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 Value Type Network Comparison Type Interaction Map green Filtered red network_comparison
    Results: HTML CSV LaTeX Showing element 551 to 600 of 3228 in total
    Value Type  : Measured
    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] 739 6434.78 5768.32 1.11554
    cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] 623 7013.19 6228.39 1.126
    cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] 629
    centaurin beta 1 (cnt-b1). [swissprot;acc:q15027] 2123 6301.76 5977.03 1.05433
    centaurin beta 2 (cnt-b2). [swissprot;acc:q15057] 2122
    centaurin beta 5 (cnt-b5). [swissprot;acc:q96p50] 2121
    centaurin gamma 1. [swissprot;acc:q99490] 2157 6000.03 5701.81 1.0523
    centaurin gamma 2. [swissprot;acc:q9upq3] 2155
    centaurin gamma 3. [swissprot;acc:q96p47] 2158
    centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451] 2499 7971.27 8186.02 1.02694
    centromere/kinetochore protein zw10 homolog. [swissprot;acc:o43264] 3167 0.00001 0.00001 1
    cerebral cell adhesion molecule. [refseq;acc:nm_016174] 1747 10241.9 9596.59 1.06724
    cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] 900 4279.17 4713.58 1.10152
    cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073] 384 5279.4 4533.74 1.16447
    cgthba protein (-14 gene protein). [swissprot;acc:q12980] 2562 5187.78 5291.65 1.02002
    channel associated protein of synapse-110 (chapsyn-110) (discs, large homolog 2). [swissprot;acc:q15700] 2085 6159.4 5835.4 1.05552
    chaperone-activity of bc1 complex-like, mitochondrial precursor (chaperone-abc1-like). [swissprot;acc:q8ni60] 1173 6305.95 5799.35 1.08735
    choline dehydrogenase. [refseq;acc:nm_018397] 1556 6302.76 5875.75 1.07267
    choline o-acetyltransferase (ec 2.3.1.6) (choactase) (choline acetylase) (chat). [swissprot;acc:p28329] 1139 6303.95 5790.66 1.08864
    cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] 1840 3375.34 3591.95 1.06417
    cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] 1846
    chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] 271 3093.78 2554.89 1.21092
    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] 468 5578.02 4869.15 1.14558
    chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192] 958 4917.77 4483.26 1.09692
    chromobox protein homolog 1 (heterochromatin protein 1 homolog beta) (hp1 beta) (modifier 1 protein) (m31) (heterochromatin protein p25). [swissprot;acc:p23197] 2598 7417.58 7538.48 1.0163
    chromobox protein homolog 3 (heterochromatin protein 1 homolog gamma) (hp1 gamma) (modifier 2 protein) (hech). [swissprot;acc:q13185] 2591 7422.01 7550.12 1.01726
    chromobox protein homolog 5 (heterochromatin protein 1 homolog alpha) (hp1 alpha) (antigen p25). [swissprot;acc:p45973] 2590 7422.68 7551.88 1.01741
    chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] 52 1390.33 779.167 1.78438
    chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] 47
    chromodomain protein, y chromosome-like isoform a; cdy-like, autosomal; testis-specific chromodomain y-like protein. [refseq;acc:nm_004824] 1758 7576.84 7101.15 1.06699
    chromodomain y-like protein 2. [refseq;acc:nm_152342] 1755 7577.75 7101.7 1.06703
    chromosome 11 open reading frame2; chromosome 11 open reading frame2. [refseq;acc:nm_013265] 2214 6199.28 5910.12 1.04893
    chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] 274 2579.49 3119.98 1.20953
    cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830] 837 4492.98 4063.64 1.10565
    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] 2291 6048.89 5783.71 1.04585
    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] 2675 7741.14 7780.98 1.00515
    clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] 2189 5033.55 5285.03 1.04996
    clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] 2197 5036.39 5285.79 1.04952
    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] 262 20431.7 24896.4 1.21852
    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] 1678 6162.98 5763.25 1.06936
    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] 1551 6149.86 5732.83 1.07274
    cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] 268 20127.8 24473.9 1.21593
    cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] 266 20369.9 24806.9 1.21782
    cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] 288 19380.3 23422.4 1.20857
    cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] 294 18702.6 22515.5 1.20387
    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] 552 13572.8 15427.2 1.13663
    cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294] 2337 5350.78 5123.89 1.04428

    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/