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 Value Type Network Comparison Type Interaction Map red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 3058 to 3107 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		Interaction Map
    		red
    		green
    		network_comparison
    383 apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] no value Squared High confidence 15043.7 18560.1 1.23375
    hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631] Measured 4533.74 5279.4 1.16447
    max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] MXD4 Ranked Low confidence 205.921 198.554 1.0371
    nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [swissprot;acc:p52594] HRB Squared 48780.6 45597.1 1.06982
    protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0] DCHS1 Measured 7115.47 7496.56 1.05356
    rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] RBM39 Ranked High confidence 237.862 217.739 1.09242
    similar to atp/gtp-binding protein. [sptrembl;acc:q8nem8] AGBL3 Rooted Low confidence 80.2902 84.1622 1.04823
    384 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] no value High confidence 50.7723 46.0607 1.10229
    cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073] Measured 4533.74 5279.4 1.16447
    flavin reductase (ec 1.5.1.30) (fr) (nadph-dependent diaphorase) (nadph-flavin reductase) (flr) (biliverdin reductase b) (ec 1.3.1.24) (bvr-b) (biliverdin-ix beta-reductase) (green heme binding protein) (ghbp). [swissprot;acc:p30043] BLVRB Squared Low confidence 44685.1 41772 1.06974
    iroquois-class homeodomain protein irx-3 (iroquois homeobox protein 3) (fragment). [swissprot;acc:p78415] IRX3 Measured 8964.52 9443.02 1.05338
    max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] RAB24 Ranked 205.918 198.554 1.03709
    ns1-associated protein 1. [refseq;acc:nm_006372] SYNCRIP Squared High confidence 15043.7 18560.1 1.23375
    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] E2F1 Ranked 266.421 244.236 1.09083
    trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] TRMU Rooted Low confidence 80.2902 84.1622 1.04823
    385 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] BCCIP High confidence 50.7723 46.0607 1.10229
    heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] HNRNPR Squared 15043.7 18560.1 1.23375
    iroquois-class homeodomain protein irx-1 (iroquois homeobox protein 1) (fragment). [swissprot;acc:p78414] IRX1 Measured Low confidence 8964.32 9442.82 1.05338
    pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222] PSIP1 High confidence 4533.74 5279.4 1.16447
    ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] SORBS1 Rooted Low confidence 69.7907 73.1569 1.04823
    protein c6orf55 (dopamine responsive protein drg-1) (my012 protein) (hspc228). [swissprot;acc:q9np79] VTA1 Squared 44685.1 41772 1.06974
    small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] SNRPD3 Ranked 201.176 193.984 1.03708
    transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] E2F2 High confidence 266.421 244.236 1.09083
    386 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] RPS14 242.238 264.11 1.09029
    60s ribosomal protein l8. [swissprot;acc:p25120] RPL8 Measured 4533.74 5279.4 1.16447
    bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] no value Squared Low confidence 49627.5 46392.9 1.06972
    ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] CUTL1 Measured 8159.45 8594.89 1.05337
    dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] POLE4 Ranked 205.821 198.494 1.03691
    monocarboxylate transporter 6 (mct 6) (mct 5). [swissprot;acc:o15375] SLC16A5 Rooted 82.9974 86.996 1.04818
    protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] EIF1B High confidence 50.0513 45.4124 1.10215
    scratch; scratch 1. [refseq;acc:nm_031309] no value Squared 40388.9 49827.5 1.23369
    387 40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] Ranked 242.238 264.11 1.09029
    60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] Rooted 50.3345 45.6718 1.10209
    eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] EIF4G1 Squared 15053 18568 1.23351
    hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858] HDGF Measured 4533.74 5279.4 1.16447
    iroquois-class homeodomain protein irx-5 (iroquois homeobox protein 5) (irx-2a). [swissprot;acc:p78411] IRX5 Low confidence 8966.17 9444.64 1.05336
    ny-ren-24 antigen (fragment). [sptrembl;acc:q9y5a4] C19orf29 Rooted 68.4471 71.745 1.04818
    protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [refseq;acc:nm_002480] PPP1R12A Squared 51030.6 54586.8 1.06969
    serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] HTRA1 Ranked 200.057 192.938 1.0369
    388 dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] no value Squared High confidence 40315.7 49716.4 1.23318
    hrd1 protein isoform a; synoviolin1. [refseq;acc:nm_032431] SYVN1 Low confidence 48960.5 45772 1.06966
    iroquois-class homeodomain protein irx-2 (iroquois homeobox protein 2) (fragment). [swissprot;acc:q9bzi1] IRX2 Measured 8966.8 9445.26 1.05336
    monocarboxylate transporter 1 (mct 1). [swissprot;acc:p53985] SLC16A1 Rooted 82.9808 86.9781 1.04817
    probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] HTRA3 Ranked 200.049 192.942 1.03683
    pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] HDGFL1 Measured High confidence 4533.74 5279.4 1.16447
    serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] SRR Rooted 50.3345 45.6718 1.10209
    small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] no value Ranked 227.575 208.756 1.09015
    389 60s ribosomal protein l34. [swissprot;acc:p49207] RPL34 Rooted 50.3345 45.6718 1.10209
    arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320] RARS2 Squared 31819.7 39222.2 1.23264
    homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] CUTL2 Measured Low confidence 8159.97 8595.12 1.05333

    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/