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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 108 to 157 of 502 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 0
    Rank
    		Hugo
    		description
    		red
    		green
    		network_comparison
    108 PYCR1 pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] 10585.3 12769.1 1.2063
    109 CSMD1 dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2] 14466.8 12031.7 1.20239
    110 TOP2B dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] 12584.5 10470.6 1.20189
    111 no value protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031] 9940.69 11929 1.20002
    112 40s ribosomal protein s26. [swissprot;acc:p02383] 14269.7 17098 1.1982
    113 DVL1 segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] 5673.33 6797.56 1.19816
    114 no value bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] 8871.11 10603.2 1.19525
    115 spir-2 protein (fragment). [sptrembl;acc:q8wwl2] 18662.8 15627 1.19427
    116 MTX1 metaxin 1. [swissprot;acc:q13505] 13761.3 16422.1 1.19335
    117 no value basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811] 11545 13771.5 1.19285
    118 AQP2 aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] 12049 14370.7 1.19269
    119 no value mesoderm induction early response 1. [refseq;acc:nm_020948] 3609 4302.5 1.19216
    120 presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] 5797 4873 1.18962
    121 ZNF232 zinc finger protein 232. [swissprot;acc:q9uny5] 11523.7 13686.9 1.18772
    122 ZNF24 zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028] 11523 13685.4 1.18766
    123 ZNF215 zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58] 11522.8 13684.9 1.18764
    124 no value zinc finger imprinted 2. [swissprot;acc:q9nzv7] 11520.7 13680.4 1.18746
    125 PIK3C2B phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750] 22038 18578 1.18624
    126 no value ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] 9722.71 11493.8 1.18216
    127 PDSS1 trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] 9411.34 11119.7 1.18152
    128 no value 60s ribosomal protein l39. [swissprot;acc:p02404] 11564.4 9794.29 1.18073
    129 isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] 14222.5 12058.6 1.17945
    130 enigma protein; lim domain protein. [refseq;acc:nm_005451] 14476.2 17069.5 1.17914
    131 MLH1 dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] 8375.43 9873.58 1.17887
    132 no value rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] 19048 22389 1.1754
    133 alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] 6814 8009 1.17537
    134 CYP4F8 cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] 12314.9 10489.3 1.17404
    135 CYP4F2 cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329]
    136 CYP4F12 cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] 12335.3 10506.8 1.17403
    137 CYP4F11 cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] 12328.5 10501
    138 CYP4X1 likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] 12384.7 10549.4 1.17397
    139 CRYAA alpha crystallin a chain. [swissprot;acc:p02489] 16372.4 13972.2 1.17178
    140 no value mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] 16411.9 14027.1 1.17001
    141 ATP2C2 probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] 7690.02 8991.19 1.1692
    142 CACNG5 voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] 8214.41 7026.41 1.16908
    143 no value dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959] 11124.8 13005.3 1.16904
    144 dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325] 11123.4 13000.1 1.16872
    145 SRI sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] 7955.61 6817.49 1.16694
    146 COPB2 coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] 12577.8 14662.1 1.16571
    147 no value 60s ribosomal protein l7. [swissprot;acc:p18124] 11080.3 9505.89 1.16562
    148 SPTBN5 spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6] 6755.71 7863.63 1.164
    149 no value block 23. [sptrembl;acc:q8nhw5] 11469.3 13334.8 1.16265
    150 ZFPL1 zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782] 8730 7516 1.16152
    151 no value u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] 7502.08 6461.83 1.16098
    152 similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9] 11438 13277.1 1.16079
    153 TUBG1 tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258] 7879.3 6789.92 1.16044
    154 no value myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] 10883 12622.8 1.15986
    155 REEP6 polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393] 12759.4 11028.8 1.15692
    156 TUB tubby protein homolog. [swissprot;acc:p50607] 12303.7 10641.7 1.15618
    157 no value transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084] 18079 15652 1.15506

    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/