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 183 to 232 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    description
    red
    green
    network_comparison
    183 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] 228.306 198.011 1.153
    184 odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] 274.027 237.79 1.15239
    185 adiponectin receptor 2. [refseq;acc:nm_024551] 281.582 246.371 1.14292
    186 filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] 226.582 198.444 1.14179
    187 rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316]
    188 protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873]
    189 protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22]
    190 u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621]
    191 filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]
    192 musashi 2 isoform a. [refseq;acc:nm_138962] 227.491 199.458 1.14055
    193 musashi 1. [refseq;acc:nm_002442]
    194 nuclear protein ukp68. [refseq;acc:nm_024824]
    195 huntingtin interacting protein c. [refseq;acc:nm_012272] 227.971 200.417 1.13748
    196 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] 263.215 231.407 1.13745
    197 forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]
    198 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] 263.191 231.394 1.13741
    199 palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] 242.735 276.059 1.13729
    200 egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] 242.718 276.018 1.1372
    201 splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] 240.133 211.382 1.13601
    202 short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] 201.478 228.784 1.13553
    203 ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] 201.515 228.752 1.13516
    204 short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62]
    205 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] 228.1 200.968 1.13501
    206 luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] 228.085 201.006 1.13472
    207 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] 285.684 252.234 1.13261
    208 s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991]
    209 f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315]
    210 cullin homolog 2 (cul-2). [swissprot;acc:q13617]
    211 presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768]
    212 cullin homolog 1 (cul-1). [swissprot;acc:q13616]
    213 pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] 210.693 186.95 1.127
    214 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] 191.644 170.192 1.12605
    215 myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] 112 126 1.125
    216 myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]
    217 myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535]
    218 myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2]
    219 myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055]
    220 myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]
    221 myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]
    222 dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430]
    223 myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]
    224 oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] 185.969 165.623 1.12285
    225 small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] 226.471 201.769 1.12243
    226 cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] 239.991 269.238 1.12187
    227 thrombospondin 3 precursor. [swissprot;acc:p49746] 239.99 269.234 1.12186
    228 sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] 226.411 202.088 1.12036
    229 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 226.401 202.094 1.12028
    230 cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] 239.35 267.915 1.11934
    231 likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] 239.336 267.881 1.11927
    232 smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] 267.879 1.11926

    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/