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 [...,...].
    Rank Gene Network Comparison Type Value Type Hugo description Interaction Map network_comparison Filtered red green
    Results: HTML CSV LaTeX Showing element 1958 to 2007 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Value Type
    		Hugo
    		description
    		Interaction Map
    		network_comparison
    		red
    		green
    245 Squared TUBA1C tubulin alpha-6 chain (alpha-tubulin 6). [swissprot;acc:q9bqe3] Low confidence 1.0937 46635.1 42639.6
    Rooted ATP2C2 probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] 1.05715 65.9913 69.763
    MYO5C myosin vc (myosin 5c). [swissprot;acc:q9nqx4] High confidence 1.13683 146.94 167.046
    246 Measured HOMER3 homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] 1.22583 4252.66 5213.05
    TP73 tumor protein p73 (p53-like transcription factor) (p53-related protein). [swissprot;acc:o15350] Low confidence 1.06312 8509.76 9046.87
    Ranked EIF4G3 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] High confidence 1.11748 237.312 212.363
    HOXA5 homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Low confidence 1.04682 162.755 155.476
    Squared PYGB glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] High confidence 1.31131 8875.01 6768.05
    SLC2A6 solute carrier family 2, facilitated glucose transporter, member 6 (glucose transporter type 6) (glucose transporter type 9). [swissprot;acc:q9ugq3] Low confidence 1.09335 51235.5 46861.2
    Rooted no value myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] High confidence 1.13683 146.94 167.046
    JAG2 jagged 2 precursor (jagged2) (hj2). [swissprot;acc:q9y219] Low confidence 1.05708 66.0188 69.7871
    247 Measured TP53 cellular tumor antigen p53 (tumor suppressor p53) (phosphoprotein p53) (antigen ny-co-13). [swissprot;acc:p04637] 1.0631 8509.51 9046.45
    WAS wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] High confidence 1.22574 6416.68 7865.15
    Ranked no value homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Low confidence 1.04682 162.755 155.476
    rna-binding protein. [refseq;acc:nm_019027] High confidence 1.11719 237.302 212.41
    Squared PYGL glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 1.31131 8875.01 6768.05
    SLC2A8 solute carrier family 2, facilitated glucose transporter, member 8 (glucose transporter type 8) (glucose transporter type x1). [swissprot;acc:q9ny64] Low confidence 1.09335 51235.5 46861.2
    Rooted DDX56 probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] High confidence 1.13668 47.3621 53.8355
    MEF2D myocyte-specific enhancer factor 2d. [swissprot;acc:q14814] Low confidence 1.05708 66.0196 69.7878
    248 Measured CRK proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] High confidence 1.22477 6417.18 7859.6
    RABEP1 rabaptin, rab gtpase binding effector protein 1; rabaptin-5; neurocrescin. [refseq;acc:nm_004703] Low confidence 1.06302 7615.71 8095.68
    Ranked no value apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] High confidence 1.11719 237.302 212.41
    HSD17B14 retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Low confidence 1.04682 162.755 155.476
    Squared MYO15A myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] High confidence 1.31131 8875.01 6768.05
    PDCD4 programmed cell death 4 isoform 1; programmed cell death 4; nuclear antigen h731. [refseq;acc:nm_014456] Low confidence 1.09312 50352.9 46063.3
    Rooted JAG1 jagged 1 precursor (jagged1) (hj1). [swissprot;acc:p78504] 1.05708 66.0195 69.7877
    LSM5 u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] High confidence 1.13264 56.0466 63.4808
    249 Measured ABL2 tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] 1.22477 6417.18 7859.59
    ATG3 apg3p; pc3-96 protein. [refseq;acc:nm_022488] Low confidence 1.06276 10547.4 9924.56
    Ranked DUOX1 dual oxidase 1 precursor; nadph thyroid oxidase 1; flavoprotein nadph oxidase; nicotinamide adenine dinucleotide phosphate oxidase. [refseq;acc:nm_017434] 1.0468 210.487 201.076
    SYNCRIP ns1-associated protein 1. [refseq;acc:nm_006372] High confidence 1.11719 237.302 212.41
    Squared PYGM glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] 1.31131 8875.01 6768.05
    RGL1 ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Low confidence 1.09241 49409.1 45229.3
    Rooted BRF1 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] High confidence 1.13199 55.5965 62.9349
    MEF2C myocyte-specific enhancer factor 2c. [swissprot;acc:q06413] Low confidence 1.05708 66.0195 69.7877
    250 Measured no value proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] High confidence 1.22477 6417.18 7859.6
    SLC7A8 large neutral amino acids transporter small subunit 2 (l-type amino acid transporter 2) (hlat2). [swissprot;acc:q9uhi5] Low confidence 1.06261 6975.98 7412.76
    Ranked DGAT1 diacylglycerol o-acyltransferase 1 (ec 2.3.1.20) (diglyceride acyltransferase) (acat related gene product 1). [swissprot;acc:o75907] 1.04671 210.443 201.051
    HNRNPR heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] High confidence 1.11719 237.302 212.41
    Squared CTBP2 c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] 1.30536 69201.8 53013.4
    RAB11FIP4 rab11-family interacting protein 4. [refseq;acc:nm_032932] Low confidence 1.09213 34469.6 37645.4
    Rooted MEF2A myocyte-specific enhancer factor 2a (serum response factor-like protein 1). [swissprot;acc:q02078] 1.05708 66.0188 69.7871
    NOLA1 nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] High confidence 1.13199 55.5965 62.9349
    251 Measured HCK tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] 1.22477 6417.18 7859.6
    KYNU kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Low confidence 1.06221 8527.55 9058.09
    Ranked NOX5 nadph oxidase, ef hand calcium-binding domain 5. [refseq;acc:nm_024505] 1.04666 210.415 201.035
    SLC15A1 oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] High confidence 1.11707 186.172 166.661
    Squared BCL6B b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] 1.30521 69165.6 52992.1
    RAB11FIP3 eferin. [swissprot;acc:o75154] Low confidence 1.09213 34469.6 37645.4
    Rooted MAX max protein. [swissprot;acc:p25912] High confidence 1.13159 56.3054 63.7148

    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/