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 [...,...].
    Value Type description Gene Rank green Network Comparison Type Interaction Map Filtered red network_comparison
    Results: HTML CSV LaTeX Showing element 551 to 600 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		green
    		red
    		network_comparison
    cell division protein kinase 9 (ec 2.7.1.-) (serine/threonine-protein kinase pitalre) (c-2k). [swissprot;acc:p50750] 2974 0.00001 0.00001 1
    cellular modulator of immune recognition. [refseq;acc:nm_145021] 1179 212.672 218.186 1.02593
    cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] 699 209.118 220.438 1.05413
    cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] 705
    centaurin beta 1 (cnt-b1). [swissprot;acc:q15027] 2037 220.812 218.919 1.00865
    centaurin beta 2 (cnt-b2). [swissprot;acc:q15057] 2035
    centaurin beta 5 (cnt-b5). [swissprot;acc:q96p50] 2034
    centaurin gamma 1. [swissprot;acc:q99490] 1924 218.452 220.659 1.0101
    centaurin gamma 2. [swissprot;acc:q9upq3] 1922
    centaurin gamma 3. [swissprot;acc:q96p47] 1925
    centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451] 1317 202.105 206.773 1.0231
    centromere/kinetochore protein zw10 homolog. [swissprot;acc:o43264] 3167 0.00001 0.00001 1
    cerebral cell adhesion molecule. [refseq;acc:nm_016174] 2508 193.871 194.349 1.00247
    cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] 172 205.556 174.667 1.17685
    cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073] 832 222.222 231.734 1.0428
    cgthba protein (-14 gene protein). [swissprot;acc:q12980] 644 230.596 217.67 1.05938
    channel associated protein of synapse-110 (chapsyn-110) (discs, large homolog 2). [swissprot;acc:q15700] 2657 216.7 216.934 1.00108
    chaperone-activity of bc1 complex-like, mitochondrial precursor (chaperone-abc1-like). [swissprot;acc:q8ni60] 1730 212.567 215.336 1.01303
    choline dehydrogenase. [refseq;acc:nm_018397] 1647 214.149 217.256 1.01451
    choline o-acetyltransferase (ec 2.3.1.6) (choactase) (choline acetylase) (chat). [swissprot;acc:p28329] 1967 213.702 211.632 1.00978
    cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] 269 267.352 241.373 1.10763
    cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] 275
    chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] 234 256.835 287.41 1.11905
    chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028] 282 228.297 252.39 1.10553
    chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192] 902 228.762 237.62 1.03872
    chromobox protein homolog 1 (heterochromatin protein 1 homolog beta) (hp1 beta) (modifier 1 protein) (m31) (heterochromatin protein p25). [swissprot;acc:p23197] 2535 188.63 188.228 1.00214
    chromobox protein homolog 3 (heterochromatin protein 1 homolog gamma) (hp1 gamma) (modifier 2 protein) (hech). [swissprot;acc:q13185] 2509 188.366 187.902 1.00247
    chromobox protein homolog 5 (heterochromatin protein 1 homolog alpha) (hp1 alpha) (antigen p25). [swissprot;acc:p45973] 2505 188.326 187.853 1.00252
    chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] 335 284 312 1.09859
    chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] 330
    chromodomain protein, y chromosome-like isoform a; cdy-like, autosomal; testis-specific chromodomain y-like protein. [refseq;acc:nm_004824] 2553 193.467 193.12 1.0018
    chromodomain y-like protein 2. [refseq;acc:nm_152342] 2556 193.46 193.119 1.00177
    chromosome 11 open reading frame2; chromosome 11 open reading frame2. [refseq;acc:nm_013265] 1211 219.759 214.364 1.02517
    chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] 153 298.263 249.663 1.19466
    cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830] 982 235.351 243.312 1.03383
    cisplatin resistance related protein crr9p. [refseq;acc:nm_030782] 3197 0.00001 0.00001 1
    clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [swissprot;acc:o60641] 1392 213.876 218.471 1.02148
    clathrin coat assembly protein ap50 (clathrin coat associated protein ap50) (plasma membrane adaptor ap-2 50 kda protein) (ha2 50 kda subunit) (clathrin assembly protein complex 2 medium chain) (ap-2 mu 2 chain). [swissprot;acc:p20172] 2208 200.413 199.129 1.00645
    clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] 399 226.226 207.889 1.08821
    clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] 405 226.209 207.931 1.0879
    cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] 850 112.329 107.842 1.04161
    cleavage and polyadenylation specific factor 5, 25 kd subunit; pre-mrna cleavage factor im (25kd); pre-mrna cleavage factor im, 25kd subunit. [refseq;acc:nm_007006] 1657 216.195 219.314 1.01443
    cleavage and polyadenylation specific factor 6, 68 kd subunit; pre-mrna cleavage factor im (68kd); cleavage and polyadenylation specific factor 6, 68kd subunit; pre-mrna cleavage factor i, 68kd subunit. [refseq;acc:nm_007007] 1480 214.55 218.664 1.01918
    cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] 871 114.552 110.2 1.03949
    cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] 854 112.772 108.289 1.0414
    cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] 1006 120.375 116.524 1.03305
    cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] 1089 125.004 121.428 1.02945
    cleavage stimulation factor, 50 kda subunit (cstf 50 kda subunit) (cf-1 50 kda subunit). [swissprot;acc:q05048] 3129 0.00001 0.00001 1
    cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] 2140 162.665 161.547 1.00692
    cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294] 756 235.583 224.434 1.04968

    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
    - 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/