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 Network Comparison Type description Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2380 to 2429 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		Network Comparison Type
    		description
    		red
    		green
    		network_comparison
    298 CAPN2 Ranked Divided 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
    CUTL2 Squared Subtracted homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] 28901.4 36762.1 7860.7
    E2F1 Ranked transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] 266.421 244.236 22.185
    FDX1 Measured adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] 8268.19 9405.85 1137.66
    SART1 Rooted Divided 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
    COPB2 Squared Subtracted coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] 51527.6 43689.1 7838.5
    CRK Divided 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
    E2F2 Ranked Subtracted transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] 266.421 244.236 22.185
    GRAP2 Rooted 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] 66.1063 74.1068 8.0005
    MTX1 Measured metaxin 1. [swissprot;acc:q13505] 9327.58 10442.2 1114.62
    300 ABL2 Squared Divided tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] 28896.2 36767 1.27238
    BRF1 Measured Subtracted transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] 4446.72 5553.79 1107.07
    COPG Squared coatomer gamma subunit (gamma-coat protein) (gamma-cop). [swissprot;acc:q9y678] 51527.6 43689.1 7838.5
    DDX56 Ranked probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] 257.017 234.945 22.072
    EIF5 Rooted eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] 43.5479 51.5473 7.9994
    MKI67IP Divided 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
    COPZ1 Squared Subtracted coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [swissprot;acc:q9y3c3] 51527.6 43689.1 7838.5
    CUTL1 Rooted ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] 66.1048 74.0977 7.9929
    MAGED4 Ranked melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] 88.2482 110.265 22.0168
    NOLA1 Measured nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] 4446.72 5553.79 1107.07
    302 ARCN1 Squared coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [swissprot;acc:p48444] 51527.6 43689.1 7838.5
    CUTL2 Rooted homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] 66.1046 74.0964 7.9918
    HCK Squared Divided tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] 28896.2 36767 1.27238
    MAGEE2 Ranked Subtracted hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] 88.2482 110.265 22.0168
    PLDN Measured Divided 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
    RRM2 Measured Subtracted ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] 6704.44 7811.45 1107.01
    303 no value Ranked melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] 88.2482 110.265 22.0168
    CRKL Squared Divided crk-like protein. [swissprot;acc:p46109] 28896.2 36767 1.27238
    PPIE Subtracted peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [swissprot;acc:q9unp9] 51527.6 43689.1 7838.5
    PPP1CC Measured Divided 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
    RRM2 Rooted Subtracted ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] 62.9007 70.8854 7.9847
    TXNL4A Measured spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] 4723.53 5828.46 1104.93
    304 no value Ranked Divided 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
    COPZ2 Subtracted coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [swissprot;acc:q9p299] 51527.6 43689.1 7838.5
    MAGEA11 Ranked melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] 88.2482 110.265 22.0168
    POLI Measured polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] 5221.28 6314.35 1093.07

    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/