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 Hugo Value Type description Network Comparison Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 1951 to 2000 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		description
    		Interaction Map
    		red
    		network_comparison
    		green
    244 RRAGB Rooted ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Low confidence 86.9838 1.05723 91.9621
    TUBA1A Squared tubulin alpha-1 chain (alpha-tubulin 1). [swissprot;acc:p05209] 46639.3 1.09401 42631.6
    245 ATP2C2 Rooted probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] 65.9913 1.05715 69.763
    GBE1 Squared 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] High confidence 8875.01 1.31131 6768.05
    HOMER1 Measured homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] 4251.65 1.22595 5212.33
    HOXB5 Ranked homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Low confidence 162.755 1.04682 155.476
    MYO5C Rooted myosin vc (myosin 5c). [swissprot;acc:q9nqx4] High confidence 146.94 1.13683 167.046
    SNRPD3 Ranked small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] 226.109 1.11751 202.333
    TP63 Measured tumor protein p73-like; tumor protein 63 kda with strong homology to p53; tumor protein p63. [refseq;acc:nm_003722] Low confidence 8509.99 1.06313 9047.26
    TUBA1C Squared tubulin alpha-6 chain (alpha-tubulin 6). [swissprot;acc:q9bqe3] 46635.1 1.0937 42639.6
    246 no value Rooted myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] High confidence 146.94 1.13683 167.046
    EIF4G3 Ranked eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] 237.312 1.11748 212.363
    HOMER3 Measured homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] 4252.66 1.22583 5213.05
    HOXA5 Ranked homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Low confidence 162.755 1.04682 155.476
    JAG2 Rooted jagged 2 precursor (jagged2) (hj2). [swissprot;acc:q9y219] 66.0188 1.05708 69.7871
    PYGB Squared glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] High confidence 8875.01 1.31131 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 51235.5 1.09335 46861.2
    TP73 Measured tumor protein p73 (p53-like transcription factor) (p53-related protein). [swissprot;acc:o15350] 8509.76 1.06312 9046.87
    247 no value Ranked homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 162.755 1.04682 155.476
    rna-binding protein. [refseq;acc:nm_019027] High confidence 237.302 1.11719 212.41
    DDX56 Rooted probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] 47.3621 1.13668 53.8355
    MEF2D myocyte-specific enhancer factor 2d. [swissprot;acc:q14814] Low confidence 66.0196 1.05708 69.7878
    PYGL Squared glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] High confidence 8875.01 1.31131 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 51235.5 1.09335 46861.2
    TP53 Measured cellular tumor antigen p53 (tumor suppressor p53) (phosphoprotein p53) (antigen ny-co-13). [swissprot;acc:p04637] 8509.51 1.0631 9046.45
    WAS wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] High confidence 6416.68 1.22574 7865.15
    248 no value Ranked apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] 237.302 1.11719 212.41
    CRK Measured proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] 6417.18 1.22477 7859.6
    HSD17B14 Ranked retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Low confidence 162.755 1.04682 155.476
    JAG1 Rooted jagged 1 precursor (jagged1) (hj1). [swissprot;acc:p78504] 66.0195 1.05708 69.7877
    LSM5 u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] High confidence 56.0466 1.13264 63.4808
    MYO15A Squared myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] 8875.01 1.31131 6768.05
    PDCD4 programmed cell death 4 isoform 1; programmed cell death 4; nuclear antigen h731. [refseq;acc:nm_014456] Low confidence 50352.9 1.09312 46063.3
    RABEP1 Measured rabaptin, rab gtpase binding effector protein 1; rabaptin-5; neurocrescin. [refseq;acc:nm_004703] 7615.71 1.06302 8095.68
    249 ABL2 tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] High confidence 6417.18 1.22477 7859.59
    ATG3 apg3p; pc3-96 protein. [refseq;acc:nm_022488] Low confidence 10547.4 1.06276 9924.56
    BRF1 Rooted 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 55.5965 1.13199 62.9349
    DUOX1 Ranked dual oxidase 1 precursor; nadph thyroid oxidase 1; flavoprotein nadph oxidase; nicotinamide adenine dinucleotide phosphate oxidase. [refseq;acc:nm_017434] Low confidence 210.487 1.0468 201.076
    MEF2C Rooted myocyte-specific enhancer factor 2c. [swissprot;acc:q06413] 66.0195 1.05708 69.7877
    PYGM Squared glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] High confidence 8875.01 1.31131 6768.05
    RGL1 ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Low confidence 49409.1 1.09241 45229.3
    SYNCRIP Ranked ns1-associated protein 1. [refseq;acc:nm_006372] High confidence 237.302 1.11719 212.41
    250 no value Measured proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] 6417.18 1.22477 7859.6
    CTBP2 Squared c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] 69201.8 1.30536 53013.4
    DGAT1 Ranked diacylglycerol o-acyltransferase 1 (ec 2.3.1.20) (diglyceride acyltransferase) (acat related gene product 1). [swissprot;acc:o75907] Low confidence 210.443 1.04671 201.051
    HNRNPR heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] High confidence 237.302 1.11719 212.41
    MEF2A Rooted myocyte-specific enhancer factor 2a (serum response factor-like protein 1). [swissprot;acc:q02078] Low confidence 66.0188 1.05708 69.7871
    NOLA1 nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] High confidence 55.5965 1.13199 62.9349
    RAB11FIP4 Squared rab11-family interacting protein 4. [refseq;acc:nm_032932] Low confidence 34469.6 1.09213 37645.4
    SLC7A8 Measured large neutral amino acids transporter small subunit 2 (l-type amino acid transporter 2) (hlat2). [swissprot;acc:q9uhi5] 6975.98 1.06261 7412.76

    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/