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 [...,...].
    description Gene Rank Hugo Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2651 to 2700 of 8289 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Filtered  : 1
    description
    		Rank
    		Hugo
    		Interaction Map
    		red
    		green
    		network_comparison
    forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] 198 FOXP3 High confidence 263.191 231.394 1.13741
    forkhead box protein q1 (hepatocyte nuclear factor 3 forkhead homolog 1) (hnf-3/forkhead-like protein 1) (hfh-1). [swissprot;acc:q9c009] 4197 FOXQ1 Low confidence 207.659 205.56 1.01021
    forkhead-related transcription factor 10 (freac-10) (fragment). [swissprot;acc:o43638] 4119 FKHL18 207.3 205.116 1.01065
    formin 2 (fragments). [swissprot;acc:q9nz56] 3772 FMN2 203.61 200.926 1.01336
    formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] 178 no value High confidence 226.887 194.72 1.1652
    442 Low confidence 201.424 194.652 1.03479
    fos-related antigen 1 (fra-1). [swissprot;acc:p15407] 46 FOSL1 High confidence 204.642 161.068 1.27053
    62 Low confidence 202.79 183.017 1.10804
    fos-related antigen 2. [swissprot;acc:p15408] 44 FOSL2 High confidence 204.641 161.046 1.2707
    60 Low confidence 202.793 182.961 1.10839
    fos39347_1. [sptrembl;acc:o75863] 2968 no value 201.618 198.273 1.01687
    fragile x mental retardation 1 protein (protein fmr-1) (fmrp). [swissprot;acc:q06787] 1828 FMR1 High confidence 202.41 200.115 1.01147
    3549 Low confidence 202.759 199.825 1.01468
    fragile x mental retardation 2 protein (protein fmr-2) (fmr2p) (ox19 protein) (fragile x e mental retardation syndrome protein). [swissprot;acc:p51816] 371 AFF2 219.599 211.723 1.0372
    fragile x mental retardation syndrome related protein 1. [swissprot;acc:p51114] 1825 FXR1 High confidence 202.386 200.086 1.0115
    3544 Low confidence 202.754 199.817 1.0147
    fragile x mental retardation syndrome related protein 2. [swissprot;acc:p51116] 1823 FXR2 High confidence 202.386 200.086 1.0115
    3542 Low confidence 202.754 199.817 1.0147
    frataxin, mitochondrial precursor (friedreich's ataxia protein) (fxn). [swissprot;acc:q16595] 1984 FXN 196.278 192.52 1.01952
    frg1 protein (fshd region gene 1 protein). [swissprot;acc:q14331] 2745 FRG1 High confidence 201.476 201.514 1.00019
    3337 Low confidence 200.117 197.047 1.01558
    fring. [refseq;acc:nm_057178] 4795 RFFL 206.644 205.76 1.0043
    frizzled 5 precursor (frizzled-5) (fz-5) (hfz5) (fze5). [swissprot;acc:q13467] 1077 FZD5 206.587 201.773 1.02386
    frizzled 8 precursor (frizzled-8) (fz-8) (hfz8). [swissprot;acc:q9h461] 1104 FZD8 206.584 201.786 1.02378
    fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:p09467] 932 FBP1 190.502 185.852 1.02502
    2561 High confidence 209.825 210.18 1.00169
    fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 936 FBP2 Low confidence 190.386 185.747 1.02497
    2551 High confidence 209.766 210.148 1.00182
    fructose-bisphosphate aldolase a (ec 4.1.2.13) (muscle-type aldolase) (lung cancer antigen ny-lu-1). [swissprot;acc:p04075] 2250 ALDOA Low confidence 206.2 202.379 1.01888
    2907 High confidence 0.00001 0.00001 1
    fructose-bisphosphate aldolase b (ec 4.1.2.13) (liver-type aldolase). [swissprot;acc:p05062] 2257 ALDOB Low confidence 206.138 202.32 1.01887
    2973 High confidence 0.00001 0.00001 1
    fructose-bisphosphate aldolase c (ec 4.1.2.13) (brain-type aldolase). [swissprot;acc:p09972] 2254 ALDOC Low confidence 206.167 202.347 1.01888
    3087 High confidence 0.00001 0.00001 1
    ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647] 726 FTSJ3 244.495 232.419 1.05196
    830 Low confidence 201.067 195.971 1.026
    fucosidase, alpha-l- 2, plasma. [refseq;acc:nm_032020] 475 FUCA2 202.311 195.778 1.03337
    fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [swissprot;acc:p07954] 731 FH High confidence 208.874 219.708 1.05187
    1488 Low confidence 201.541 197.306 1.02146
    fumarylacetoacetase (ec 3.7.1.2) (fumarylacetoacetate hydrolase) (beta-diketonase) (faa). [swissprot;acc:p16930] 1284 FAH 202.294 197.852 1.02245
    fuse binding protein 3 (fragment). [sptrembl;acc:q92946] 2668 FUBP3 High confidence 217.176 216.944 1.00107
    3715 Low confidence 203.863 201.112 1.01368
    fuse-binding protein-interacting repressor isoform b; siah binding protein 1; pyrimidine tract binding splicing factor; ro ribonucleoprotein-binding protein 1; poly-u binding splicing factor puf60. [refseq;acc:nm_014281] 350 PUF60 204.762 197.135 1.03869
    1864 High confidence 203.071 200.89 1.01086
    fused toes homolog; likely ortholog of mouse fused toes. [refseq;acc:nm_022476] 2124 AKTIP 221.248 222.788 1.00696
    3573 Low confidence 203.212 200.303 1.01452
    fyve finger-containing phosphoinositide kinase (ec 2.7.1.68) (1- phosphatidylinositol-4-phosphate 5-kinase) (pip5k) (ptdins(4)p-5- kinase) (p235) (fragment). [swissprot;acc:q9y2i7] 1975 PIP5K3 194.796 191.061 1.01955
    fyve-finger-containing rab5 effector protein rabenosyn-5. [refseq;acc:nm_022340] 2998 ZFYVE20 High confidence 0.00001 0.00001 1
    3331 Low confidence 200.825 197.742 1.01559
    fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] 848 FZR1 High confidence 147.211 153.371 1.04184

    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/