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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1180 to 1229 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		description
    		red
    		green
    		network_comparison
    295 SCYE1 Ranked multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] 223.273 202.423 1.103
    296 MRPL4 mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] 241.282 266.12 1.10294
    SF3A2 Measured splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] 4911.81 5909.18 1.20306
    TBC1D10A Rooted ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] 63.0663 56.4667 1.11688
    WAS Squared wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] 28878.8 36783.5 1.27372
    297 no value Ranked 60s ribosomal protein l7. [swissprot;acc:p18124] 235.727 259.984 1.1029
    KLF5 Measured 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] 4911.81 5909.18 1.20306
    RPS6KC1 Squared ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] 14247.4 18142.1 1.27336
    TRPC5 Rooted short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] 63.0663 56.4667 1.11688
    298 no value Measured u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] 4633.92 5572.85 1.20262
    Squared ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] 14247.4 18142.1 1.27336
    CAPN2 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] 268.632 243.588 1.10281
    SART1 Rooted 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] 57.6823 64.4212 1.11683
    299 no value Measured ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] 4914.27 5907.12 1.20203
    CAPN1 Ranked calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] 268.635 243.592 1.10281
    CRK Squared proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] 28896.2 36767 1.27238
    DVL3 Rooted segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] 59.026 65.8955 1.11638
    300 ABL2 Squared tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] 28896.2 36767 1.27238
    MKI67IP Rooted mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] 48.1584 53.7378 1.11586
    PITRM1 Ranked metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] 150.959 166.351 1.10196
    SNRPA1 Measured u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] 4914.27 5907.12 1.20203
    301 no value cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] 13768.2 11466 1.20078
    Squared proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] 28896.2 36767 1.27238
    Rooted 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] 203.673 182.638 1.11517
    ALG1 Ranked beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] 150.982 166.372 1.10193
    302 HCK Squared tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] 28896.2 36767 1.27238
    PLDN Measured pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] 5894.75 7073.65 1.19999
    PSCD1 Rooted cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 203.673 182.638 1.11517
    RPL26 Ranked 60s ribosomal protein l26. [swissprot;acc:q02877] 242.326 267.008 1.10185
    303 CRKL Squared crk-like protein. [swissprot;acc:p46109] 28896.2 36767 1.27238
    PPP1CC Measured serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] 22268.8 18560.4 1.1998
    PSCD2 Rooted cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 203.673 182.638 1.11517
    RPL35 Ranked 60s ribosomal protein l35. [swissprot;acc:p42766] 242.333 266.999 1.10179
    304 no value 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] 242.339 266.986 1.1017
    ABL1 Squared proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] 28896.2 36767 1.27238
    PRPF31 Measured pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] 4855.46 5824.52 1.19958
    PSCD4 Rooted cytohesin 4. [swissprot;acc:q9uia0] 203.673 182.638 1.11517
    305 FYN Squared proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] 28896.2 36767 1.27238
    MRPL2 Ranked mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] 242.339 266.986 1.1017
    OSR1 Measured odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] 3856.29 4624.15 1.19912
    PSCD3 Rooted cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 203.673 182.638 1.11517
    306 no value Measured pnas-18. [sptrembl;acc:q9bzu3] 13680.5 11409.6 1.19903
    Ranked 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] 242.153 266.673 1.10126
    FGR Squared proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] 28896.2 36767 1.27238
    RBM39 Rooted rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] 56.3935 62.8817 1.11505
    307 CCT3 Measured t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] 12365.2 14824.9 1.19892
    GRAP2 Squared grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791] 28896.4 36766.8 1.27237
    SIN3A Rooted transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] 50.4687 45.2733 1.11476
    SRR Ranked serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] 242.153 266.673 1.10126
    308 AGPAT3 Squared 1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7] 30596.2 38919.9 1.27205

    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/