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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2101 to 2150 of 14920 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Rank
    		description
    		Value Type
    		Filtered
    		red
    		green
    		network_comparison
    263 paxillin. [swissprot;acc:p49023] Rooted 1 59.4073 66.7002 1.12276
    ribosomal protein l10-like protein. [refseq;acc:nm_080746] Squared 0 2463.98 3102.52 1.25915
    sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] Measured 1843 1633 1.1286
    trs85 homolog. [swissprot;acc:q9y2l5] 1 24896.4 20431.7 1.21852
    264 60s ribosomal protein l12. [swissprot;acc:p30050] Squared 0 3686.65 4639.46 1.25845
    adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] 1 26157.6 20236.2 1.29261
    arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681] Ranked 0 10037.1 10935.1 1.08947
    cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] Measured 1 4987.58 4094.57 1.2181
    mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] Ranked 219.421 196.978 1.11394
    sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993] Measured 0 3336.48 2957.12 1.12829
    transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193] Rooted 11.0015 9.99917 1.10024
    wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] 1 66.1122 74.1438 1.12148
    265 40s ribosomal protein s29. [swissprot;acc:p30054] 0 26.1023 28.6733 1.0985
    60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] Squared 3687.69 4640.77 1.25845
    60s ribosomal protein l9. [swissprot;acc:p32969] Measured 1685.44 1894.01 1.12375
    glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488] Ranked 13653.8 14874 1.08937
    leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Squared 1 26157.6 20236.2 1.29261
    splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Ranked 225.217 202.459 1.11241
    u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] Rooted 56.031 62.8281 1.12131
    wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Measured 24806.9 20369.9 1.21782
    266 aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448] 0 1475.05 1312.91 1.1235
    cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] 1 24806.9 20369.9 1.21782
    dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] Squared 0 3687.33 4640.32 1.25845
    fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] 1 26157.6 20236.2 1.29261
    proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Rooted 66.1064 74.1074 1.12103
    transcription factor btf3 homolog 3. [swissprot;acc:q13892] Ranked 0 13483.3 14685.4 1.08915
    transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] Rooted 39.5626 36.099 1.09595
    transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] Ranked 1 241.07 267.88 1.11121
    267 density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583]
    leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] Squared 26157.6 20236.2 1.29261
    mitogen-activated protein kinase kinase kinase 5 (ec 2.7.1.-) (mapk/erk kinase kinase 5) (mek kinase 5) (mekk 5) (apoptosis signal- regulating kinase 1) (ask-1). [swissprot;acc:q99683] 0 181.291 144.478 1.2548
    ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] Measured 1 14021.4 11523 1.21682
    transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [swissprot;acc:o60675] Rooted 0 12.9585 14.1963 1.09552
    transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268] Ranked 8054.34 8772.02 1.0891
    tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Rooted 1 66.1064 74.1073 1.12103
    uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452] Measured 0 1475.05 1312.91 1.1235
    268 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] 1 24473.9 20127.8 1.21593
    eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] Ranked 271.016 244.167 1.10996
    far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [refseq;acc:nm_003902] Measured 0 604.529 538.094 1.12346
    laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] Squared 1 26157.6 20236.2 1.29261
    maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] Ranked 0 14257.4 13134.5 1.08549
    protein cgi-147. [swissprot;acc:q9y3e5] Squared 75129.2 94178 1.25355
    proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Rooted 1 66.1064 74.1074 1.12103
    transcription factor mafg (v-maf musculoaponeurotic fibrosarcoma oncogene homolog g) (hmaf). [swissprot;acc:o15525] 0 13.0249 14.2577 1.09465
    269 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] Measured 1217.92 1367.83 1.12309
    60s ribosomal protein l17 (l23). [swissprot;acc:p18621] Squared 4121.56 5159.2 1.25176
    cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] Ranked 1 241.373 267.352 1.10763
    ischemia/reperfusion inducible protein. [refseq;acc:nm_024640] 0 12463.5 11482.6 1.08542
    similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] Rooted 90.4079 98.9265 1.09422
    thymic stromal co-transporter. [refseq;acc:nm_033051] Squared 1 26157.6 20236.2 1.29261

    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
    - 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/