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 Interaction Map Hugo network_comparison Filtered red green
    Results: HTML CSV LaTeX Showing element 1925 to 1974 of 66312 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Value Type
    		description
    		Interaction Map
    		Hugo
    		network_comparison
    		red
    		green
    241 Squared atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] Low confidence ATP5F1 1.09465 52929.8 48353.2
    neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] High confidence CHRNA4 1.31573 42411.6 55802.1
    Rooted melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] MAGEB4 1.13758 137.446 120.823
    spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813] Low confidence no value 1.05748 72.5948 76.7678
    242 Measured glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] GNPDA1 1.06356 4585.58 4311.52
    max protein. [swissprot;acc:p25912] High confidence MAX 1.22943 4640.26 5704.87
    Ranked homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Low confidence HOXC5 1.04682 162.755 155.476
    j domain containing protein 1. [swissprot;acc:q9ukb3] High confidence DNAJC12 1.11785 227.357 254.15
    Squared neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] CHRNA3 1.31573 42411.6 55802.1
    tubulin alpha-8 chain (alpha-tubulin 8). [swissprot;acc:q9ny65] Low confidence no value 1.09454 46646.5 42617.6
    Rooted 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] High confidence MAGED2 1.13758 137.446 120.823
    splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Low confidence SF3B1 1.05744 71.0451 75.1259
    243 Measured dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804] DDX39 1.06338 7648.9 8133.69
    homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] High confidence HOMER2 1.22652 4246.95 5208.98
    Ranked homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Low confidence no value 1.04682 162.755 155.476
    sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] High confidence SNX13 1.11785 227.357 254.15
    Squared sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] SPHK2 1.31573 42411.6 55802.1
    valyl-trna synthetase 2 (ec 6.1.1.9) (valine--trna ligase 2) (valrs 2) (g7a). [swissprot;acc:p26640] Low confidence VARS 1.09426 51669.9 47219.1
    Rooted anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [refseq;acc:nm_014885] ANAPC10 1.05726 67.7543 71.6341
    trophinin. [swissprot;acc:q12816] High confidence TRO 1.13758 137.446 120.823
    244 Measured protein phosphatase 1, regulatory (inhibitor) subunit 12b isoform a; myosin phosphatase regulatory subunit; myosin phosphatase, target subunit 2. [refseq;acc:nm_002481] Low confidence PPP1R12B 1.06331 8759.92 9314.48
    ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] High confidence COQ7 1.22614 4250.14 5211.25
    Ranked ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] GSTO2 1.11785 227.357 254.15
    homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Low confidence HOXD4 1.04682 162.755 155.476
    Squared dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] High confidence NCBP2L 1.31245 14728.8 19330.8
    tubulin alpha-1 chain (alpha-tubulin 1). [swissprot;acc:p05209] Low confidence TUBA1A 1.09401 46639.3 42631.6
    Rooted myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] High confidence MYO5B 1.13683 146.94 167.046
    ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Low confidence RRAGB 1.05723 86.9838 91.9621
    245 Measured homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] High confidence HOMER1 1.22595 4251.65 5212.33
    tumor protein p73-like; tumor protein 63 kda with strong homology to p53; tumor protein p63. [refseq;acc:nm_003722] Low confidence TP63 1.06313 8509.99 9047.26
    Ranked homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] HOXB5 1.04682 162.755 155.476
    small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] High confidence SNRPD3 1.11751 226.109 202.333
    Squared 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] GBE1 1.31131 8875.01 6768.05
    tubulin alpha-6 chain (alpha-tubulin 6). [swissprot;acc:q9bqe3] Low confidence TUBA1C 1.0937 46635.1 42639.6
    Rooted myosin vc (myosin 5c). [swissprot;acc:q9nqx4] High confidence MYO5C 1.13683 146.94 167.046
    probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] Low confidence ATP2C2 1.05715 65.9913 69.763
    246 Measured homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] High confidence HOMER3 1.22583 4252.66 5213.05
    tumor protein p73 (p53-like transcription factor) (p53-related protein). [swissprot;acc:o15350] Low confidence TP73 1.06312 8509.76 9046.87
    Ranked eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] High confidence EIF4G3 1.11748 237.312 212.363
    homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Low confidence HOXA5 1.04682 162.755 155.476
    Squared glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] High confidence PYGB 1.31131 8875.01 6768.05
    solute carrier family 2, facilitated glucose transporter, member 6 (glucose transporter type 6) (glucose transporter type 9). [swissprot;acc:q9ugq3] Low confidence SLC2A6 1.09335 51235.5 46861.2
    Rooted jagged 2 precursor (jagged2) (hj2). [swissprot;acc:q9y219] JAG2 1.05708 66.0188 69.7871
    myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] High confidence no value 1.13683 146.94 167.046
    247 Measured cellular tumor antigen p53 (tumor suppressor p53) (phosphoprotein p53) (antigen ny-co-13). [swissprot;acc:p04637] Low confidence TP53 1.0631 8509.51 9046.45
    wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] High confidence WAS 1.22574 6416.68 7865.15
    Ranked homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Low confidence no value 1.04682 162.755 155.476
    rna-binding protein. [refseq;acc:nm_019027] High confidence 1.11719 237.302 212.41
    Squared glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] PYGL 1.31131 8875.01 6768.05
    solute carrier family 2, facilitated glucose transporter, member 8 (glucose transporter type 8) (glucose transporter type x1). [swissprot;acc:q9ny64] Low confidence SLC2A8 1.09335 51235.5 46861.2

    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/