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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 958 to 1007 of 8289 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Filtered  : 1
    description
    		Rank
    		Hugo
    		Interaction Map
    		red
    		green
    		network_comparison
    band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [swissprot;acc:o43491] 2146 EPB41L2 High confidence 206.443 207.864 1.00688
    2666 Low confidence 199.624 196.156 1.01768
    band 4.1-like protein 3 (4.1b) (differentially expressed in adenocarcinoma of the lung protein 1) (dal-1). [swissprot;acc:q9y2j2] 2145 EPB41L3 High confidence 206.442 207.862 1.00688
    2661 Low confidence 199.622 196.153 1.01769
    bardet-biedl syndrome 7 protein isoform a; bbs2-like 1. [refseq;acc:nm_176824] 635 BBS7 207.763 201.882 1.02913
    1567 High confidence 221.128 224.767 1.01646
    barrier-to-autointegration factor (breakpoint cluster region protein 1). [swissprot;acc:o75531] 2804 BANF1 0.00001 0.00001 1
    3579 Low confidence 202.517 199.628 1.01447
    basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] 933 BHLHB5 High confidence 159.165 164.951 1.03635
    4972 Low confidence 197.202 197.037 1.00084
    basic leucine zipper nuclear factor 1 (jem-1); basic-leucine zipper nuclear factor; likely ortholog of mouse golgin-45. [refseq;acc:nm_003666] 4086 BLZF1 201.76 199.573 1.01096
    basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811] 1732 no value 201.552 197.517 1.02043
    2715 High confidence 216.018 215.903 1.00053
    bax inhibitor-1 (bi-1) (testis enhanced gene transcript). [swissprot;acc:p55061] 2950 TEGT 0.00001 0.00001 1
    3005 Low confidence 140.432 138.122 1.01672
    bcl-6 interacting corepressor isoform 1. [refseq;acc:nm_017745] 2776 BCOR High confidence 0.00001 0.00001 1
    4959 Low confidence 202.187 201.971 1.00107
    bcl2-related ovarian killer. [refseq;acc:nm_032515] 30 BOK 265.638 223.235 1.18995
    bcl2/adenovirus e1b 19-kda protein-interacting protein 1. [swissprot;acc:q12981] 4497 BNIP1 202.09 203.853 1.00872
    beclin 1 (coiled-coil myosin-like bcl2-interacting protein) (protein gt197). [swissprot;acc:q14457] 1636 BECN1 High confidence 202.358 199.408 1.01479
    2036 Low confidence 199.664 195.869 1.01938
    bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] 11 BEST1 37.318 28.4944 1.30966
    bet3 homolog. [swissprot;acc:o43617] 327 TRAPPC3 197.221 189.574 1.04034
    567 High confidence 129.219 121.261 1.06563
    bet5 homolog (multiple myeloma protein 2) (mum-2). [swissprot;acc:q9y5r8] 1058 TRAPPC1 Low confidence 198.804 194.142 1.02401
    beta adducin (erythrocyte adducin beta subunit). [swissprot;acc:p35612] 1549 ADD2 205.847 201.577 1.02118
    1945 High confidence 224.343 222.151 1.00987
    beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929] 2361 ENO3 207.186 208.046 1.00415
    4628 Low confidence 201.961 200.622 1.00667
    beta tubulin 1, class vi. [refseq;acc:nm_030773] 2985 TUBB1 200.1 196.798 1.01678
    beta-1,3-galactosyltransferase 5 (ec 2.4.1.-) (beta-1,3-galtase 5) (beta3gal-t5) (b3gal-t5) (udp-galactose:beta-n-acetylglucosamine beta- 1,3-galactosyltransferase 5) (udp-gal:beta-glcnac beta-1,3- galactosyltransferase 5) (beta-3-gx-t5). [swissprot;acc:q9y2c3] 3631 B3GALT5 200.633 197.828 1.01418
    beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] 301 ALG1 High confidence 150.982 166.372 1.10193
    4906 Low confidence 179.202 179.551 1.00195
    beta-1-syntrophin (59 kda dystrophin-associated protein a1, basic component 1) (dapa1b) (tax interaction protein 43) (tip-43) (syntrophin 2) (bsyn2). [swissprot;acc:q13884] 2576 SNTB1 High confidence 213.422 213.75 1.00154
    3276 Low confidence 202.385 199.258 1.01569
    beta-2-syntrophin (59 kda dystrophin-associated protein a1, basic component 2) (syntrophin 3) (snt3) (syntrophin-like) (sntl). [swissprot;acc:q13425] 2578 SNTB2 High confidence 213.422 213.75 1.00154
    3277 Low confidence 202.385 199.258 1.01569
    beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 50 ARRB1 High confidence 133 105 1.26667
    439 Low confidence 194.237 187.689 1.03489
    beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 49 ARRB2 High confidence 133 105 1.26667
    428 Low confidence 194.137 187.552 1.03511
    beta-carotene 15, 15'-dioxygenase; beta-carotene 15,15'-monooxygenase. [refseq;acc:nm_017429] 2222 BCMO1 High confidence 221.509 220.108 1.00637
    3074 Low confidence 203.19 199.882 1.01655
    beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] 2221 no value High confidence 221.509 220.108 1.00637
    3073 Low confidence 203.19 199.882 1.01655
    beta-catenin (pro2286). [swissprot;acc:p35222] 801 CTNNB1 High confidence 224.445 214.894 1.04445
    4878 Low confidence 207.082 206.548 1.00259
    beta-centractin (actin-related protein 1b) (arp1b). [swissprot;acc:p42025] 1510 ACTR1B High confidence 225.148 221.177 1.01795
    3620 Low confidence 198.688 195.899 1.01424
    beta-galactosidase precursor (ec 3.2.1.23) (lactase) (acid beta- galactosidase). [swissprot;acc:p16278] 1324 GLB1 203.758 199.335 1.02219

    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/