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 [...,...].
    description Rank Gene Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2608 to 2657 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		green
    		network_comparison
    small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678] 3012 SNRPB 0.00001 0.00001 1
    small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 388 no value 227.575 208.756 1.09015
    small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] 389 SNRPF
    small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] 173 SNRPD1 227.032 193.056 1.17599
    small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] 225 SNRPD2 226.471 201.769 1.12243
    small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] 245 SNRPD3 226.109 202.333 1.11751
    small optic lobes homolog; small optic lobes, drosophila, homolog of. [refseq;acc:nm_005632] 1346 SOLH 216.772 221.594 1.02224
    smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] 232 CSRP2 239.336 267.879 1.11926
    snare associated protein snapin. [refseq;acc:nm_012437] 1163 SNAPAP 220.758 215.097 1.02632
    snrna activating protein complex 50 kda subunit (snapc 50 kda subunit) (proximal sequence element-binding transcription factor beta subunit) (pse-binding factor beta subunit) (ptf beta subunit). [swissprot;acc:q92966] 2849 SNAPC3 0.00001 0.00001 1
    sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289] 2000 SLC5A6 204.626 202.739 1.00931
    sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911] 1996 SLC5A5 204.682 202.784 1.00936
    sodium/potassium-transporting atpase alpha-1 chain precursor (ec 3.6.3.9) (sodium pump 1) (na+/k+ atpase 1). [swissprot;acc:p05023] 1424 ATP1A1 214.717 219.157 1.02068
    sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993] 1428 ATP1A2
    sodium/potassium-transporting atpase alpha-3 chain (ec 3.6.3.9) (sodium pump 3) (na+/k+ atpase 3) (alpha(iii)). [swissprot;acc:p13637] 1427 ATP1A3
    soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825] 1911 SEPSECS 217.48 215.256 1.01033
    solute carrier family 13, member 1 (renal sodium/sulfate cotransporter) (na(+)/sulfate cotransporter) (hnasi-1). [swissprot;acc:q9bzw2] 2456 SLC13A1 204.683 205.326 1.00314
    solute carrier family 13, member 2 (renal sodium/dicarboxylate cotransporter) (na(+)/dicarboxylate cotransporter 1) (nadc-1). [swissprot;acc:q13183] 2458 SLC13A2
    solute carrier family 13, member 3 (sodium-dependent high-affinity dicarboxylate transporter 2) (na(+)/dicarboxylate cotransporter 3) (nadc-3) (hnadc3). [swissprot;acc:q8wwt9] 2455 SLC13A3
    solute carrier family 13, member 4 (na+/sulfate cotransporter sut-1). [swissprot;acc:q9ukg4] 2454 SLC13A4
    solute carrier family 2, facilitated glucose transporter, member 6 (glucose transporter type 6) (glucose transporter type 9). [swissprot;acc:q9ugq3] 2047 SLC2A6 224.124 226.003 1.00838
    solute carrier family 2, facilitated glucose transporter, member 8 (glucose transporter type 8) (glucose transporter type x1). [swissprot;acc:q9ny64] 2048 SLC2A8
    solute carrier family 20 (phosphate transporter), member 1; glvr-1; pit-1; gibbon ape leukemia virus receptor 1. [refseq;acc:nm_005415] 2464 SLC20A1 235.812 235.088 1.00308
    solute carrier family 20 (phosphate transporter), member 2; glvr-2; pit-2; gibbon ape leukemia virus receptor 2; murine leukemia virus, amphotropic; receptor. [refseq;acc:nm_006749] 2461 SLC20A2
    solute carrier family 21 member 15 (organic anion transporter polypeptide-related protein 4) (oatp-rp4) (oatprp4). [swissprot;acc:q9h2y9] 2965 SLCO5A1 0.00001 0.00001 1
    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] 2120 SLC23A1 221.248 222.788 1.00696
    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] 2138 SLC23A2
    solute carrier family 27 (fatty acid transporter), member 4; fatty acid transport protein 4. [refseq;acc:nm_005094] 1900 SLC27A4 191.401 193.38 1.01034
    solute carrier family 27 (fatty acid transporter), member 5; very long-chain acyl-coa synthetase homolog 2; very long-chain acyl-coa synthetase-related protein; likely ortholog of mouse solute carrier family 27 (fatty acid transporter), member 5. [refseq;acc:nm_012254] 1907 SLC27A5 191.408 193.387
    solute carrier family 27 member 3; fatty acid transport protein 3. [refseq;acc:nm_024330] 1903 SLC27A3 191.406 193.385
    solute carrier family 35, member b1; udp-galactose transporter related. [refseq;acc:nm_005827] 745 SLC35B1 214.679 225.568 1.05072
    solute carrier family 36 member 1; proton / amino acid symporter; lysosomal amino acid transporter 1. [refseq;acc:nm_078483] 3026 SLC36A1 0.00001 0.00001 1
    solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [refseq;acc:nm_018158] 1832 SLC4A1AP 180.409 182.459 1.01136
    solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913] 1999 SLC5A8 204.636 202.748 1.00931
    son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889] 560 SOS1 205.74 193.021 1.06589
    son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890] 561 SOS2 205.89 193.183 1.06578
    son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] 131 SON 294.053 242.562 1.21228
    sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] 943 SRI 212.442 205.087 1.03586
    sorting nexin 1. [swissprot;acc:q13596] 1150 SNX1 209.868 215.522 1.02694
    sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] 243 SNX13 227.357 254.15 1.11785
    sorting nexin 16. [swissprot;acc:p57768] 3108 SNX16 0.00001 0.00001 1
    sorting nexin 17. [swissprot;acc:q15036] 638 SNX17 228.639 242.258 1.05957
    sorting nexin 5. [swissprot;acc:q9y5x3] 678 SNX5 208.482 220.175 1.05609
    sorting nexin 6 (traf4-associated factor 2). [swissprot;acc:q9unh7] 778 SNX6 209.191 219.332 1.04848
    sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1] 2335 SNX9 229.258 230.294 1.00452
    source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] 254 STT3B 200.691 179.88 1.11569
    sparc precursor (secreted protein acidic and rich in cysteine) (osteonectin) (on) (basement membrane protein bm-40). [swissprot;acc:p09486] 3062 SPARC 0.00001 0.00001 1
    sparc-like protein 1 precursor (high endothelial venule protein) (hevin) (mast 9). [swissprot;acc:q14515] 2899 SPARCL1
    spartin; trans-activated by hepatitis c virus core protein 1. [refseq;acc:nm_015087] 2987 SPG20
    speckle-type poz protein. [swissprot;acc:o43791] 3031 SPOP

    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/