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 330 to 379 of 3228 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		green
    		network_comparison
    ataxin 2-binding protein. [swissprot;acc:q9nwb1] 1704 no value 218.514 215.577 1.01362
    ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] 1059 228.105 221.293 1.03078
    ataxin-1 ubiquitin-like interacting protein. [refseq;acc:nm_020131] 2041 UBQLN4 196.808 195.141 1.00854
    atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 149 no value 142 170 1.19718
    atp synthase alpha chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p25705] 1658 ATP5A1 217.925 214.826 1.01443
    atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] 241 ATP5F1 227.357 254.15 1.11785
    atp synthase beta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p06576] 1655 ATP5B 219.062 215.942 1.01445
    atp synthase coupling factor 6, mitochondrial precursor (ec 3.6.3.14) (f6). [swissprot;acc:p18859] 2893 ATP5J 0.00001 0.00001 1
    atp synthase coupling factor b, mitochondrial precursor. [swissprot;acc:q99766] 2022 ATP5S 208.601 210.464 1.00893
    atp synthase delta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p30049] 1687 ATP5D 215.345 212.386 1.01393
    atp synthase f chain, mitochondrial (ec 3.6.3.14). [swissprot;acc:p56134] 2644 ATP5J2 194.097 194.328 1.00119
    atp synthase g chain, mitochondrial (ec 3.6.3.14) (atpase subunit g). [swissprot;acc:o75964] 2834 ATP5L 0.00001 0.00001 1
    atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p36542] 1563 ATP5C1 218.277 214.739 1.01648
    atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691] 456 ATPAF2 210.225 226.578 1.07779
    atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047] 1564 ATP5O 218.277 214.739 1.01648
    atp-binding cassette, sub-family c, member 10; multidrug resistance-associated protein 7. [refseq;acc:nm_033450] 2209 ABCC10 199.129 200.413 1.00645
    atp-binding cassette, sub-family d, member 3 (70 kda peroxisomal membrane protein) (pmp70). [swissprot;acc:p28288] 2166 ABCD3 215.925 214.481 1.00673
    atp-citrate synthase (ec 2.3.3.8) (atp-citrate (pro-s-)-lyase) (citrate cleavage enzyme). [swissprot;acc:p53396] 2689 ACLY 213.792 213.619 1.00081
    atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031] 1871 CLPX 222.819 225.228 1.01081
    atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956] 2727 no value 221.001 220.927 1.00033
    atp-dependent dna helicase ii, 80 kda subunit (lupus ku autoantigen protein p86) (ku86) (ku80) (86 kda subunit of ku antigen) (thyroid- lupus autoantigen) (tlaa) (ctc box binding factor 85 kda subunit) (ctcbf) (ctc85) (nuclear factor iv) (dna-repair protein xrcc5). [swissprot;acc:p13010] 2728 XRCC5
    atp-dependent dna helicase q5 (recq protein-like 5) (recq5). [swissprot;acc:o94762] 1703 RECQL5 216.079 219.024 1.01363
    atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] 529 DDX18 251.653 235.506 1.06856
    atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] 328 DDX24 258.437 235.183 1.09888
    atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] 428 DDX54 253.852 234.808 1.0811
    atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010] 990 DDX52 243.297 235.373 1.03367
    atpase inhibitor, mitochondrial precursor. [swissprot;acc:q9uii2] 1365 ATPIF1 228.644 223.736 1.02194
    atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [refseq;acc:nm_152565] 1126 ATP6V0D2 218.487 212.656 1.02742
    atpase, h+ transporting, lysosomal v0 subunit a isoform 4; vacuolar proton pump 116 kda accessory subunit; vacuolar proton pump, subunit 2; h(+)-transporting two-sector atpase, noncatalytic accessory protein 1b; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1b; renal tubular acidosis; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 2 (38kd). [refseq;acc:nm_020632] 1120 ATP6V0A4 218.528 212.676 1.02752
    atrophin-1 (dentatorubral-pallidoluysian atrophy protein). [swissprot;acc:p54259] 1384 ATN1 218.471 213.876 1.02148
    atrophin-1 interacting protein 1; activin receptor interacting protein 1; likely ortholog of mouse activin receptor interacting protein 1; atrophin-1 interacting protein a; membrane associated guanylate kinase 2; activin receptor interacting p. [refseq;acc:nm_012301] 1035 MAGI2 221.682 228.68 1.03157
    au rna-binding protein/enoyl-coenzyme a hydratase precursor; au rna-binding protein/enoyl-coenzyme a hydratase; 3-methylglutaconyl-coa hydratase; mga type i. [refseq;acc:nm_001698] 2913 AUH 0.00001 0.00001 1
    autoantigen ngp-1. [swissprot;acc:q13823] 670 GNL2 250.302 236.817 1.05694
    autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] 1729 ATG12 187.582 190.028 1.01304
    autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] 1540 ATG5 240.077 236.015 1.01721
    axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] 2003 DNALI1 208.315 206.41 1.00923
    b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] 1559 BCL6B 196.191 192.996 1.01655
    b-cell lymphoma 3-encoded protein (bcl-3 protein). [swissprot;acc:p20749] 2655 BCL3 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
    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 130.289 134.713 1.03396
    b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] 181 B9D1 229.818 267.265 1.16294
    ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] 244 GSTO2 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
    ba203i16.1 (hypothetical protein kiaa0970). [sptrembl;acc:q9h1w1] 3117 FNDC3A 0.00001 0.00001 1
    ba207c16.2 (fragment). [sptrembl;acc:q9nql7] 2599 KIAA1432 211.662 211.361 1.00142
    ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9] 2148 no value 217.871 219.366 1.00686
    ba304i5.1 (novel lipase) (fragment). [sptrembl;acc:q96lg2] 2115 LIPM 214.632 213.14 1.007
    ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] 931 BHLHB4 159.13 164.917 1.03637
    ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] 452 no value 224.161 207.972 1.07784
    ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 1568 221.128 224.767 1.01646

    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/