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 Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2108 to 2157 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    2108 argininosuccinate lyase (ec 4.3.2.1) (arginosuccinase) (asal). [swissprot;acc:p04424] ASL 216.36 217.93 1.00726
    2109 ran-binding protein 2 (ranbp2) (nuclear pore complex protein nup358) (nucleoporin nup358) (358 kda nucleoporin) (p270). [swissprot;acc:p49792] RANBP2 219.032 217.47 1.00718
    2110 conserved oligomeric golgi complex component 6. [swissprot;acc:q9y2v7] COG6 211.099 209.607 1.00712
    2111 ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] no value 219.047 217.511 1.00706
    2112 dna-directed rna polymerases iii 12.5 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c11 subunit) (hsc11p) (hrpc11) (my010 protein). [swissprot;acc:q9y2y1] POLR3K 223.415 224.989 1.00705
    2113 ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] no value 219.055 217.533 1.007
    2114 triacylglycerol lipase, gastric precursor (ec 3.1.1.3) (gastric lipase) (gl). [swissprot;acc:p07098] LIPF 214.632 213.14
    2115 ba304i5.1 (novel lipase) (fragment). [sptrembl;acc:q96lg2] LIPM
    2116 lysosomal acid lipase/cholesteryl ester hydrolase precursor (ec 3.1.1.13) (lal) (acid cholesteryl ester hydrolase) (sterol esterase) (lipase a) (cholesteryl esterase). [swissprot;acc:p38571] LIPA
    2117 seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [swissprot;acc:q9np81] SARS2
    2118 seryl-trna synthetase (ec 6.1.1.11) (serine--trna ligase) (serrs). [swissprot;acc:p49591] SARS
    2119 potassium channel modulatory factor 1; potassium channel modulatory factor; differentially expressed in branching tubulogenesis 91; zinc finger, zz domain containing 1. [refseq;acc:nm_020122] KCMF1 221.248 222.788 1.00696
    2120 solute carrier family 23, member 1 (sodium-dependent vitamin c transporter 1) (hsvct1) (na(+)/l-ascorbic acid transporter 1) (yolk sac permease-like molecule 3). [swissprot;acc:q9uhi7] SLC23A1
    2121 heterogeneous nuclear ribonucleoprotein a3 (hnrnp a3) (d10s102). [swissprot;acc:p51991] HNRPA3
    2122 galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182] LGALS9 206.473 207.911
    2123 adp-ribosylation factor 4. [swissprot;acc:p18085] ARF4 221.248 222.788
    2124 fused toes homolog; likely ortholog of mouse fused toes. [refseq;acc:nm_022476] AKTIP
    2125 shc transforming protein. [swissprot;acc:p29353] SHC1
    2126 zinc finger protein 289, id1 regulated; likely ortholog of mouse zfp289. [refseq;acc:nm_032389] ZNF289
    2127 neuronal shc. [refseq;acc:nm_016848] SHC3
    2128 adp-ribosylation factor 1. [swissprot;acc:p32889] ARF1
    2129 heterogeneous nuclear ribonucleoprotein a1 (helix-destabilizing protein) (single-strand binding protein) (hnrnp core protein a1). [swissprot;acc:p09651] HNRNPA1
    2130 adp-ribosylation factor 3. [swissprot;acc:p16587] ARF3
    2131 gtp cyclohydrolase i (ec 3.5.4.16) (gtp-ch-i). [swissprot;acc:p30793] GCH1 226.277 227.851
    2132 protein sck (fragment). [swissprot;acc:p98077] SHC2 221.248 222.788
    2133 orphan nuclear receptor hmr (early response protein nak1) (tr3 orphan receptor). [swissprot;acc:p22736] NR4A1 207.74 206.305
    2134 heterogeneous nuclear ribonucleoproteins a2/b1 (hnrnp a2 / hnrnp b1). [swissprot;acc:p22626] HNRNPA2B1 221.248 222.788
    2135 nuclear hormone receptor nor-1 (neuron-derived orphan receptor 1) (mitogen induced nuclear orphan receptor). [swissprot;acc:q92570] NR4A3 207.743 206.308
    2136 ovarian carcinoma immunoreactive antigen. [refseq;acc:nm_017830] OCIAD1 221.248 222.788
    2137 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] ARFGAP3
    2138 solute carrier family 23, member 2 (sodium-dependent vitamin c transporter 2) (hsvct2) (na(+)/l-ascorbic acid transporter 2) (yolk sac permease-like molecule 2) (nucleobase transporter-like 1 protein). [swissprot;acc:q9ugh3] SLC23A2
    2139 dual specificity mitogen-activated protein kinase kinase 7 (ec 2.7.1.-) (map kinase kinase 7) (mapkk 7) (mapk/erk kinase 7) (jnk activating kinase 2) (c-jun n-terminal kinase kinase 2) (jnk kinase 2) (jnkk 2). [swissprot;acc:o14733] MAP2K7
    2140 cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] CSTF2 161.547 162.665 1.00692
    2141 orphan nuclear receptor nurr1 (immediate-early response protein not) (transcriptionally inducible nuclear receptor). [swissprot;acc:p43354] NR4A2 207.765 206.343 1.00689
    2142 protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [swissprot;acc:p11171] EPB41 206.443 207.864 1.00688
    2143 spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6] SPTBN5 206.442 207.862
    2144 band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [swissprot;acc:q9h4g0] EPB41L1 206.443 207.864
    2145 band 4.1-like protein 3 (4.1b) (differentially expressed in adenocarcinoma of the lung protein 1) (dal-1). [swissprot;acc:q9y2j2] EPB41L3 206.442 207.862
    2146 band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [swissprot;acc:o43491] EPB41L2 206.443 207.864
    2147 45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5] SDF4 206.442 207.862
    2148 ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9] no value 217.871 219.366 1.00686
    2149 40s ribosomal protein s7 (s8). [swissprot;acc:p23821] RPS7
    2150 26s proteasome-associated pad1 homolog. [refseq;acc:nm_005805] PSMD14
    2151 apolipoprotein b-100 precursor (apo b-100) [contains: apolipoprotein b-48 (apo b-48)]. [swissprot;acc:p04114] APOB
    2152 vesicle-associated membrane protein 2 (vamp-2) (synaptobrevin 2). [swissprot;acc:p19065] VAMP2 200.063 198.71 1.00681
    2153 vesicle-associated membrane protein 1 (vamp-1) (synaptobrevin 1). [swissprot;acc:p23763] VAMP1
    2154 vesicule-associated membrane protein 4 (vamp-4). [swissprot;acc:o75379] VAMP4
    2155 cdp-diacylglycerol--inositol 3-phosphatidyltransferase (ec 2.7.8.11) (phosphatidylinositol synthase) (ptdins synthase) (pi synthase). [swissprot;acc:o14735] CDIPT
    2156 adp-ribosylation factor gtpase activating protein 1 (adp-ribosylation factor 1 gtpase activating protein) (arf1 gap) (arf1-directed gtpase- activating protein) (gap protein). [swissprot;acc:q8n6t3] ARFGAP1
    2157 vesicle-associated membrane protein 3 (vamp-3) (synaptobrevin 3) (cellubrevin) (ceb). [swissprot;acc:q15836] VAMP3

    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/