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 [...,...].
    description Rank Gene Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 2051 to 2100 of 3228 in total
    Value Type  : Measured
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		red
    		network_comparison
    		green
    polybromo 1. [refseq;acc:nm_018165] 2052 5634.8 1.05642 5952.7
    polyglutamine binding protein 1; nuclear protein containing ww domain 38 kd. [refseq;acc:nm_005710] 2579 4979.44 1.01849 5071.53
    polyhomeotic like 3; early development regulator 3; polyhomeotic 3. [refseq;acc:nm_024947] 2809 0.00001 1 0.00001
    polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] 283 5221.28 1.20935 6314.35
    polymerase (dna directed) sigma; topoisomerase-related function protein 4-1; polymerase (dna-directed) sigma. [refseq;acc:nm_006999] 765 4726.38 1.11268 5258.95
    polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467] 2583 3926.4 1.01776 3857.88
    polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468] 2630 3985.17 1.01446 3928.38
    polymerase delta-interacting protein 1; tnfaip1-like. [refseq;acc:nm_178863] 1156 5840.77 1.08819 6355.89
    polymyositis/scleroderma autoantigen 2 (autoantigen pm/scl 2) (polymyositis/scleroderma autoantigen 100 kda) (pm/scl-100) (p100 polymyositis-scleroderma overlap syndrome associated autoantigen). [swissprot;acc:q01780] 2531 6141.97 1.02428 6291.08
    polypeptide n-acetylgalactosaminyltransferase 2; udp-galnac transferase 2. [refseq;acc:nm_004481] 2097 6024.47 1.05512 6356.56
    polyposis locus protein 1 (tb2 protein). [swissprot;acc:q00765] 2611 6380.6 1.01498 6476.18
    polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393] 2613
    polypyrimidine tract binding protein 2; neural polypyrimidine tract binding protein; ptb-like protein. [refseq;acc:nm_021190] 2281 5783.73 1.04585 6048.91
    polypyrimidine tract-binding protein 1 (ptb) (heterogeneous nuclear ribonucleoprotein i) (hnrnp i) (57 kda rna-binding protein pptb-1). [swissprot;acc:p26599] 2293 5783.76 6048.94
    ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] 448 6259.3 1.14884 7190.91
    porphobilinogen deaminase (ec 4.3.1.8) (hydroxymethylbilane synthase) (hmbs) (pre-uroporphyrinogen synthase) (pbg-d). [swissprot;acc:p08397] 1202 4913.07 1.08648 5337.95
    possible global transcription activator snf2l1. [swissprot;acc:p28370] 2055 5634.8 1.05642 5952.7
    possible global transcription activator snf2l2 (snf2-alpha). [swissprot;acc:p51531] 2057
    possible global transcription activator snf2l4 (snf2-beta) (brg-1 protein) (mitotic growth and transcription activator) (brahma protein homolog 1). [swissprot;acc:p51532] 2054
    postsynaptic protein cript; hspc139 protein. [refseq;acc:nm_014171] 3034 0.00001 1 0.00001
    potassium channel modulatory factor 1; potassium channel modulatory factor; differentially expressed in branching tubulogenesis 91; zinc finger, zz domain containing 1. [refseq;acc:nm_020122] 1816 5633.44 1.06454 5997
    potassium channel tetramerisation domain containing 3; ny-ren-45 antigen. [refseq;acc:nm_016121] 2975 0.00001 1 0.00001
    potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] 139 2759.61 1.31442 2099.49
    potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470] 2188 6682.7 1.05022 7018.29
    potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389] 2176 6674.58 1.05114 7015.93
    potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459] 2196 6688.64 1.04954 7020.02
    potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] 91 2416.53 1.42082 1700.8
    potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] 88 2411.93 1.42259 1695.45
    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] 90 2414.77 1.4215 1698.75
    potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] 720 6593.17 1.117 7364.55
    potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] 716
    potential phospholipid-transporting atpase ih (ec 3.6.3.1) (atpase class i type 11a) (atpase is). [swissprot;acc:p98196] 1349 6153.36 1.07921 6640.77
    potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] 1453 5602.01 1.07659 6031.05
    pp1201 protein. [refseq;acc:nm_022152] 709 5317.78 1.11781 5944.25
    pp3111 protein. [refseq;acc:nm_022156] 1964 4374.32 1.05994 4126.96
    pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] 2559 5291.65 1.02002 5187.78
    pre-b-cell leukemia transcription factor 4. [refseq;acc:nm_025245] 2473 7765.3 1.03074 8004
    pre-b-cell leukemia transcription factor-1 (homeobox protein pbx1) (homeobox protein prl). [swissprot;acc:p40424] 2466
    pre-b-cell leukemia transcription factor-2 (homeobox protein pbx2) (g17 protein). [swissprot;acc:p40425] 2472
    pre-b-cell leukemia transcription factor-3 (homeobox protein pbx3). [swissprot;acc:p40426] 2467
    pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989] 554 14830.5 1.13641 13050.3
    pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] 331 20287.2 1.18751 17083.8
    pre-mrna cleavage factor i, 59 kda subunit. [refseq;acc:nm_024811] 1942 5805.06 1.06083 6158.16
    pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] 304 4855.46 1.19958 5824.52
    pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] 368 5082.66 1.17261 5959.99
    prefoldin subunit 1. [swissprot;acc:o60925] 1554 5875.75 1.07267 6302.76
    prefoldin subunit 2 (hspc231). [swissprot;acc:q9uhv9] 1073 5207.39 1.09214 5687.2
    prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] 1072
    prefoldin subunit 4 (protein c-1). [swissprot;acc:q9nqp4] 3130 0.00001 1 0.00001
    prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471] 911 4982.81 1.09996 5480.91

    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
    - 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/