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 Value Type Network Comparison Type Interaction Map red Filtered network_comparison green
    Results: HTML CSV LaTeX Showing element 558 to 607 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		network_comparison
    		green
    centaurin gamma 1. [swissprot;acc:q99490] 1924 CENTG1 220.659 1.0101 218.452
    centaurin gamma 2. [swissprot;acc:q9upq3] 1922 CENTG2
    centaurin gamma 3. [swissprot;acc:q96p47] 1925 CENTG3
    centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451] 1317 CENPJ 206.773 1.0231 202.105
    centromere/kinetochore protein zw10 homolog. [swissprot;acc:o43264] 3167 ZW10 0.00001 1 0.00001
    cerebral cell adhesion molecule. [refseq;acc:nm_016174] 2508 CEECAM1 194.349 1.00247 193.871
    cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] 172 TIPRL 174.667 1.17685 205.556
    cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073] 832 no value 231.734 1.0428 222.222
    cgthba protein (-14 gene protein). [swissprot;acc:q12980] 644 C16orf35 217.67 1.05938 230.596
    channel associated protein of synapse-110 (chapsyn-110) (discs, large homolog 2). [swissprot;acc:q15700] 2657 DLG2 216.934 1.00108 216.7
    chaperone-activity of bc1 complex-like, mitochondrial precursor (chaperone-abc1-like). [swissprot;acc:q8ni60] 1730 CABC1 215.336 1.01303 212.567
    choline dehydrogenase. [refseq;acc:nm_018397] 1647 CHDH 217.256 1.01451 214.149
    choline o-acetyltransferase (ec 2.3.1.6) (choactase) (choline acetylase) (chat). [swissprot;acc:p28329] 1967 CHAT 211.632 1.00978 213.702
    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 PCYT1A 241.373 1.10763 267.352
    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 PCYT1B
    chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] 234 CHRAC1 287.41 1.11905 256.835
    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 RBBP4 252.39 1.10553 228.297
    chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192] 902 SUPT16H 237.62 1.03872 228.762
    chromobox protein homolog 1 (heterochromatin protein 1 homolog beta) (hp1 beta) (modifier 1 protein) (m31) (heterochromatin protein p25). [swissprot;acc:p23197] 2535 CBX1 188.228 1.00214 188.63
    chromobox protein homolog 3 (heterochromatin protein 1 homolog gamma) (hp1 gamma) (modifier 2 protein) (hech). [swissprot;acc:q13185] 2509 CBX3 187.902 1.00247 188.366
    chromobox protein homolog 5 (heterochromatin protein 1 homolog alpha) (hp1 alpha) (antigen p25). [swissprot;acc:p45973] 2505 CBX5 187.853 1.00252 188.326
    chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] 335 CHD5 312 1.09859 284
    chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] 330 CHD3
    chromodomain protein, y chromosome-like isoform a; cdy-like, autosomal; testis-specific chromodomain y-like protein. [refseq;acc:nm_004824] 2553 CDYL 193.12 1.0018 193.467
    chromodomain y-like protein 2. [refseq;acc:nm_152342] 2556 CDYL2 193.119 1.00177 193.46
    chromosome 11 open reading frame2; chromosome 11 open reading frame2. [refseq;acc:nm_013265] 1211 C11orf2 214.364 1.02517 219.759
    chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] 153 RBM15B 249.663 1.19466 298.263
    cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830] 982 CIRH1A 243.312 1.03383 235.351
    cisplatin resistance related protein crr9p. [refseq;acc:nm_030782] 3197 CLPTM1L 0.00001 1 0.00001
    clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [swissprot;acc:o60641] 1392 SNAP91 218.471 1.02148 213.876
    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 AP2M1 199.129 1.00645 200.413
    clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] 399 CLTC 207.889 1.08821 226.226
    clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] 405 CLTCL1 207.931 1.0879 226.209
    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 CPSF4 107.842 1.04161 112.329
    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 NUDT21 219.314 1.01443 216.195
    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 CPSF6 218.664 1.01918 214.55
    cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] 871 CPSF2 110.2 1.03949 114.552
    cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] 854 CPSF1 108.289 1.0414 112.772
    cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] 1006 CPSF3 116.524 1.03305 120.375
    cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] 1089 CSTF3 121.428 1.02945 125.004
    cleavage stimulation factor, 50 kda subunit (cstf 50 kda subunit) (cf-1 50 kda subunit). [swissprot;acc:q05048] 3129 CSTF1 0.00001 1 0.00001
    cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] 2140 CSTF2 161.547 1.00692 162.665
    cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294] 756 CLPTM1 224.434 1.04968 235.583
    clll6 protein. [refseq;acc:nm_020456] 3028 C13orf1 0.00001 1 0.00001
    coactosin-like protein. [swissprot;acc:q14019] 1219 COTL1 211.959 1.025 217.258
    coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [swissprot;acc:p53621] 1093 COPA 177.432 1.02939 182.647
    coatomer beta subunit (beta-coat protein) (beta-cop). [swissprot;acc:p53618] 1036 COPB1 171.341 1.03155 176.746
    coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] 1074 COPB2 174.387 1.03045 179.697
    coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [swissprot;acc:p48444] 1077 ARCN1
    coatomer epsilon subunit (epsilon-coat protein) (epsilon-cop). [swissprot;acc:o14579] 1174 COPE 187.964 1.02599 192.849

    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/