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 Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 1358 to 1407 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Interaction Map
    		red
    		network_comparison
    		green
    170 MAGEB4 melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Measured High confidence 23693.7 1.29736 18263
    SLC15A1 oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] Rooted Low confidence 70.7428 1.06479 75.3259
    TIA1 nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Ranked High confidence 227.199 1.17894 192.715
    171 CTPS ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] Squared 96602.7 1.39577 69211.2
    FOXP3 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Ranked Low confidence 219.889 1.05683 208.064
    LASS2 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] 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
    NFU1 hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Rooted 96.9641 1.06474 103.242
    SENP8 sentrin-specific protease 8 (ec 3.4.22.-) (sentrin/sumo-specific protease senp8) (cysteine protease fksg8). [swissprot;acc:q96ld8] Measured 7012.61 1.08158 7584.69
    TIAL1 nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Ranked High confidence 227.202 1.17829 192.823
    172 CAPZA1 f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] Low confidence 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
    NEDD8 ubiquitin-like protein nedd8. [swissprot;acc:q15843] Measured Low confidence 7012.61 1.08158 7584.69
    SF3B1 splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Rooted High confidence 56.7592 1.16261 65.9889
    TIPRL cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] Ranked 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 BCAR3 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 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
    SEPT2 septin 2 (nedd5 protein homolog). [swissprot;acc:q15019] 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
    UNC84A sad1/unc-84 protein-like 1. [swissprot;acc:o94901] 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
    FOXP1 forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Low confidence 219.6 1.05624 207.907
    MXD1 mad protein (max dimerizer). [swissprot;acc:q05195] Measured High confidence 4455.95 1.2958 5774.03
    PANK1 pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] Rooted 145.551 1.1597 168.796
    PSCD4 cytohesin 4. [swissprot;acc:q9uia0] Measured Low confidence 12315 1.08115 11390.6
    RBM5 rna-binding protein 5 (rna binding motif protein 5) (putative tumor suppressor luca15) (g15 protein). [swissprot;acc:p52756] Squared 67801.5 1.11409 60858
    TNS3 tumor endothelial marker 6; thyroid specific ptb domain protein; tensin 3. [refseq;acc:nm_022748] Rooted 65.8885 1.06398 70.104
    ZNF547 sedlin. [swissprot;acc:o14582] Squared High confidence 112820 1.39189 157033
    175 no value synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]
    COPS3 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] Ranked 199.949 1.17123 234.187
    CTPS2 cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] Squared Low confidence 65119.3 1.11223 58548.3
    FOXP3 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Rooted 63.3478 1.06343 67.3658
    FOXP4 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Ranked 219.593 1.05623 207.903
    MAN1B1 endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase (ec 3.2.1.113) (er alpha-1,2-mannosidase) (mannosidase alpha class 1b member 1) (man9glcnac2-specific processing alpha-mannosidase). [swissprot;acc:q9ukm7] Measured 7004.28 1.08076 7569.94
    MXI1 max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] High confidence 4456.67 1.29553 5773.77
    PANK2 pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Rooted 145.551 1.1597 168.796
    176 CTPS ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] Squared Low confidence 65033.7 1.11214 58476.1
    FER proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591] Rooted 66.7098 1.06339 70.9384
    MXD4 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Measured High confidence 4456.93 1.29544 5773.67
    PANK3 pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] Rooted 145.551 1.1597 168.796
    POLE4 dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] Ranked 275.754 1.1689 235.908
    PSEN2 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Measured Low confidence 7004.28 1.08076 7569.94
    TNS3 tumor endothelial marker 6; thyroid specific ptb domain protein; tensin 3. [refseq;acc:nm_022748] Ranked 219.336 1.05601 207.703

    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/