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 description Value Type Hugo Interaction Map Filtered network_comparison red green
    Results: HTML CSV LaTeX Showing element 1951 to 2000 of 66312 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		description
    		Value Type
    		Hugo
    		Interaction Map
    		network_comparison
    		red
    		green
    244 tubulin alpha-1 chain (alpha-tubulin 1). [swissprot;acc:p05209] Squared TUBA1A Low confidence 1.09401 46639.3 42631.6
    ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Measured COQ7 High confidence 1.22614 4250.14 5211.25
    245 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Squared GBE1 1.31131 8875.01 6768.05
    homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Ranked HOXB5 Low confidence 1.04682 162.755 155.476
    homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Measured HOMER1 High confidence 1.22595 4251.65 5212.33
    myosin vc (myosin 5c). [swissprot;acc:q9nqx4] Rooted MYO5C 1.13683 146.94 167.046
    probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] ATP2C2 Low confidence 1.05715 65.9913 69.763
    small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Ranked SNRPD3 High confidence 1.11751 226.109 202.333
    tubulin alpha-6 chain (alpha-tubulin 6). [swissprot;acc:q9bqe3] Squared TUBA1C Low confidence 1.0937 46635.1 42639.6
    tumor protein p73-like; tumor protein 63 kda with strong homology to p53; tumor protein p63. [refseq;acc:nm_003722] Measured TP63 1.06313 8509.99 9047.26
    246 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Ranked EIF4G3 High confidence 1.11748 237.312 212.363
    glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Squared PYGB 1.31131 8875.01 6768.05
    homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Ranked HOXA5 Low confidence 1.04682 162.755 155.476
    homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] Measured HOMER3 High confidence 1.22583 4252.66 5213.05
    jagged 2 precursor (jagged2) (hj2). [swissprot;acc:q9y219] Rooted JAG2 Low confidence 1.05708 66.0188 69.7871
    myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] no value High confidence 1.13683 146.94 167.046
    solute carrier family 2, facilitated glucose transporter, member 6 (glucose transporter type 6) (glucose transporter type 9). [swissprot;acc:q9ugq3] Squared SLC2A6 Low confidence 1.09335 51235.5 46861.2
    tumor protein p73 (p53-like transcription factor) (p53-related protein). [swissprot;acc:o15350] Measured TP73 1.06312 8509.76 9046.87
    247 cellular tumor antigen p53 (tumor suppressor p53) (phosphoprotein p53) (antigen ny-co-13). [swissprot;acc:p04637] TP53 1.0631 8509.51 9046.45
    glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Squared PYGL High confidence 1.31131 8875.01 6768.05
    homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Ranked no value Low confidence 1.04682 162.755 155.476
    myocyte-specific enhancer factor 2d. [swissprot;acc:q14814] Rooted MEF2D 1.05708 66.0196 69.7878
    probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] DDX56 High confidence 1.13668 47.3621 53.8355
    rna-binding protein. [refseq;acc:nm_019027] Ranked no value 1.11719 237.302 212.41
    solute carrier family 2, facilitated glucose transporter, member 8 (glucose transporter type 8) (glucose transporter type x1). [swissprot;acc:q9ny64] Squared SLC2A8 Low confidence 1.09335 51235.5 46861.2
    wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Measured WAS High confidence 1.22574 6416.68 7865.15
    248 apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Ranked no value 1.11719 237.302 212.41
    jagged 1 precursor (jagged1) (hj1). [swissprot;acc:p78504] Rooted JAG1 Low confidence 1.05708 66.0195 69.7877
    myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Squared MYO15A High confidence 1.31131 8875.01 6768.05
    programmed cell death 4 isoform 1; programmed cell death 4; nuclear antigen h731. [refseq;acc:nm_014456] PDCD4 Low confidence 1.09312 50352.9 46063.3
    proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Measured CRK High confidence 1.22477 6417.18 7859.6
    rabaptin, rab gtpase binding effector protein 1; rabaptin-5; neurocrescin. [refseq;acc:nm_004703] RABEP1 Low confidence 1.06302 7615.71 8095.68
    retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Ranked HSD17B14 1.04682 162.755 155.476
    u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Rooted LSM5 High confidence 1.13264 56.0466 63.4808
    249 apg3p; pc3-96 protein. [refseq;acc:nm_022488] Measured ATG3 Low confidence 1.06276 10547.4 9924.56
    dual oxidase 1 precursor; nadph thyroid oxidase 1; flavoprotein nadph oxidase; nicotinamide adenine dinucleotide phosphate oxidase. [refseq;acc:nm_017434] Ranked DUOX1 1.0468 210.487 201.076
    glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Squared PYGM High confidence 1.31131 8875.01 6768.05
    myocyte-specific enhancer factor 2c. [swissprot;acc:q06413] Rooted MEF2C Low confidence 1.05708 66.0195 69.7877
    ns1-associated protein 1. [refseq;acc:nm_006372] Ranked SYNCRIP High confidence 1.11719 237.302 212.41
    ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Squared RGL1 Low confidence 1.09241 49409.1 45229.3
    transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] Rooted BRF1 High confidence 1.13199 55.5965 62.9349
    tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Measured ABL2 1.22477 6417.18 7859.59
    250 c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] Squared CTBP2 1.30536 69201.8 53013.4
    diacylglycerol o-acyltransferase 1 (ec 2.3.1.20) (diglyceride acyltransferase) (acat related gene product 1). [swissprot;acc:o75907] Ranked DGAT1 Low confidence 1.04671 210.443 201.051
    heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] HNRNPR High confidence 1.11719 237.302 212.41
    large neutral amino acids transporter small subunit 2 (l-type amino acid transporter 2) (hlat2). [swissprot;acc:q9uhi5] Measured SLC7A8 Low confidence 1.06261 6975.98 7412.76
    myocyte-specific enhancer factor 2a (serum response factor-like protein 1). [swissprot;acc:q02078] Rooted MEF2A 1.05708 66.0188 69.7871
    nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] NOLA1 High confidence 1.13199 55.5965 62.9349
    proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Measured no value 1.22477 6417.18 7859.6
    rab11-family interacting protein 4. [refseq;acc:nm_032932] Squared RAB11FIP4 Low confidence 1.09213 34469.6 37645.4

    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/