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 green network_comparison
    Results: HTML CSV LaTeX Showing element 5408 to 5457 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		Value Type
    		red
    		green
    		network_comparison
    676 SPRY1 sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609] Divided Measured 5549.2 6215.42 1.12006
    677 COX11 cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1] Squared 22335.8 26232.2 1.17445
    FBL fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] Subtracted Ranked 245.246 233.483 11.763
    GABPA ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] Rooted 57.2007 61.7615 4.5608
    LEF1 lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2] Divided 59.2629 63.7418 1.07558
    LSM4 u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Ranked 228.944 216.745 1.05628
    OTC ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480] Subtracted Squared 24614 28973.4 4359.4
    POLE dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] Measured 4024.4 4719.35 694.95
    SPRY2 sprouty homolog 2 (spry-2). [swissprot;acc:o43597] Divided 5549.2 6215.42 1.12006
    678 no value ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545] Subtracted Rooted 57.2007 61.7615 4.5608
    transcription factor btf3 homolog 3. [swissprot;acc:q13892] Divided Measured 6938.22 7770.65 1.11998
    KPNA6 importin alpha-6 subunit (karyopherin alpha-5 subunit). [swissprot;acc:o15131] Subtracted Squared 23534.9 27890.2 4355.3
    MYEF2 myelin gene expression factor 2. [refseq;acc:nm_016132] Divided Rooted 56.8369 52.8585 1.07527
    NCK1 cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [swissprot;acc:p16333] Subtracted Measured 6784.67 7475.48 690.81
    PPIL4 peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126] Ranked 226.135 214.405 11.73
    SNX5 sorting nexin 5. [swissprot;acc:q9y5x3] Divided 208.482 220.175 1.05609
    SURF1 surfeit locus protein 1. [swissprot;acc:q15526] Squared 22335.8 26232.2 1.17445
    679 no value homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Ranked 132.413 125.389 1.05602
    putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231] Rooted 61.5558 66.1861 1.07522
    ADSSL1 adenylosuccinate synthase-like 1. [refseq;acc:nm_152328] Measured 6503.1 7282.94 1.11992
    DPP6 dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658] Squared 22337.3 26234.1 1.17445
    GALK2 n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [swissprot;acc:q01415] Subtracted Measured 4910.6 5600.61 690.01
    KCNAB3 voltage-gated potassium channel beta-3 subunit (k+ channel beta-3 subunit) (kv-beta-3). [swissprot;acc:o43448] Squared 23526.4 27879.4 4353
    NDUFS8 nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [swissprot;acc:o00217] Rooted 57.2007 61.7615 4.5608
    SNX5 sorting nexin 5. [swissprot;acc:q9y5x3] Ranked 208.482 220.175 11.693
    680 no value galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [swissprot;acc:p07902] Measured 4910.6 5600.61 690.01
    ADSS adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] Divided 6503.03 7282.5 1.11986
    ELOVL1 elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] Subtracted Rooted 57.2008 61.7614 4.5606
    FAP seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884] Divided Squared 22336.8 26233.5 1.17445
    GPKOW t54 protein. [swissprot;acc:q92917] Rooted 61.5558 66.1861 1.07522
    HOXB4 homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Ranked 132.413 125.389 1.05602
    SFRS18 sr rich protein. [refseq;acc:nm_032870] Subtracted 225.293 213.64 11.653
    YIF1A yip1 interacting factor homolog; yip1p-interacting factor; putative rab5-interacting protein; putative transmembrane protein 54tmp. [refseq;acc:nm_020470] Squared 23526.4 27879.3 4352.9
    681 C15orf15 ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] Divided Measured 7170.83 8029.64 1.11976
    COX15 cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376] Squared 22335.8 26232.2 1.17445
    GALE udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] Subtracted Measured 4910.6 5600.61 690.01
    HOXC5 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Divided Ranked 132.413 125.389 1.05602
    KCNAB1 voltage-gated potassium channel beta-1 subunit (k+ channel beta-1 subunit) (kv-beta-1). [swissprot;acc:q14722] Subtracted Squared 23526.4 27879.3 4352.9
    MYC myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] Rooted 57.208 61.7592 4.5512
    SLC15A2 oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] Divided 80.2562 86.277 1.07502
    SNW1 nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] Subtracted Ranked 220.593 208.987 11.606
    682 no value 60s ribosomal protein l12. [swissprot;acc:p30050] Rooted 49.9858 45.4433 4.5425
    homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Divided Ranked 132.413 125.389 1.05602
    CLEC11A stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] Rooted 86.5959 93.0684 1.07474
    COX10 protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887] Squared 22335.8 26232.2 1.17445
    MARS methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] Subtracted Measured 5560.06 6248.27 688.21
    NAT10 upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] Ranked 246.055 234.458 11.597
    STX12 syntaxin 12. [refseq;acc:nm_177424] Divided Measured 5552.92 6217.59 1.1197
    YIF1B similar to putative transmembrane protein; homolog of yeast golgi membrane protein yif1p (yip1p-interacting factor). [refseq;acc:nm_033557] Subtracted Squared 23526.4 27879.3 4352.9
    683 no value 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] Rooted 49.9856 45.4431 4.5425

    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/