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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Rank Gene Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 830 to 879 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
Network Comparison Type
red
green
network_comparison
104 Squared likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] Subtracted 121579 87259.3 34319.7
Rooted jun dimerization protein. [refseq;acc:nm_130469] Divided 60.8365 77.7233 1.27758
ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Subtracted 19.9625 35.798 15.8355
105 Measured musashi 1. [refseq;acc:nm_002442] Divided 4241.57 5810.79 1.36996
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Subtracted 11068 8508.5 2559.5
Ranked guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] Divided 266.716 333.165 1.24914
transcription factor jun-d. [swissprot;acc:p17535] Subtracted 200.941 158.941 42
Squared cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Divided 407289 263351 1.54656
ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] Subtracted 90432.9 56304.2 34128.7
Rooted fos-related antigen 2. [swissprot;acc:p15408] Divided 60.8675 77.7168 1.27682
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] Subtracted 63.7477 48.1588 15.5889
106 Measured nuclear protein ukp68. [refseq;acc:nm_024824] Divided 4241.57 5810.79 1.36996
protein hspc134 (protein cda04). [swissprot;acc:q9by43] Subtracted 11068 8508.5 2559.5
Ranked nostrin. [refseq;acc:nm_052946] 209.299 249.187 39.888
ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Divided 252.329 202.004 1.24913
Squared cytohesin 4. [swissprot;acc:q9uia0] 407289 263351 1.54656
septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] Subtracted 82624.3 115061 32436.7
Rooted protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Divided 60.8692 77.7165 1.27678
uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Subtracted 63.7477 48.1589 15.5888
107 Measured 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Divided 4266.04 5843.51 1.36977
septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] Subtracted 14229.2 16780.7 2551.5
Ranked eap30 subunit of ell complex. [refseq;acc:nm_007241] 209.299 249.187 39.888
homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Divided 252.309 201.998 1.24907
Squared cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 407289 263351 1.54656
ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Subtracted 84857.8 53402.4 31455.4
Rooted fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Divided 60.875 77.7152 1.27664
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 63.7477 48.1594 15.5883
108 Measured filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] Divided 4366.44 5899.76 1.35116
ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] Subtracted 14021.4 11523 2498.4
Ranked homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] Divided 252.296 201.995 1.24902
liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] Subtracted 209.299 249.187 39.888
Squared myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Divided 19321 12542.6 1.54043
septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] Subtracted 78383 108483 30100
Rooted 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] 63.7475 48.1615 15.586
voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] Divided 49.2925 62.397 1.26585
109 Measured 44050 protein. [refseq;acc:nm_178832] Subtracted 17385.9 14889.2 2496.7
rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] Divided 4366.44 5899.76 1.35116
Ranked glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] Subtracted 209.299 249.187 39.888
guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] Divided 266.933 333.281 1.24856
Squared cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] Subtracted 88432.6 58423.3 30009.3
myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] Divided 19321 12542.6 1.54043
Rooted nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Subtracted 30.8986 46.4619 15.5633
voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] Divided 49.2923 62.3969 1.26585
110 Measured nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972] Subtracted 17385.9 14889.2 2496.7
protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Divided 4366.44 5899.76 1.35116
Ranked deltex 2. [refseq;acc:nm_020892] 333.144 267.393 1.2459
gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] Subtracted 209.299 249.187 39.888
Squared myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] Divided 19321 12542.6 1.54043
pnas-18. [sptrembl;acc:q9bzu3] Subtracted 87787.3 58155.8 29631.5
Rooted junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 33.9632 18.4255 15.5377

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/