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 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
    		Value Type
    		description
    		Hugo
    		Interaction Map
    		network_comparison
    		red
    		green
    244 Rooted myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] MYO5B High confidence 1.13683 146.94 167.046
    ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] RRAGB Low confidence 1.05723 86.9838 91.9621
    245 Measured homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] HOMER1 High confidence 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] TP63 Low confidence 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] SNRPD3 High confidence 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] TUBA1C Low confidence 1.0937 46635.1 42639.6
    Rooted myosin vc (myosin 5c). [swissprot;acc:q9nqx4] MYO5C High confidence 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
    246 Measured homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] HOMER3 High confidence 1.22583 4252.66 5213.05
    tumor protein p73 (p53-like transcription factor) (p53-related protein). [swissprot;acc:o15350] TP73 Low confidence 1.06312 8509.76 9046.87
    Ranked eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] EIF4G3 High confidence 1.11748 237.312 212.363
    homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] HOXA5 Low confidence 1.04682 162.755 155.476
    Squared glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] PYGB High confidence 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] SLC2A6 Low confidence 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] no value High confidence 1.13683 146.94 167.046
    247 Measured cellular tumor antigen p53 (tumor suppressor p53) (phosphoprotein p53) (antigen ny-co-13). [swissprot;acc:p04637] TP53 Low confidence 1.0631 8509.51 9046.45
    wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] WAS High confidence 1.22574 6416.68 7865.15
    Ranked homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] no value Low confidence 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] SLC2A8 Low confidence 1.09335 51235.5 46861.2
    Rooted myocyte-specific enhancer factor 2d. [swissprot;acc:q14814] 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
    248 Measured proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] CRK 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
    Ranked apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] no value High confidence 1.11719 237.302 212.41
    retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] HSD17B14 Low confidence 1.04682 162.755 155.476
    Squared myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] 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
    Rooted jagged 1 precursor (jagged1) (hj1). [swissprot;acc:p78504] JAG1 1.05708 66.0195 69.7877
    u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] LSM5 High confidence 1.13264 56.0466 63.4808
    249 Measured apg3p; pc3-96 protein. [refseq;acc:nm_022488] ATG3 Low confidence 1.06276 10547.4 9924.56
    tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] ABL2 High confidence 1.22477 6417.18 7859.59
    Ranked dual oxidase 1 precursor; nadph thyroid oxidase 1; flavoprotein nadph oxidase; nicotinamide adenine dinucleotide phosphate oxidase. [refseq;acc:nm_017434] DUOX1 Low confidence 1.0468 210.487 201.076
    ns1-associated protein 1. [refseq;acc:nm_006372] SYNCRIP High confidence 1.11719 237.302 212.41
    Squared glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] PYGM 1.31131 8875.01 6768.05
    ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] RGL1 Low confidence 1.09241 49409.1 45229.3
    Rooted myocyte-specific enhancer factor 2c. [swissprot;acc:q06413] MEF2C 1.05708 66.0195 69.7877
    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] BRF1 High confidence 1.13199 55.5965 62.9349
    250 Measured large neutral amino acids transporter small subunit 2 (l-type amino acid transporter 2) (hlat2). [swissprot;acc:q9uhi5] SLC7A8 Low confidence 1.06261 6975.98 7412.76
    proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] no value High confidence 1.22477 6417.18 7859.6
    Ranked diacylglycerol o-acyltransferase 1 (ec 2.3.1.20) (diglyceride acyltransferase) (acat related gene product 1). [swissprot;acc:o75907] 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
    Squared c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] CTBP2 1.30536 69201.8 53013.4
    rab11-family interacting protein 4. [refseq;acc:nm_032932] RAB11FIP4 Low confidence 1.09213 34469.6 37645.4
    Rooted myocyte-specific enhancer factor 2a (serum response factor-like protein 1). [swissprot;acc:q02078] 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

    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/