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 2113 to 2162 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		red
    		green
    		network_comparison
    2113 no value ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] 219.055 217.533 1.007
    2114 LIPF triacylglycerol lipase, gastric precursor (ec 3.1.1.3) (gastric lipase) (gl). [swissprot;acc:p07098] 214.632 213.14
    2115 LIPM ba304i5.1 (novel lipase) (fragment). [sptrembl;acc:q96lg2]
    2116 LIPA 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]
    2117 SARS2 seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [swissprot;acc:q9np81]
    2118 SARS seryl-trna synthetase (ec 6.1.1.11) (serine--trna ligase) (serrs). [swissprot;acc:p49591]
    2119 KCMF1 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] 221.248 222.788 1.00696
    2120 SLC23A1 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]
    2121 HNRPA3 heterogeneous nuclear ribonucleoprotein a3 (hnrnp a3) (d10s102). [swissprot;acc:p51991]
    2122 LGALS9 galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182] 206.473 207.911
    2123 ARF4 adp-ribosylation factor 4. [swissprot;acc:p18085] 221.248 222.788
    2124 AKTIP fused toes homolog; likely ortholog of mouse fused toes. [refseq;acc:nm_022476]
    2125 SHC1 shc transforming protein. [swissprot;acc:p29353]
    2126 ZNF289 zinc finger protein 289, id1 regulated; likely ortholog of mouse zfp289. [refseq;acc:nm_032389]
    2127 SHC3 neuronal shc. [refseq;acc:nm_016848]
    2128 ARF1 adp-ribosylation factor 1. [swissprot;acc:p32889]
    2129 HNRNPA1 heterogeneous nuclear ribonucleoprotein a1 (helix-destabilizing protein) (single-strand binding protein) (hnrnp core protein a1). [swissprot;acc:p09651]
    2130 ARF3 adp-ribosylation factor 3. [swissprot;acc:p16587]
    2131 GCH1 gtp cyclohydrolase i (ec 3.5.4.16) (gtp-ch-i). [swissprot;acc:p30793] 226.277 227.851
    2132 SHC2 protein sck (fragment). [swissprot;acc:p98077] 221.248 222.788
    2133 NR4A1 orphan nuclear receptor hmr (early response protein nak1) (tr3 orphan receptor). [swissprot;acc:p22736] 207.74 206.305
    2134 HNRNPA2B1 heterogeneous nuclear ribonucleoproteins a2/b1 (hnrnp a2 / hnrnp b1). [swissprot;acc:p22626] 221.248 222.788
    2135 NR4A3 nuclear hormone receptor nor-1 (neuron-derived orphan receptor 1) (mitogen induced nuclear orphan receptor). [swissprot;acc:q92570] 207.743 206.308
    2136 OCIAD1 ovarian carcinoma immunoreactive antigen. [refseq;acc:nm_017830] 221.248 222.788
    2137 ARFGAP3 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]
    2138 SLC23A2 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]
    2139 MAP2K7 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]
    2140 CSTF2 cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] 161.547 162.665 1.00692
    2141 NR4A2 orphan nuclear receptor nurr1 (immediate-early response protein not) (transcriptionally inducible nuclear receptor). [swissprot;acc:p43354] 207.765 206.343 1.00689
    2142 EPB41 protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [swissprot;acc:p11171] 206.443 207.864 1.00688
    2143 SPTBN5 spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6] 206.442 207.862
    2144 EPB41L1 band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [swissprot;acc:q9h4g0] 206.443 207.864
    2145 EPB41L3 band 4.1-like protein 3 (4.1b) (differentially expressed in adenocarcinoma of the lung protein 1) (dal-1). [swissprot;acc:q9y2j2] 206.442 207.862
    2146 EPB41L2 band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [swissprot;acc:o43491] 206.443 207.864
    2147 SDF4 45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5] 206.442 207.862
    2148 no value ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9] 217.871 219.366 1.00686
    2149 RPS7 40s ribosomal protein s7 (s8). [swissprot;acc:p23821]
    2150 PSMD14 26s proteasome-associated pad1 homolog. [refseq;acc:nm_005805]
    2151 APOB apolipoprotein b-100 precursor (apo b-100) [contains: apolipoprotein b-48 (apo b-48)]. [swissprot;acc:p04114]
    2152 VAMP2 vesicle-associated membrane protein 2 (vamp-2) (synaptobrevin 2). [swissprot;acc:p19065] 200.063 198.71 1.00681
    2153 VAMP1 vesicle-associated membrane protein 1 (vamp-1) (synaptobrevin 1). [swissprot;acc:p23763]
    2154 VAMP4 vesicule-associated membrane protein 4 (vamp-4). [swissprot;acc:o75379]
    2155 CDIPT cdp-diacylglycerol--inositol 3-phosphatidyltransferase (ec 2.7.8.11) (phosphatidylinositol synthase) (ptdins synthase) (pi synthase). [swissprot;acc:o14735]
    2156 ARFGAP1 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]
    2157 VAMP3 vesicle-associated membrane protein 3 (vamp-3) (synaptobrevin 3) (cellubrevin) (ceb). [swissprot;acc:q15836]
    2158 LGALS4 galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] 206.401 207.796 1.00676
    2159 MAPK3 mitogen-activated protein kinase 3 (ec 2.7.1.37) (extracellular signal-regulated kinase 1) (erk-1) (insulin-stimulated map2 kinase) (map kinase 1) (mapk 1) (p44-erk1) (ert2) (p44-mapk) (microtubule- associated protein-2 kinase). [swissprot;acc:p27361] 215.921 214.474 1.00675
    2160 RPS6KA3 ribosomal protein s6 kinase alpha 3 (ec 2.7.1.37) (s6k-alpha 3) (90 kda ribosomal protein s6 kinase 3) (p90-rsk 3) (ribosomal s6 kinase 2) (rsk-2) (pp90rsk2) (insulin-stimulated protein kinase 1) (ispk-1). [swissprot;acc:p51812] 215.925 214.481 1.00673
    2161 CAMK2G calcium/calmodulin-dependent protein kinase type ii gamma chain (ec 2.7.1.123) (cam-kinase ii gamma chain) (cam kinase ii gamma subunit) (camk-ii gamma subunit) (fragment). [swissprot;acc:q13555]
    2162 CAMK2D calcium/calmodulin-dependent protein kinase type ii delta chain (ec 2.7.1.123) (cam-kinase ii delta chain) (cam kinase ii delta subunit) (camk-ii delta subunit). [swissprot;acc:q13557]

    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/