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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1175 to 1224 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Value Type
    		red
    		green
    		network_comparison
    294 cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] Measured 22515.5 18702.6 1.20387
    segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Rooted 59.0296 65.951 1.11725
    295 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] Squared 30807.7 39351.7 1.27733
    multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] Ranked 223.273 202.423 1.103
    ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Measured 13261.9 11017.8 1.20368
    segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Rooted 59.029 65.9421 1.11711
    296 ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] 63.0663 56.4667 1.11688
    mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] Ranked 241.282 266.12 1.10294
    splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] Measured 4911.81 5909.18 1.20306
    wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Squared 28878.8 36783.5 1.27372
    297 60s ribosomal protein l7. [swissprot;acc:p18124] Ranked 235.727 259.984 1.1029
    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] Measured 4911.81 5909.18 1.20306
    ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] Squared 14247.4 18142.1 1.27336
    short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] Rooted 63.0663 56.4667 1.11688
    298 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] Ranked 268.632 243.588 1.10281
    ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Squared 14247.4 18142.1 1.27336
    squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] Rooted 57.6823 64.4212 1.11683
    u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] Measured 4633.92 5572.85 1.20262
    299 ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] 4914.27 5907.12 1.20203
    calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] Ranked 268.635 243.592 1.10281
    proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Squared 28896.2 36767 1.27238
    segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Rooted 59.026 65.8955 1.11638
    300 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Ranked 150.959 166.351 1.10196
    mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] Rooted 48.1584 53.7378 1.11586
    tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Squared 28896.2 36767 1.27238
    u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] Measured 4914.27 5907.12 1.20203
    301 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Ranked 150.982 166.372 1.10193
    cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] Measured 13768.2 11466 1.20078
    mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] Rooted 203.673 182.638 1.11517
    proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Squared 28896.2 36767 1.27238
    302 60s ribosomal protein l26. [swissprot;acc:q02877] Ranked 242.326 267.008 1.10185
    cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Rooted 203.673 182.638 1.11517
    pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] Measured 5894.75 7073.65 1.19999
    tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Squared 28896.2 36767 1.27238
    303 60s ribosomal protein l35. [swissprot;acc:p42766] Ranked 242.333 266.999 1.10179
    crk-like protein. [swissprot;acc:p46109] Squared 28896.2 36767 1.27238
    cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Rooted 203.673 182.638 1.11517
    serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Measured 22268.8 18560.4 1.1998
    304 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] Ranked 242.339 266.986 1.1017
    cytohesin 4. [swissprot;acc:q9uia0] Rooted 203.673 182.638 1.11517
    pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Measured 4855.46 5824.52 1.19958
    proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Squared 28896.2 36767 1.27238
    305 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Rooted 203.673 182.638 1.11517
    mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] Ranked 242.339 266.986 1.1017
    odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Measured 3856.29 4624.15 1.19912
    proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Squared 28896.2 36767 1.27238
    306 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] Ranked 242.153 266.673 1.10126
    pnas-18. [sptrembl;acc:q9bzu3] Measured 13680.5 11409.6 1.19903
    proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] Squared 28896.2 36767 1.27238
    rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] Rooted 56.3935 62.8817 1.11505

    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
    - 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/