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.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Value Type Rank Gene description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 686 to 735 of 29840 in total
Value Type  : Measured
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
red
green
network_comparison
172 suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] Subtracted 0 1890.86 2081.91 191.05
trophinin. [swissprot;acc:q12816] Divided 1 23693.7 18263 1.29736
williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158] 0 112.666 141.702 1.25772
173 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 1 4579.34 5940.64 1.29727
cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] 0 3265.25 4102.97 1.25656
mesoderm induction early response 1. [refseq;acc:nm_020948] Subtracted 1914.5 1723.5 191
uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] 1 4556.79 2945.28 1611.51
174 dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2] Divided 0 488.43 612.604 1.25423
mad protein (max dimerizer). [swissprot;acc:q05195] 1 4455.95 5774.03 1.2958
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] Subtracted 4556.83 2945.38 1611.45
uridine kinase-like 1. [swissprot;acc:q9nwz5] 0 633.433 821.711 188.278
175 cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247] Divided 1382.5 1107 1.24887
histone deacetylase 2 (hd2). [swissprot;acc:q92769] Subtracted 2056.14 2244.06 187.92
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Divided 1 4456.67 5773.77 1.29553
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4] Subtracted 4556.99 2945.8 1611.19
176 40s ribosomal protein s29. [swissprot;acc:p30054] 0 1711.6 1895.38 183.78
hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] 1 10235.2 11830.8 1595.6
max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Divided 4456.93 5773.67 1.29544
small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] 0 3023.85 2436.4 1.24111
177 acrc protein; putative nuclear protein. [refseq;acc:nm_052957] 4131.06 3340.03 1.23683
lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Subtracted 1 4110.14 5694.99 1584.85
max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Divided 4457.06 5773.63 1.29539
pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] Subtracted 0 1124.15 943.423 180.727
178 dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7] Divided 498.07 615.233 1.23523
mstp028 protein. [refseq;acc:nm_031954] Subtracted 9988.45 9808.48 179.97
myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] Divided 1 21591.5 27904.5 1.29238
stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] Subtracted 10908.6 12491.8 1583.2
179 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] 4266.04 5843.51 1577.47
hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934] Divided 0 556 681 1.22482
myosin vc (myosin 5c). [swissprot;acc:q9nqx4] 1 21591.5 27904.5 1.29238
ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916] Subtracted 0 304.664 483.809 179.145
180 c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] 1 10872.4 12447 1574.6
dc11 protein. [refseq;acc:nm_020186] Divided 0 556 681 1.22482
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] 1 21591.5 27904.5 1.29238
thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445] Subtracted 0 304.664 483.809 179.145
181 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] 1318.22 1495.66 177.44
enigma protein; lim domain protein. [refseq;acc:nm_005451] Divided 187.25 153 1.22386
eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] 1 4068.56 5252.6 1.29102
musashi 2 isoform a. [refseq;acc:nm_138962] Subtracted 4241.57 5810.79 1569.22
182 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 0 1317.84 1495.22 177.38
musashi 1. [refseq;acc:nm_002442] 1 4241.57 5810.79 1569.22
rna-binding protein. [refseq;acc:nm_019027] Divided 4069.83 5252.17 1.29051
transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664] 0 971.889 794.63 1.22307
183 apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] 1 4069.83 5252.17 1.29051
blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161] 0 375.07 306.727 1.22281
nuclear protein ukp68. [refseq;acc:nm_024824] Subtracted 1 4241.57 5810.79 1569.22
transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664] 0 971.889 794.63 177.259
184 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 736.737 561.038 175.699
blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] Divided 375.07 306.727 1.22281
ns1-associated protein 1. [refseq;acc:nm_006372] 1 4069.83 5252.17 1.29051

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/