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 Hugo Network Comparison Type Value Type Interaction Map red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 2408 to 2457 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Network Comparison Type
    		Value Type
    		red
    		green
    		network_comparison
    301 proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] no value Divided Squared 28896.2 36767 1.27238
    302 60s ribosomal protein l26. [swissprot;acc:q02877] RPL26 Ranked 242.326 267.008 1.10185
    coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [swissprot;acc:p48444] ARCN1 Subtracted Squared 51527.6 43689.1 7838.5
    cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] PSCD1 Divided Rooted 203.673 182.638 1.11517
    hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] MAGEE2 Subtracted Ranked 88.2482 110.265 22.0168
    homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] CUTL2 Rooted 66.1046 74.0964 7.9918
    pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] PLDN Divided Measured 5894.75 7073.65 1.19999
    ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] RRM2 Subtracted 6704.44 7811.45 1107.01
    tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] HCK Divided Squared 28896.2 36767 1.27238
    303 60s ribosomal protein l35. [swissprot;acc:p42766] RPL35 Ranked 242.333 266.999 1.10179
    crk-like protein. [swissprot;acc:p46109] CRKL Squared 28896.2 36767 1.27238
    cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] PSCD2 Rooted 203.673 182.638 1.11517
    melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] no value Subtracted Ranked 88.2482 110.265 22.0168
    peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [swissprot;acc:q9unp9] PPIE Squared 51527.6 43689.1 7838.5
    ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] RRM2 Rooted 62.9007 70.8854 7.9847
    serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] PPP1CC Divided Measured 22268.8 18560.4 1.1998
    spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] TXNL4A Subtracted 4723.53 5828.46 1104.93
    304 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] no value Divided Ranked 242.339 266.986 1.1017
    coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [swissprot;acc:q9p299] COPZ2 Subtracted Squared 51527.6 43689.1 7838.5
    cytohesin 4. [swissprot;acc:q9uia0] PSCD4 Divided Rooted 203.673 182.638 1.11517
    melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] MAGEA11 Subtracted Ranked 88.2482 110.265 22.0168
    polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] POLI Measured 5221.28 6314.35 1093.07
    pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] PRPF31 Divided 4855.46 5824.52 1.19958
    proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] ABL1 Squared 28896.2 36767 1.27238
    splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] SF4 Subtracted Rooted 53.6107 61.5862 7.9755
    305 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] no value 75.6323 67.6572 7.9751
    cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] PSCD3 Divided 203.673 182.638 1.11517
    melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] MAGEA2B Subtracted Ranked 88.2482 110.265 22.0168
    mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] MRPL2 Divided 242.339 266.986 1.1017
    neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] WASL Subtracted Squared 28918.3 36746 7827.7
    odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] OSR1 Divided Measured 3856.29 4624.15 1.19912
    paxillin. [swissprot;acc:p49023] PXN Subtracted 5221.28 6314.35 1093.07
    proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] FYN Divided Squared 28896.2 36767 1.27238
    306 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] no value Ranked 242.153 266.673 1.10126
    hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Subtracted 88.2482 110.265 22.0168
    kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] KYNU Measured 8430.03 9518.11 1088.08
    ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926] ODC1 Squared 33044.9 40781.4 7736.5
    pnas-18. [sptrembl;acc:q9bzu3] no value Divided 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] FGR Squared 28896.2 36767 1.27238
    rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] RBM39 Rooted 56.3935 62.8817 1.11505
    serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] PPP1CC Subtracted 127.967 120.003 7.964
    307 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] AGPAT2 Measured 7556.75 8636.87 1080.12
    aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763] AASS Squared 33010.8 40732.2 7721.4
    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] GRAP2 Divided 28896.4 36766.8 1.27237
    melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] MAGEA6 Subtracted Ranked 88.2482 110.265 22.0168
    neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] WASL Rooted 66.0989 74.0609 7.962
    serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] SRR Divided Ranked 242.153 266.673 1.10126
    t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] CCT3 Measured 12365.2 14824.9 1.19892
    transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] SIN3A Rooted 50.4687 45.2733 1.11476
    308 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] AGPAT3 Squared 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/