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 Network Comparison Type red Value Type Interaction Map Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 958 to 1007 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		Value Type
    		Interaction Map
    		green
    		network_comparison
    120 potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] KCND2 269.278 Ranked High confidence 327.709 1.21699
    segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] DVL1 203.016 Low confidence 189.965 1.0687
    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 64.712 Rooted 69.8815 1.07988
    121 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] ALG1 43800.4 Squared 38358.3 1.14188
    cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] CTH 269.254 Ranked High confidence 327.655 1.2169
    homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] HOMER3 50.339 Rooted 62.9975 1.25147
    melanoma antigen, family b, 6. [refseq;acc:nm_173523] MAGEB6B 11285.3 Measured Low confidence 10318.5 1.0937
    segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] DVL2 203.007 Ranked 189.985 1.06854
    serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] PPP1CC 199594 Squared High confidence 130021 1.53509
    transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] E2F2 64.712 Rooted Low confidence 69.8815 1.07988
    transcription factor jun-b. [swissprot;acc:p17275] JUNB 5579.18 Measured High confidence 7488.4 1.3422
    122 c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] CTBP1 82257.5 Squared Low confidence 72122.5 1.14052
    cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] CSTF3 201896 High confidence 131906 1.53061
    high-mobility group 20a. [refseq;acc:nm_018200] HMG20A 5140.14 Measured 6893.53 1.34112
    melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] no value 11285.3 Low confidence 10318.5 1.0937
    nanos (fragment). [sptrembl;acc:q8wy41] 203.66 Ranked 217.479 1.06785
    potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] KCND3 269.248 High confidence 327.642 1.21688
    serine/threonine-protein kinase plk (ec 2.7.1.-) (plk-1) (serine- threonine protein kinase 13) (stpk13). [swissprot;acc:p53350] PLK1 68.1979 Rooted Low confidence 73.5829 1.07896
    transcription factor jun-d. [swissprot;acc:p17535] JUND 63.636 High confidence 79.6225 1.25122
    123 b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] BCL6B 81989.8 Squared Low confidence 71910.8 1.14016
    cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2] CTSZ 68.1979 Rooted 73.5829 1.07896
    cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] ATG4A 24260.3 Measured High confidence 18172.1 1.33503
    melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] MAGEA9 11285.3 Low confidence 10318.5 1.0937
    nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] TIA1 54.6527 Rooted High confidence 67.9743 1.24375
    potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] KCND1 269.23 Ranked 327.601 1.21681
    protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] PPP1R2 192904 Squared 126167 1.52896
    segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] DVL3 202.96 Ranked Low confidence 190.094 1.06768
    124 b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182] BCL6 81993.8 Squared 71914 1.14016
    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 208.52 Ranked High confidence 171.595 1.21519
    melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] MAGEA8 11285.3 Measured Low confidence 10318.5 1.0937
    microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] MAP1LC3B 24255.7 High confidence 18168.9 1.33501
    mouse mammary turmor virus receptor homolog 1. [refseq;acc:nm_152832] FAM89B 63.5737 Rooted Low confidence 68.4785 1.07715
    natural resistance-associated macrophage protein 2 (nramp 2) (divalent metal transporter 1) (dmt1). [swissprot;acc:p49281] SLC11A2 224.763 Ranked 210.566 1.06742
    nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] TIAL1 54.6625 Rooted High confidence 67.9477 1.24304
    type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] PPP1R2P9 192779 Squared 126095 1.52884
    125 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] B9D1 213.243 Ranked Low confidence 227.616 1.0674
    c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] CTBP2 81761.4 Squared 71730.2 1.13985
    high-mobility group 20a. [refseq;acc:nm_018200] HMG20A 208.588 Ranked High confidence 171.778 1.21429
    melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] MAGEC1 11285.3 Measured Low confidence 10318.5 1.0937
    microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] MAP1LC3A 24255.7 High confidence 18168.9 1.33501
    ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] RRS1 189976 Squared 124480 1.52616
    small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] SNRPD1 54.8203 Rooted 67.934 1.23921
    sperm associated antigen 7. [refseq;acc:nm_004890] SPAG7 132.137 Low confidence 122.736 1.0766
    126 adiponectin receptor 2. [refseq;acc:nm_024551] ADIPOR2 66.1599 71.1967 1.07613
    associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] STAMBPL1 94 Ranked High confidence 114 1.21277
    cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] ATG4B 24250 Measured 18164.9 1.33499
    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 60.9342 Rooted 75.1387 1.23311
    lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] LASS2 191.688 Ranked Low confidence 179.639 1.06707
    melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] MAGEA4 11285.3 Measured 10318.5 1.0937
    rho guanine nucleotide exchange factor 5 (guanine nucleotide regulatory protein tim) (oncogene tim) (p60 tim) (transforming immortalized mammary oncogene). [swissprot;acc:q12774] ARHGEF5 58231.9 Squared 51117.1 1.13919

    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/