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 [...,...].
    Network Comparison Type Rank Gene Value Type description Hugo Interaction Map network_comparison Filtered red green
    Results: HTML CSV LaTeX Showing element 1325 to 1374 of 66312 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Value Type
    		description
    		Hugo
    		Interaction Map
    		network_comparison
    		red
    		green
    166 Squared homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] HOXA5 High confidence 1.40126 173408 242989
    transcription regulator protein bach2 (btb and cnc homolog 2). [swissprot;acc:q9byv9] BACH2 Low confidence 1.11844 37094.3 41487.9
    Rooted max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] MXD4 High confidence 1.17064 55.6495 65.1458
    ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [refseq;acc:nm_003968] UBE1C Low confidence 1.06689 72.46 77.3071
    167 Measured cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] PSCD2 1.08219 12376.5 11436.5
    melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] MAGEA4 High confidence 1.29736 23693.7 18263
    Ranked glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] GAD1 1.19058 209.299 249.187
    rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] RHOBTB2 Low confidence 1.05749 212.695 201.131
    Squared cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] ATF3 1.11468 23804.2 26534
    homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] no value High confidence 1.40126 173408 242989
    Rooted max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] RAB24 1.17062 55.65 65.1448
    rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] RHOBTB2 Low confidence 1.06594 68.0417 72.5283
    168 Measured 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] no value 1.08218 12376.4 11436.5
    melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] High confidence 1.29736 23693.7 18263
    Ranked gaba-a receptor-associated protein. [sptrembl;acc:q9by60] 1.18722 82.5916 98.0548
    proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591] FER Low confidence 1.05717 216.796 205.073
    Squared retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] HSD17B14 High confidence 1.40126 173408 242989
    ring finger protein 20. [refseq;acc:nm_019592] RNF20 Low confidence 1.11461 53551.4 48045.1
    Rooted beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] ARRB2 1.0657 72.4531 77.213
    small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] SNRPD3 High confidence 1.16895 56.3709 65.8949
    169 Measured cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] PSCD3 Low confidence 1.08217 12375.5 11435.8
    melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] MAGEA10 High confidence 1.29736 23693.7 18263
    Ranked 60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914] RPL29 Low confidence 1.05715 216.79 205.07
    apg3p; pc3-96 protein. [refseq;acc:nm_022488] ATG3 High confidence 1.18722 82.5916 98.0548
    Squared rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [swissprot;acc:p98175] RBM10 Low confidence 1.1146 67930.9 60946.6
    symplekin. [swissprot;acc:q92797] SYMPK High confidence 1.39979 124118 88668.8
    Rooted beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] ARRB1 Low confidence 1.06533 72.4389 77.1711
    cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] COPS3 High confidence 1.1671 62.762 53.7761
    170 Measured 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 Low confidence 1.08194 6131.26 6633.65
    melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] MAGEB4 High confidence 1.29736 23693.7 18263
    Ranked nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] TIA1 1.17894 227.199 192.715
    proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332] FES Low confidence 1.05714 216.783 205.066
    Squared cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] CTPS2 High confidence 1.39609 96730.5 69286.7
    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 Low confidence 1.11441 67882.7 60913.7
    Rooted b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] B9D1 High confidence 1.16499 53.4993 45.9227
    oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] SLC15A1 Low confidence 1.06479 70.7428 75.3259
    171 Measured 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 High confidence 1.29736 23693.7 18263
    sentrin-specific protease 8 (ec 3.4.22.-) (sentrin/sumo-specific protease senp8) (cysteine protease fksg8). [swissprot;acc:q96ld8] SENP8 Low confidence 1.08158 7012.61 7584.69
    Ranked forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] FOXP3 1.05683 219.889 208.064
    nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] TIAL1 High confidence 1.17829 227.202 192.823
    Squared ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] CTPS 1.39577 96602.7 69211.2
    multiple pdz domain protein. [refseq;acc:nm_003829] MPDZ Low confidence 1.11438 67876.4 60909.3
    Rooted hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] NFU1 1.06474 96.9641 103.242
    lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] LASS2 High confidence 1.16333 61.6639 71.7355
    172 Measured trophinin. [swissprot;acc:q12816] TRO 1.29736 23693.7 18263
    ubiquitin-like protein nedd8. [swissprot;acc:q15843] NEDD8 Low confidence 1.08158 7012.61 7584.69
    Ranked cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] TIPRL High confidence 1.17685 174.667 205.556
    f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] CAPZA1 Low confidence 1.0567 213.671 202.205
    Squared likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] CSTF2T High confidence 1.39331 121579 87259.3
    ww domain binding protein 11; npw38-binding protein npwbp; sh3 domain-binding protein snp70. [refseq;acc:nm_016312] WBP11 Low confidence 1.11437 67872.2 60906.5

    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/