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 description Network Comparison Type Value Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 2725 to 2774 of 66312 in total
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		Value Type
    		Interaction Map
    		red
    		network_comparison
    		green
    171 LASS2 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Divided Rooted High confidence 61.6639 1.16333 71.7355
    MAGED2 melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] Measured 23693.7 1.29736 18263
    MPDZ multiple pdz domain protein. [refseq;acc:nm_003829] Squared Low confidence 67876.4 1.11438 60909.3
    NCBP2L dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Subtracted Measured High confidence 4117.67 1683.37 5801.04
    NFU1 hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Divided Rooted Low confidence 96.9641 1.06474 103.242
    RNF20 ring finger protein 20. [refseq;acc:nm_019592] Subtracted Squared 53551.4 5506.3 48045.1
    SENP8 sentrin-specific protease 8 (ec 3.4.22.-) (sentrin/sumo-specific protease senp8) (cysteine protease fksg8). [swissprot;acc:q96ld8] Divided Measured 7012.61 1.08158 7584.69
    SNAI2 zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] Subtracted Squared High confidence 69165 16173.3 52991.7
    SNRP70 u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Rooted 55.6161 11.1171 66.7332
    TIAL1 nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Divided Ranked 227.202 1.17829 192.823
    TRAPPC3 bet3 homolog. [swissprot;acc:o43617] Subtracted Measured Low confidence 8749.42 622.91 9372.33
    TRPC4 short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Ranked High confidence 201.478 27.306 228.784
    172 no value filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Rooted 55.6161 11.1171 66.7332
    serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] Measured 4556.78 1611.52 2945.26
    ATG3 apg3p; pc3-96 protein. [refseq;acc:nm_022488] Low confidence 10547.4 622.84 9924.56
    CAPZA1 f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] Divided Ranked 213.671 1.0567 202.205
    CSTF2T likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] Squared High confidence 121579 1.39331 87259.3
    CTBP1 c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] Subtracted 69123.3 16156.3 52967
    NEDD8 ubiquitin-like protein nedd8. [swissprot;acc:q15843] Divided Measured Low confidence 7012.61 1.08158 7584.69
    PPM1B protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] Subtracted Ranked 196.714 10.956 185.758
    SF3B1 splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Divided Rooted High confidence 56.7592 1.16261 65.9889
    SNRPA u1 small nuclear ribonucleoprotein a (u1 snrnp a protein). [swissprot;acc:p09012] Subtracted Low confidence 70.5964 4.5235 75.1199
    SRM spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [swissprot;acc:p19623] Squared 54936 5461.3 49474.7
    TBC1D10A ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] Ranked High confidence 201.515 27.237 228.752
    TIPRL cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] Divided 174.667 1.17685 205.556
    TRO trophinin. [swissprot;acc:q12816] Measured 23693.7 1.29736 18263
    UNC84A sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Rooted Low confidence 65.0717 1.06436 69.26
    WBP11 ww domain binding protein 11; npw38-binding protein npwbp; sh3 domain-binding protein snp70. [refseq;acc:nm_016312] Squared 67872.2 1.11437 60906.5
    173 no value guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Subtracted Ranked 211.679 10.944 222.623
    methyltransferase like 2. [refseq;acc:nm_018396] Squared High confidence 71576.8 15250.1 56326.7
    ALG1 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Low confidence 43800.4 5442.1 38358.3
    BCAR3 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] Divided Measured High confidence 4579.34 1.29727 5940.64
    ELAC2 elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [refseq;acc:nm_018127] Squared Low confidence 67872.2 1.11437 60906.5
    MRPS17 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Rooted High confidence 145.551 1.1597 168.796
    PPP2R2D uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Subtracted Measured 4556.79 1611.51 2945.28
    PSEN2 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Rooted 37.3005 11.1136 48.4141
    SEPT2 septin 2 (nedd5 protein homolog). [swissprot;acc:q15019] Divided Measured Low confidence 10168.5 1.08145 10996.7
    SEPT4 septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] Squared High confidence 82624.3 1.39258 115061
    SNRPA u1 small nuclear ribonucleoprotein a (u1 snrnp a protein). [swissprot;acc:p09012] Rooted Low confidence 70.5964 1.06408 75.1199
    SNRPD1 small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Ranked High confidence 227.032 1.17599 193.056
    TAGLN transgelin (smooth muscle protein 22-alpha) (sm22-alpha) (ws3-10) (22 kda actin-binding protein). [swissprot;acc:q01995] Subtracted Rooted Low confidence 65.5094 4.5141 70.0235
    TOB2 tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Measured 3098.94 620.72 3719.66
    TRPC5 short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] Ranked High confidence 201.515 27.237 228.752
    UNC84A sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Divided Low confidence 221.678 1.05664 209.795
    174 DGCR14 dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] High confidence 335 1.17133 286
    DYNLT1 cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] Subtracted Squared 71576.8 15250.1 56326.7
    FOXP1 forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Divided Ranked Low confidence 219.6 1.05624 207.907
    GNG12 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Subtracted 211.679 10.944 222.623
    LUC7L2 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] High confidence 228.1 27.132 200.968
    MXD1 mad protein (max dimerizer). [swissprot;acc:q05195] Divided Measured 4455.95 1.2958 5774.03

    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/