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 [...,...].
    Network Comparison Type Rank Gene Value Type description Interaction Map Hugo network_comparison Filtered red green
    Results: HTML CSV LaTeX Showing element 2330 to 2379 of 66312 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Value Type
    		description
    		Interaction Map
    		Hugo
    		network_comparison
    		red
    		green
    292 Measured nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] High confidence NUBP1 1.20419 4641.09 5588.75
    Ranked 40s ribosomal protein s15a. [swissprot;acc:p39027] RPS15A 1.10357 241.411 266.414
    lysosomal-associated transmembrane protein 4a (golgi 4-transmembrane spanning transporter mtp). [swissprot;acc:q15012] Low confidence LAPTM4A 1.04308 209.995 201.322
    Squared neuralized-like. [refseq;acc:nm_004210] High confidence NEURL 1.27831 6828.26 8728.66
    phosphoserine aminotransferase (ec 2.6.1.52) (psat). [swissprot;acc:q9y617] Low confidence PSAT1 1.08461 56826.7 61634.7
    Rooted splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459] SF3A1 1.05461 71.0039 74.8814
    u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] High confidence LSM6 1.11755 56.48 63.119
    293 Measured nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] NUBP2 1.20419 4641.09 5588.75
    splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] Low confidence SF3B2 1.05915 7675.19 8129.16
    Ranked 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] High confidence no value 1.10356 240.782 265.717
    probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] Low confidence ATP2C2 1.04301 218.785 209.763
    Squared kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] High confidence KYNU 1.27815 35991.8 46002.9
    mothers against decapentaplegic homolog 3 (smad 3) (mothers against dpp homolog 3) (mad3) (hmad-3) (mmad3) (jv15-2) (hsmad3). [swissprot;acc:q92940] Low confidence SMAD3 1.08456 49043.9 45220
    Rooted potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] KCND3 1.05439 61.2714 58.111
    short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] High confidence TRPC4 1.11729 63.0715 56.4506
    294 Measured cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] CSTF3 1.20387 22515.5 18702.6
    ubiquitin-conjugating enzyme e2 g1 (ec 6.3.2.19) (ubiquitin-protein ligase g1) (ubiquitin carrier protein g1) (e217k) (ubc7). [swissprot;acc:q99462] Low confidence UBE2G1 1.05913 7590.39 8039.23
    Ranked brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567] High confidence BCCIP 1.10356 240.782 265.717
    jagged 2 precursor (jagged2) (hj2). [swissprot;acc:q9y219] Low confidence JAG2 1.04294 218.715 209.71
    Squared 1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120] High confidence AGPAT2 1.2776 30826.5 39383.9
    fatty acid-binding protein, heart (h-fabp) (muscle fatty acid-binding protein) (m-fabp) (mammary-derived growth inhibitor) (mdgi). [swissprot;acc:p05413] Low confidence FABP3 1.08402 49635.2 45787.9
    Rooted nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] NUBP1 1.05423 70.1377 73.9413
    segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] High confidence DVL1 1.11725 59.0296 65.951
    295 Measured 5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [swissprot;acc:q99707] Low confidence MTR 1.05895 9113.16 9650.42
    ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] High confidence RGL1 1.20368 13261.9 11017.8
    Ranked multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] SCYE1 1.103 223.273 202.423
    myocyte-specific enhancer factor 2d. [swissprot;acc:q14814] Low confidence MEF2D 1.04294 218.713 209.709
    Squared 1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943] High confidence no value 1.27733 30807.7 39351.7
    ubiquitin-like protein gdx (ubiquitin-like protein 4). [swissprot;acc:p11441] Low confidence UBL4A 1.08399 57470.4 53017.7
    Rooted segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] High confidence DVL2 1.11711 59.029 65.9421
    tankyrase 2 (ec 2.4.2.30) (tank2) (tankyrase ii) (tnks-2) (trf1- interacting ankyrin-related adp-ribose polymerase 2) (tankyrase-like protein) (tankyrase-related protein). [swissprot;acc:q9h2k2] Low confidence TNKS2 1.054 66.6351 70.2333
    296 Measured splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] High confidence SF3A2 1.20306 4911.81 5909.18
    tissue alpha-l-fucosidase precursor (ec 3.2.1.51) (alpha-l-fucosidase i) (alpha-l-fucoside fucohydrolase). [swissprot;acc:p04066] Low confidence FUCA1 1.05868 8417.28 8911.22
    Ranked jagged 1 precursor (jagged1) (hj1). [swissprot;acc:p78504] JAG1 1.04294 218.714 209.709
    mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] High confidence MRPL4 1.10294 241.282 266.12
    Squared fibulin-1 precursor. [swissprot;acc:p23142] Low confidence FBLN1 1.0838 51225 47264.3
    wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] High confidence WAS 1.27372 28878.8 36783.5
    Rooted ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] TBC1D10A 1.11688 63.0663 56.4667
    septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] Low confidence SEPT1 1.0539 84.7416 89.3094
    297 Measured fucosidase, alpha-l- 2, plasma. [refseq;acc:nm_032020] FUCA2 1.05859 8414.05 8907.06
    krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887] High confidence KLF5 1.20306 4911.81 5909.18
    Ranked 60s ribosomal protein l7. [swissprot;acc:p18124] no value 1.1029 235.727 259.984
    myocyte-specific enhancer factor 2c. [swissprot;acc:q06413] Low confidence MEF2C 1.04294 218.714 209.709
    Squared mothers against decapentaplegic homolog 2 (smad 2) (mothers against dpp homolog 2) (mad-related protein 2) (hmad-2) (jv18-1) (hsmad2). [swissprot;acc:q15796] SMAD2 1.08377 48958.6 45174.5
    ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] High confidence RPS6KC1 1.27336 14247.4 18142.1
    Rooted potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Low confidence KCND1 1.05383 61.3254 58.1927
    short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] High confidence TRPC5 1.11688 63.0663 56.4667
    298 Measured fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] Low confidence FZR1 1.05855 8708.47 9218.39
    u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] High confidence no value 1.20262 4633.92 5572.85
    Ranked calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] CAPN2 1.10281 268.632 243.588

    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/