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 313 to 362 of 8289 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Filtered  : 1
    description
    		Rank
    		Hugo
    		Interaction Map
    		red
    		green
    		network_comparison
    60s ribosomal protein l32, mitochondrial precursor (l32mt) (hspc283). [swissprot;acc:q9byc8] 4034 MRPL32 Low confidence 203.062 200.757 1.01148
    60s ribosomal protein l32. [swissprot;acc:p02433] 276 SNORA7A High confidence 241.13 266.969 1.10716
    3156 Low confidence 207.568 210.937 1.01623
    60s ribosomal protein l34, mitochondrial precursor (l34mt). [swissprot;acc:q9bq48] 1333 MRPL34 High confidence 220.681 215.78 1.02271
    3852 Low confidence 204.301 201.678 1.01301
    60s ribosomal protein l34. [swissprot;acc:p49207] 308 RPL34 High confidence 242.153 266.673 1.10126
    4903 Low confidence 204.23 204.633 1.00197
    60s ribosomal protein l35. [swissprot;acc:p42766] 303 RPL35 High confidence 242.333 266.999 1.10179
    4224 Low confidence 206.836 208.898 1.00997
    60s ribosomal protein l35a. [swissprot;acc:p18077] 2451 RPL35A 200.987 197.369 1.01833
    60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6] 365 MRPL36 High confidence 242.744 266.07 1.09609
    4899 Low confidence 207.159 207.572 1.00199
    60s ribosomal protein l36. [swissprot;acc:q9y3u8] 604 RPL36 205.116 211.234 1.02983
    60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403] 635 RPL37 High confidence 228.639 242.258 1.05957
    3174 Low confidence 203.428 200.191 1.01617
    60s ribosomal protein l37a. [swissprot;acc:p12751] 68 no value 239.692 217.005 1.10455
    2959 High confidence 0.00001 0.00001 1
    60s ribosomal protein l38. [swissprot;acc:p23411] 4235 RPL38 Low confidence 202.55 200.576 1.00984
    60s ribosomal protein l39. [swissprot;acc:p02404] 859 no value High confidence 234.025 224.958 1.04031
    3220 Low confidence 202.665 199.481 1.01596
    60s ribosomal protein l4 (l1). [swissprot;acc:p36578] 359 RPL4 High confidence 239.277 262.434 1.09678
    4517 Low confidence 206.721 208.457 1.0084
    60s ribosomal protein l5. [swissprot;acc:p46777] 326 RPL5 High confidence 241.899 265.924 1.09932
    4179 Low confidence 207.337 209.485 1.01036
    60s ribosomal protein l6 (tax-responsive enhancer element binding protein 107) (taxreb107) (neoplasm-related protein c140). [swissprot;acc:q02878] 179 RPL6 209.954 221.607 1.0555
    60s ribosomal protein l7. [swissprot;acc:p18124] 297 no value High confidence 235.727 259.984 1.1029
    4752 Low confidence 205.499 206.566 1.00519
    60s ribosomal protein l7a (surfeit locus protein 3) (pla-x polypeptide). [swissprot;acc:p11518] 1822 205.672 201.635 1.02002
    60s ribosomal protein l8. [swissprot;acc:p25120] 834 RPL8 High confidence 231.734 222.222 1.0428
    3288 Low confidence 199.513 196.433 1.01568
    60s ribosomal protein l9, mitochondrial precursor (l9mt). [swissprot;acc:q9byd2] 3758 MRPL9 201.668 198.992 1.01345
    60s ribosomal protein l9. [swissprot;acc:p32969] 341 no value High confidence 240.243 263.798 1.09805
    3742 Low confidence 207.443 210.24 1.01348
    65 kda yes-associated protein (yap65). [swissprot;acc:p46937] 1986 YAP1 High confidence 219.26 217.193 1.00952
    3095 Low confidence 202.795 199.503 1.0165
    69 kda islet cell autoantigen (ica69) (islet cell autoantigen 1) (islet cell autoantigen p69) (icap69). [swissprot;acc:q05084] 2604 ICA1 202.113 205.73 1.0179
    3227 High confidence 0.00001 0.00001 1
    7-dehydrocholesterol reductase (ec 1.3.1.21) (7-dhc reductase) (sterol delta-7-reductase) (putative sterol reductase sr-2). [swissprot;acc:q9ubm7] 1225 DHCR7 Low confidence 203.51 198.973 1.0228
    70 kda wd-repeat tumor rejection antigen homolog. [swissprot;acc:p57737] 3659 CORO7 201.605 198.82 1.01401
    78 kda glucose-regulated protein precursor (grp 78) (immunoglobulin heavy chain binding protein) (bip) (endoplasmic reticulum lumenal ca(2+) binding protein grp78). [swissprot;acc:p11021] 4037 HSPA5 206.348 204.01 1.01146
    80 kda nuclear cap binding protein (ncbp 80 kda subunit) (cbp80). [swissprot;acc:q09161] 3969 NCBP1 202.356 199.945 1.01206
    85 kda calcium-independent phospholipase a2 (ec 3.1.1.4) (ipla2) (cai- pla2) (group vi phospholipase a2) (gvi pla2). [swissprot;acc:o60733] 1195 PLA2G6 202.297 197.738 1.02306
    9 kda protein. [swissprot;acc:p13994] 1988 CCDC130 High confidence 219.26 217.193 1.00952
    2931 Low confidence 204.222 200.808 1.017
    a kinase anchor protein 1, mitochondrial precursor (protein kinase a anchoring protein 1) (prka1) (a-kinase anchor protein 149 kda) (akap 149) (dual specificity a-kinase anchoring protein 1) (d-akap-1) (spermatid a-kinase anchor protein 84) (s-akap84). [swissprot;acc:q92667] 2167 AKAP1 202.625 198.833 1.01907
    a kindred of iglon. [refseq;acc:nm_173808] 215 NEGR1 199.671 209.654 1.05
    804 High confidence 212.386 221.785 1.04425
    a-kinase anchor protein 5 (a-kinase anchor protein 79 kda) (akap 79) (camp-dependent protein kinase regulatory subunit ii high affinity binding protein) (h21). [swissprot;acc:p24588] 1602 AKAP5 Low confidence 206.235 202.009 1.02092
    2788 High confidence 0.00001 0.00001 1
    a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] 957 ARAF 129.913 134.399 1.03453

    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/