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 980 to 1029 of 66312 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Value Type
    		description
    		Hugo
    		Interaction Map
    		network_comparison
    		red
    		green
    123 Ranked segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] DVL3 Low confidence 1.06768 202.96 190.094
    Squared b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] BCL6B 1.14016 81989.8 71910.8
    protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] PPP1R2 High confidence 1.52896 192904 126167
    Rooted cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2] CTSZ Low confidence 1.07896 68.1979 73.5829
    nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] TIA1 High confidence 1.24375 54.6527 67.9743
    124 Measured melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] MAGEA8 Low confidence 1.0937 11285.3 10318.5
    microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] MAP1LC3B High confidence 1.33501 24255.7 18168.9
    Ranked high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] HMG20B 1.21519 208.52 171.595
    natural resistance-associated macrophage protein 2 (nramp 2) (divalent metal transporter 1) (dmt1). [swissprot;acc:p49281] SLC11A2 Low confidence 1.06742 224.763 210.566
    Squared b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182] BCL6 1.14016 81993.8 71914
    type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] PPP1R2P9 High confidence 1.52884 192779 126095
    Rooted mouse mammary turmor virus receptor homolog 1. [refseq;acc:nm_152832] FAM89B Low confidence 1.07715 63.5737 68.4785
    nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] TIAL1 High confidence 1.24304 54.6625 67.9477
    125 Measured melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] MAGEC1 Low confidence 1.0937 11285.3 10318.5
    microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] MAP1LC3A High confidence 1.33501 24255.7 18168.9
    Ranked b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] B9D1 Low confidence 1.0674 213.243 227.616
    high-mobility group 20a. [refseq;acc:nm_018200] HMG20A High confidence 1.21429 208.588 171.778
    Squared c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] CTBP2 Low confidence 1.13985 81761.4 71730.2
    ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] RRS1 High confidence 1.52616 189976 124480
    Rooted small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] SNRPD1 1.23921 54.8203 67.934
    sperm associated antigen 7. [refseq;acc:nm_004890] SPAG7 Low confidence 1.0766 132.137 122.736
    126 Measured cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] ATG4B High confidence 1.33499 24250 18164.9
    melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] MAGEA4 Low confidence 1.0937 11285.3 10318.5
    Ranked associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] STAMBPL1 High confidence 1.21277 94 114
    lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] LASS2 Low confidence 1.06707 191.688 179.639
    Squared rho guanine nucleotide exchange factor 5 (guanine nucleotide regulatory protein tim) (oncogene tim) (p60 tim) (transforming immortalized mammary oncogene). [swissprot;acc:q12774] ARHGEF5 1.13919 58231.9 51117.1
    serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] PPP1CA High confidence 1.52616 189976 124480
    Rooted adiponectin receptor 2. [refseq;acc:nm_024551] ADIPOR2 Low confidence 1.07613 66.1599 71.1967
    high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] HMG20B High confidence 1.23311 60.9342 75.1387
    127 Measured melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] no value Low confidence 1.0937 11285.3 10318.5
    transcription factor jun-d. [swissprot;acc:p17535] JUND High confidence 1.33436 5638.2 7523.39
    Ranked putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] CHMP2A 1.21277 94 114
    vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] VPS33B Low confidence 1.06705 203.678 190.88
    Squared cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] no value High confidence 1.51365 88432.6 58423.3
    monocarboxylate transporter 8 (mct 8) (x-linked pest-containing transporter) (mct 7). [swissprot;acc:p36021] SLC16A2 Low confidence 1.13908 63904 72791.6
    Rooted high-mobility group 20a. [refseq;acc:nm_018200] HMG20A High confidence 1.23236 60.9353 75.094
    vacuolar assembly protein vps41 homolog (s53). [swissprot;acc:p49754] VPS41 Low confidence 1.07532 70.0842 75.3627
    128 Measured luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] LUC7L2 High confidence 1.3341 4355.61 5810.82
    melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] MAGEA10 Low confidence 1.0937 11285.3 10318.5
    Ranked associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] STAMBP High confidence 1.21277 94 114
    striatin. [swissprot;acc:o43815] STRN Low confidence 1.06618 214.085 200.796
    Squared pnas-18. [sptrembl;acc:q9bzu3] no value High confidence 1.50952 87787.3 58155.8
    solute carrier family 16 (monocarboxylic acid transporters), member 10; t-type amino acid transporter 1. [refseq;acc:nm_018593] SLC16A10 Low confidence 1.13907 63903.1 72790.2
    Rooted malignant cell expression-enhanced gene/tumor progression-enhanc. [refseq;acc:nm_024298] LENG4 1.0739 64.4748 60.0381
    tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] TARDBP High confidence 1.23069 48.0515 39.0445
    129 Measured luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] LUC7L 1.33348 4358.13 5811.49
    melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] MAGEB4 Low confidence 1.0937 11285.3 10318.5
    Ranked goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4] COL4A3BP 1.06609 220.969 235.572
    neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] VPS24 High confidence 1.21277 94 114
    Squared pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] PCF11 1.50257 178263 118639

    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/