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 [...,...].
    Gene Rank description Hugo Value Type Network Comparison Type Interaction Map red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 2682 to 2731 of 66312 in total
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		Network Comparison Type
    		Interaction Map
    		red
    		green
    		network_comparison
    168 proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591] FER Ranked Divided Low confidence 216.796 205.073 1.05717
    protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0] DCHS1 Subtracted 218.925 207.441 11.484
    retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] HSD17B14 Squared Divided High confidence 173408 242989 1.40126
    rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] REV1 Rooted Subtracted 55.6161 66.7332 11.1171
    ring finger protein 20. [refseq;acc:nm_019592] RNF20 Squared Divided Low confidence 53551.4 48045.1 1.11461
    septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] SEPT1 Rooted Subtracted 84.7416 89.3094 4.5678
    small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] SNRPD3 Divided High confidence 56.3709 65.8949 1.16895
    169 60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914] RPL29 Ranked Low confidence 216.79 205.07 1.05715
    apg3p; pc3-96 protein. [refseq;acc:nm_022488] ATG3 High confidence 82.5916 98.0548 1.18722
    beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] ARRB1 Rooted Low confidence 72.4389 77.1711 1.06533
    cop-coated vesicle membrane protein p24 precursor (p24a). [swissprot;acc:q15363] TMED2 Squared Subtracted 64485.5 70068.3 5582.8
    cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] COPS3 Rooted Divided High confidence 62.762 53.7761 1.1671
    cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] CDK2AP1 Ranked Subtracted 312 284 28
    cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] PSCD3 Measured Divided Low confidence 12375.5 11435.8 1.08217
    f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] CAPZA1 Ranked Subtracted 213.671 202.205 11.466
    formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] no value Measured High confidence 4245.52 5942.75 1697.23
    melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] MAGEA10 Divided 23693.7 18263 1.29736
    pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148] PASK Squared Subtracted 69165 52991.7 16173.3
    protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] PRMT1 Rooted 55.6161 66.7332 11.1171
    putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] no value Low confidence 69.4376 64.8818 4.5558
    rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [swissprot;acc:p98175] RBM10 Squared Divided 67930.9 60946.6 1.1146
    symplekin. [swissprot;acc:q92797] SYMPK High confidence 124118 88668.8 1.39979
    tho complex 3. [refseq;acc:nm_032361] no value Measured Subtracted Low confidence 7401.51 8028.16 626.65
    170 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] PRKAG2 Squared 54860.1 49344.1 5516
    amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] APBA1 Measured Divided 6131.26 6633.65 1.08194
    b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182] BCL6 Squared Subtracted High confidence 69165 52991.7 16173.3
    b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] B9D1 Rooted Divided 53.4993 45.9227 1.16499
    cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] CTPS2 Squared 96730.5 69286.7 1.39609
    huntingtin interacting protein c. [refseq;acc:nm_012272] PRPF40B Ranked Subtracted 227.971 200.417 27.554
    huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] no value Measured 4247.86 5941.88 1694.02
    inad-like protein isoform 3; pdz domain protein (drosophila inad-like); protein associated to tight junctions; pals1-associated tight junction protein; inactivation no after-potential d-like protein. [refseq;acc:nm_005799] INADL Squared Divided Low confidence 67882.7 60913.7 1.11441
    melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] MAGEB4 Measured High confidence 23693.7 18263 1.29736
    nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] TIA1 Ranked 227.199 192.715 1.17894
    oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] SLC15A1 Rooted Low confidence 70.7428 75.3259 1.06479
    protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] PRMT8 Subtracted High confidence 55.6161 66.7332 11.1171
    protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [refseq;acc:nm_002480] PPP1R12A Measured Low confidence 8973.23 9597.94 624.71
    proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332] FES Ranked Divided 216.783 205.066 1.05714
    striatin. [swissprot;acc:o43815] STRN Rooted Subtracted 66.4354 70.987 4.5516
    vacuolar assembly protein vps41 homolog (s53). [swissprot;acc:p49754] VPS41 Ranked 202.698 191.393 11.305
    171 bet3 homolog. [swissprot;acc:o43617] TRAPPC3 Measured 8749.42 9372.33 622.91
    ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] CTPS Squared Divided High confidence 96602.7 69211.2 1.39577
    cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] ATG4B Rooted Subtracted Low confidence 98.0366 93.4864 4.5502
    defender against cell death 1 (dad-1). [swissprot;acc:p46966] DAD1 Ranked 197.99 186.913 11.077
    dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] NCBP2L Measured High confidence 4117.67 5801.04 1683.37
    forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] FOXP3 Ranked Divided Low confidence 219.889 208.064 1.05683
    hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] NFU1 Rooted 96.9641 103.242 1.06474
    lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] LASS2 High confidence 61.6639 71.7355 1.16333
    melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] MAGED2 Measured 23693.7 18263 1.29736
    multiple pdz domain protein. [refseq;acc:nm_003829] MPDZ Squared Low confidence 67876.4 60909.3 1.11438
    nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] TIAL1 Ranked High confidence 227.202 192.823 1.17829

    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/