.79 1259.58
    189 adenylosuccinate synthase-like 1. [refseq;acc:nm_152328] 9955.22 11213.7 1258.48
    cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] 1 241.373 267.352 25.979
    protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Divided 226.582 198.444 1.14179
    sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4] 0 10634.4 9465 1.12355
    190 fad synthetase. [refseq;acc:nm_025207] Subtracted 1 241.373 267.352 25.979

    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
    - 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/