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 Network Comparison Type Hugo Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 501 to 550 of 16578 in total
    Value Type  : Ranked
    Filtered  : 1
    description
    		Rank
    		Network Comparison Type
    		Hugo
    		Interaction Map
    		red
    		green
    		network_comparison
    60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993] 808 Subtracted HTATIP High confidence 223.186 213.912 9.274
    826 Divided 1.04335
    3722 Low confidence 200.338 197.651 1.01359
    3751 Subtracted 2.687
    60s acidic ribosomal protein p0 (l10e). [swissprot;acc:p05388] 1022 RPLP0 High confidence 226.203 232.855 6.652
    1092 Divided 1.02941
    3894 Subtracted Low confidence 202.202 199.673 2.529
    3897 Divided 1.01267
    60s acidic ribosomal protein p1. [swissprot;acc:p05386] 831 Subtracted no value High confidence 229.171 238.048 8.877
    898 Divided 1.03874
    4994 Low confidence 203.12 203.189 1.00034
    Subtracted 0.069
    60s acidic ribosomal protein p2. [swissprot;acc:p05387] 621 RPLP2 High confidence 231.92 244.435 12.515
    720 Divided 1.05396
    1863 Subtracted Low confidence 204.808 200.886 3.922
    1982 Divided 1.01952
    60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] 267 Subtracted no value High confidence 243.12 266.661 23.541
    357 Divided 1.09683
    4704 Subtracted Low confidence 207.452 208.569 1.117
    4740 Divided 1.00538
    60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] 264 Subtracted High confidence 243.24 266.796 23.556
    356 Divided 1.09684
    4855 Subtracted Low confidence 207.503 208.103 0.6
    4858 Divided 1.00289
    60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] 283 Subtracted MRPL11 High confidence 242.37 265.255 22.885
    373 Divided 1.09442
    4582 Subtracted Low confidence 208.668 210.165 1.497
    4601 Divided 1.00717
    60s ribosomal protein l11. [swissprot;acc:p39026] 201 Subtracted RPL11 High confidence 241.828 267.346 25.518
    283 Divided 1.10552
    2323 Subtracted Low confidence 208.542 212.217 3.675
    2678 Divided 1.01762
    60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] 246 Subtracted no value High confidence 243.583 267.528 23.945
    338 Divided 1.0983
    4651 Subtracted Low confidence 206.86 208.125 1.265
    4667 Divided 1.00612
    60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] 281 Subtracted MRPL12 High confidence 242.159 265.104 22.945
    369 Divided 1.09475
    3863 Subtracted Low confidence 204.522 201.949 2.573
    3886 Divided 1.01274
    60s ribosomal protein l12. [swissprot;acc:p30050] 247 Subtracted no value High confidence 243.583 267.527 23.944
    337 Divided 1.0983
    4655 Subtracted Low confidence 206.837 208.096 1.259
    4669 Divided 1.00609
    60s ribosomal protein l13 (breast basic conserved protein 1). [swissprot;acc:p26373] 3620 Subtracted RPL13 203.892 201.053 2.839
    3643 Divided 1.01412
    60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] 325 Subtracted MRPL13 High confidence 241.828 263.62 21.792
    390 Divided 1.09011
    4858 Subtracted Low confidence 206.138 205.562 0.576
    4867 Divided 1.0028

    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/