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 901 to 950 of 8289 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Filtered  : 1
    description
    		Rank
    		Hugo
    		Interaction Map
    		red
    		green
    		network_comparison
    b(0,+)-type amino acid transporter 1 (b(0,+)at) (glycoprotein- associated amino acid transporter b0,+at1). [swissprot;acc:p82251] 100 SLC7A9 Low confidence 200.497 185.679 1.0798
    b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] 1559 BCL6B High confidence 196.191 192.996 1.01655
    2972 Low confidence 193.996 190.784 1.01684
    b-cell lymphoma 3-encoded protein (bcl-3 protein). [swissprot;acc:p20749] 1565 BCL3 199.975 195.839 1.02112
    2655 High confidence 201.445 201.667 1.0011
    b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182] 1556 BCL6 196.192 192.996 1.01656
    2973 Low confidence 193.996 190.784 1.01684
    b-cell receptor-associated protein 29 (bcr-associated protein bap29). [swissprot;acc:q9uhq4] 3019 BCAP29 201.261 197.953 1.01671
    b-cell receptor-associated protein 31 (bcr-associated protein bap31) (p28 bap31) (cdm protein) (6c6-ag tumor-associated antigen) (dxs1357e). [swissprot;acc:p51572] 3011 BCAP31
    b-lymphocyte activation-related protein. [sptrembl;acc:q96pn3] 4286 no value 197.793 195.963 1.00934
    b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] 980 BRAF High confidence 130.289 134.713 1.03396
    4824 Low confidence 184.583 183.88 1.00382
    b/k protein. [refseq;acc:nm_016524] 2533 SYT17 200.555 196.985 1.01812
    b24o18.3 (pom121 membrane glycoprotein (rat homolog)-like 2). [sptrembl;acc:q96kw2] 3359 POM121L2 203.07 199.966 1.01552
    b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] 125 B9D1 213.243 227.616 1.0674
    181 High confidence 229.818 267.265 1.16294
    ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] 41 GSTO2 Low confidence 228.147 200.55 1.13761
    244 High confidence 227.357 254.15 1.11785
    ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6] 464 FNBP1 210.578 226.764 1.07686
    983 Low confidence 201.215 196.378 1.02463
    ba161i19.3 (similar to ribosomal protein l36). [sptrembl;acc:q8wx03] 608 no value 205.117 211.213 1.02972
    ba203i16.1 (hypothetical protein kiaa0970). [sptrembl;acc:q9h1w1] 3117 FNDC3A High confidence 0.00001 0.00001 1
    3814 Low confidence 205.397 202.717 1.01322
    ba207c16.2 (fragment). [sptrembl;acc:q9nql7] 2599 KIAA1432 High confidence 211.662 211.361 1.00142
    3146 Low confidence 201.676 198.45 1.01626
    ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9] 1596 no value 205.496 201.273 1.02098
    2148 High confidence 217.871 219.366 1.00686
    ba304i5.1 (novel lipase) (fragment). [sptrembl;acc:q96lg2] 2115 LIPM 214.632 213.14 1.007
    2524 Low confidence 196.878 193.373 1.01813
    ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] 931 BHLHB4 High confidence 159.13 164.917 1.03637
    4976 Low confidence 197.195 197.038 1.0008
    ba371l19.2 (novel protein similar to 40s ribosomal protein s10 (rps10)). [sptrembl;acc:q9nq39] 3258 no value 202.738 199.588 1.01578
    ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] 313 202.05 193.94 1.04182
    452 High confidence 224.161 207.972 1.07784
    ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 1568 221.128 224.767 1.01646
    1999 Low confidence 205.081 201.165 1.01947
    ba526d8.2 (novel protein similar to kiaa1074). [sptrembl;acc:q9h560] 261 ANKRD19 216.845 207.333 1.04588
    ba526d8.4 (novel krab box containing c2h2 type zinc finger protein) (fragment). [sptrembl;acc:q9h559] 4383 ZNF484 197.793 195.963 1.00934
    ba528a10.3.2 (novel protein similar to kiaa0161, isoform 2) (fragment). [sptrembl;acc:q9bx39] 667 RNF144B 208.62 202.855 1.02842
    2968 High confidence 0.00001 0.00001 1
    bactericidal permeability-increasing protein precursor (bpi) (cap 57). [swissprot;acc:p17213] 757 BPI 224.434 235.583 1.04968
    3102 Low confidence 202.125 198.846 1.01649
    baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392] 2500 BIRC5 High confidence 218.949 219.552 1.00275
    4088 Low confidence 201.76 199.573 1.01096
    bag-family molecular chaperone regulator-1 (bcl-2 binding athanogene- 1) (bag-1) (glucocorticoid receptor-associated protein rap46). [swissprot;acc:q99933] 2185 BAG1 High confidence 211.713 210.318 1.00663
    2472 Low confidence 202.189 198.561 1.01827
    bag-family molecular chaperone regulator-2. [swissprot;acc:o95816] 1785 BAG2 High confidence 206.332 203.874 1.01206
    4241 Low confidence 202.144 200.188 1.00977
    bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817] 459 BAG3 High confidence 233.529 216.737 1.07748
    2878 Low confidence 203.113 199.699 1.0171

    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/