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 green network_comparison
    Results: HTML CSV LaTeX Showing element 5336 to 5385 of 8289 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Interaction Map
    		red
    		green
    		network_comparison
    2668 ROS1 proto-oncogene tyrosine-protein kinase ros precursor (ec 2.7.1.112) (c-ros-1). [swissprot;acc:p08922] Low confidence 202.995 199.473 1.01766
    2669 no value sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] 202.994 1.01765
    GPD1 glycerol-3-phosphate dehydrogenase [nad+], cytoplasmic (ec 1.1.1.8) (gpd-c) (gpdh-c). [swissprot;acc:p21695] High confidence 214.575 214.354 1.00103
    2670 HMHA1 myeloblast kiaa0223 (fragment). [sptrembl;acc:q92619] Low confidence 197.843 194.412 1.01765
    KRAS transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] High confidence 144.391 144.538 1.00102
    2671 GNPNAT1 similar to glucosamine-phosphate n-acetyltransferase (hypothetical protein flj33258). [sptrembl;acc:q96ek6] 216.288 216.067
    SPRY3 sprouty homolog 3 (spry-3). [swissprot;acc:o43610] Low confidence 202.994 199.473 1.01765
    2672 BCAT1 branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [swissprot;acc:p54687] High confidence 210.957 210.741 1.00102
    SPRY1 sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609] Low confidence 202.994 199.473 1.01765
    2673 ARHGAP29 ptpl1-associated rhogap 1. [refseq;acc:nm_004815] 197.842 194.411
    RAD9A rad9 homolog; cell cycle checkpoint control protein; rad9 homolog (s. pombe). [refseq;acc:nm_004584] High confidence 216.372 216.588 1.001
    2674 DCX doublecortin (lissencephalin-x) (lis-x) (doublin). [swissprot;acc:o43602] Low confidence 201.053 197.566 1.01765
    GLUL glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104] High confidence 203.151 202.948 1.001
    2675 MID1IP1 protein strait11499. [swissprot;acc:q9npa3] Low confidence 196.277 192.877 1.01763
    MRPS26 28s ribosomal protein s26, mitochondrial precursor (mrp-s26) (mrp- s13). [swissprot;acc:q9byn8] High confidence 214.893 215.108 1.001
    2676 CRIM1 cysteine-rich motor neuron 1; cysteine-rich repeat-containing protein s52 precursor. [refseq;acc:nm_016441] Low confidence 204.508 200.964 1.01763
    ERH enhancer of rudimentary homolog. [swissprot;acc:q14259] High confidence 214.893 215.108 1.001
    2677 C10orf118 ctcl tumor antigen l14-2. [refseq;acc:nm_018017] Low confidence 203.566 200.041 1.01762
    SHOC2 leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] High confidence 144.412 144.553 1.00098
    2678 no value ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] 144.411 144.552
    RPL11 60s ribosomal protein l11. [swissprot;acc:p39026] Low confidence 208.542 212.217 1.01762
    2679 ANAPC2 anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [refseq;acc:nm_013366] High confidence 190.142 189.959 1.00096
    C13orf1 clll6 protein. [refseq;acc:nm_020456] Low confidence 203.566 200.041 1.01762
    2680 HRAS transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] High confidence 144.422 144.56 1.00096
    TMEM147 seven transmembrane domain protein. [refseq;acc:nm_032635] Low confidence 208.542 212.217 1.01762
    2681 OTUB2 ubiquitin-specific protease otubain 2. [refseq;acc:nm_023112] High confidence 203.592 203.787 1.00096
    TMED10 transmembrane protein tmp21 precursor (21 kda transmembrane trafficking protein) (p24delta) (s31iii125) (s31i125) (tmp-21-i). [swissprot;acc:p49755] Low confidence 182.789 179.625 1.01761
    2682 no value transforming protein n-ras. [swissprot;acc:p01111] High confidence 144.427 144.564 1.00095
    SUPV3L1 suppressor of var1, 3-like 1. [refseq;acc:nm_003171] Low confidence 200.492 197.022 1.01761
    2683 DCLK1 serine/threonine-protein kinase dcamkl1 (ec 2.7.1.-) (doublecortin- like and cam kinase-like 1). [swissprot;acc:o15075] 201.045 197.566
    YBX1 nuclease sensitive element binding protein 1 (y box binding protein-1) (y-box transcription factor) (yb-1) (ccaat-binding transcription factor i subunit a) (cbf-a) (enhancer factor i subunit a) (efi-a) (dna-binding protein b) (dbpb). [swissprot;acc:p16991] High confidence 208.438 208.635 1.00095
    2684 CSDA dna-binding protein a (cold shock domain protein a) (single-strand dna binding protein nf-gmb). [swissprot;acc:p16989]
    PFDN5 prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471] Low confidence 200.242 196.776 1.01761
    2685 PIGB phosphatidylinositol glycan, class b. [refseq;acc:nm_004855] 182.789 179.625
    YBX2 germ cell specific y-box binding protein; contrin. [refseq;acc:nm_015982] High confidence 208.438 208.635 1.00095
    2686 PSMB7 proteasome subunit beta type 7 precursor (ec 3.4.25.1) (proteasome subunit z) (macropain chain z) (multicatalytic endopeptidase complex chain z). [swissprot;acc:q99436] 219.829 219.629 1.00091
    STIP1 stress-induced-phosphoprotein 1 (sti1) (hsp70/hsp90-organizing protein) (transformation-sensitive protein ief ssp 3521). [swissprot;acc:p31948] Low confidence 197.695 194.276 1.0176
    2687 BCAT2 branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382] High confidence 210.939 210.755 1.00087
    ERCC3 tfiih basal transcription factor complex helicase xpb subunit (ec 3.6.1.-) (basic transcription factor 2 89 kda subunit) (btf2-p89) (tfiih 89 kda subunit) (dna-repair protein complementing xp-b cells) (xeroderma pigmentosum group b complementing protein) (dna excision repair protein ercc-3). [swissprot;acc:p19447] Low confidence 197.695 194.276 1.0176
    2688 no value peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521] High confidence 194.557 194.392 1.00085
    AARS alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [swissprot;acc:p49588] Low confidence 201.799 198.308 1.0176
    2689 ACLY atp-citrate synthase (ec 2.3.3.8) (atp-citrate (pro-s-)-lyase) (citrate cleavage enzyme). [swissprot;acc:p53396] High confidence 213.792 213.619 1.00081
    CRISP1 cysteine-rich secretory protein-1 precursor (crisp-1) (acidic epididymal glycoprotein homolog) (aeg-like protein) (arp). [swissprot;acc:p54107] Low confidence 205.763 202.207 1.01759
    2690 AQP4 aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] High confidence 188.191 188.046 1.00077
    CRISP2 testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562] Low confidence 205.763 202.207 1.01759
    2691 AQP2 aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] High confidence 188.193 188.048 1.00077
    PEX14 peroxisomal membrane protein pex14 (peroxin-14) (peroxisomal membrane anchor protein pex14) (pts1 receptor docking protein). [swissprot;acc:o75381] Low confidence 201.441 197.96 1.01758
    2692 AQP5 aquaporin 5. [swissprot;acc:p55064] High confidence 188.192 188.048 1.00077
    EIF2B4 translation initiation factor eif-2b delta subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9ui10] Low confidence 202.466 198.969 1.01758
    2693 DDX43 dead-box protein. [refseq;acc:nm_018665] 202.135 198.643

    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/