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 Gene Rank Network Comparison Type Hugo Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2651 to 2700 of 3228 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		green
    		network_comparison
    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
    spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813] 3038 no value
    spectrin beta chain, brain 1 (spectrin, non-erythroid beta chain 1) (beta-ii spectrin) (fodrin beta chain). [swissprot;acc:q01082] 1773 SPTBN1 223.032 225.739 1.01214
    spectrin beta chain, brain 2 (spectrin, non-erythroid beta chain 2) (beta-iii spectrin). [swissprot;acc:o15020] 1772 SPTBN2
    spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6] 2143 SPTBN5 206.442 207.862 1.00688
    spectrin sh3 domain binding protein 1; eps8 binding protein; interactor protein ablbp4; abl-interactor protein 1 long; nap1 binding protein. [refseq;acc:nm_005470] 1846 ABI1 217.066 214.698 1.01103
    sperm tail protein shippo1; h-shippo 1. [refseq;acc:nm_053280] 2797 ODF3 0.00001 0.00001 1
    spermatogenesis associated 6. [refseq;acc:nm_019073] 51 SPATA6 133 105 1.26667
    spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [swissprot;acc:p19623] 1471 SRM 221.412 217.199 1.0194
    spermine synthase (ec 2.5.1.22) (spermidine aminopropyltransferase) (spmsy). [swissprot;acc:p52788] 3118 SMS 0.00001 0.00001 1
    sphingolipid delta 4 desaturase; membrane fatty acid (lipid) desaturase; dihydroceramide desaturase. [refseq;acc:nm_003676] 2648 DEGS1 213.169 213.417 1.00116
    sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906] 75 SMPD2 288 362 1.25694
    sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] 1264 SPHK1 171.231 167.177 1.02425
    sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] 1277 SPHK2
    sphingosine-1-phosphate lyase 1; sphingosine-1-phosphate lyase. [refseq;acc:nm_003901] 1744 SGPL1 219.423 222.215 1.01272
    spir-2 protein (fragment). [sptrembl;acc:q8wwl2] 2879 no value 0.00001 0.00001 1
    spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] 393 TXNL4A 225.719 207.072 1.09005
    splicing coactivator subunit srm300; rna binding protein; at-rich element binding factor. [refseq;acc:nm_016333] 2281 SRRM2 219.652 218.482 1.00536
    splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459] 938 SF3A1 220.246 212.618 1.03588
    splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] 460 SF3A2 223.648 207.62 1.0772
    splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874] 937 SF3A3 220.246 212.618 1.03588
    splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] 265 SF3B1 225.217 202.459 1.11241
    splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] 578 SF3B2 224.606 210.944 1.06477
    splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] 317 no value 224.445 204.044 1.09998
    splicing factor 3b subunit 4 (spliceosome associated protein 49) (sap 49) (sf3b50) (pre-mrna splicing factor sf3b 49 kda subunit). [swissprot;acc:q15427] 1404 SF3B4 232.752 237.65 1.02104
    splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] 201 SF4 240.133 211.382 1.13601
    splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519] 570 SFRS11 229.709 215.631 1.06529
    splicing factor u2af 35 kda subunit (u2 auxiliary factor 35 kda subunit) (u2 snrnp auxiliary factor small subunit). [swissprot;acc:q01081] 2282 U2AF1 219.652 218.482 1.00536
    splicing factor u2af 65 kda subunit (u2 auxiliary factor 65 kda subunit) (u2 snrnp auxiliary factor large subunit) (hu2af(65)). [swissprot;acc:p26368] 2285 U2AF2
    splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [swissprot;acc:q07955] 636 SFRS1 228.639 242.258 1.05957
    splicing factor, arginine/serine-rich 3 (pre-mrna splicing factor srp20) (x16 protein). [swissprot;acc:p23152] 1194 SFRS3 220.742 215.237 1.02558
    splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872] 824 SFRS8 206.068 197.471 1.04354
    splicing factor, proline-and glutamine-rich (polypyrimidine tract- binding protein-associated splicing factor) (ptb-associated splicing factor) (psf) (dna-binding p52/p100 complex, 100 kda subunit). [swissprot;acc:p23246] 2538 SFPQ 190.765 191.163 1.00209
    sporulation-induced transcript 4-associated protein. [refseq;acc:nm_018312] 2318 SAPS3 194.834 195.794 1.00493
    sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609] 1002 SPRY1 225.167 217.922 1.03325
    sprouty homolog 2 (spry-2). [swissprot;acc:o43597] 1003 SPRY2
    sprouty homolog 3 (spry-3). [swissprot;acc:o43610] 1001 SPRY3
    sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] 1000 no value
    spry domain-containing socs box protein ssb-1. [refseq;acc:nm_025106] 2814 SPSB1 0.00001 0.00001 1
    spry domain-containing socs box protein ssb-4. [refseq;acc:nm_080862] 2806 SPSB4
    squalene monooxygenase (ec 1.14.99.7) (squalene epoxidase) (se). [swissprot;acc:q14534] 2199 SQLE 193.787 195.064 1.00659
    squamous cell carcinoma antigen 1 (scca-1) (protein t4-a). [swissprot;acc:p29508] 2420 SERPINB4 218.2 218.984 1.00359
    squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] 488 SART1 225.026 209.798 1.07258
    sqv-7-like protein (fragment). [sptrembl;acc:o95454] 520 SLC35D2 214.754 229.565 1.06897

    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/