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.


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 [...,...].
Rank Gene Network Comparison Type Hugo Value Type description Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 836 to 885 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
Hugo
Value Type
description
red
network_comparison
green
105 Divided PSCD2 Squared cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 407289 1.54656 263351
Subtracted no value Rooted 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] 63.7477 15.5889 48.1588
JUND Ranked transcription factor jun-d. [swissprot;acc:p17535] 200.941 42 158.941
RALGDS Squared ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] 90432.9 34128.7 56304.2
VPS24 Measured neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] 11068 2559.5 8508.5
106 Divided COQ7 Ranked ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] 252.329 1.24913 202.004
FOSB Rooted protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] 60.8692 1.27678 77.7165
PSCD4 Squared cytohesin 4. [swissprot;acc:q9uia0] 407289 1.54656 263351
ZC3H14 Measured nuclear protein ukp68. [refseq;acc:nm_024824] 4241.57 1.36996 5810.79
Subtracted CHMP4A protein hspc134 (protein cda04). [swissprot;acc:q9by43] 11068 2559.5 8508.5
NOSTRIN Ranked nostrin. [refseq;acc:nm_052946] 209.299 39.888 249.187
PPP2R2D Rooted uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] 63.7477 15.5888 48.1589
SEPT4 Squared 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] 82624.3 32436.7 115061
107 Divided FOSL1 Rooted fos-related antigen 1 (fra-1). [swissprot;acc:p15407] 60.875 1.27664 77.7152
HOMER1 Ranked homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] 252.309 1.24907 201.998
NCBP2 Measured 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] 4266.04 1.36977 5843.51
PSCD3 Squared cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 407289 1.54656 263351
Subtracted PPP2R2B Rooted 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] 63.7477 15.5883 48.1594
RGL1 Squared ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] 84857.8 31455.4 53402.4
SEPT1 Measured septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] 14229.2 2551.5 16780.7
SNF8 Ranked eap30 subunit of ell complex. [refseq;acc:nm_007241] 209.299 39.888 249.187
108 Divided no value Squared myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] 19321 1.54043 12542.6
CACNG2 Rooted voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] 49.2925 1.26585 62.397
FLNB 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] 4366.44 1.35116 5899.76
HOMER3 Ranked homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] 252.296 1.24902 201.995
Subtracted PPP2R2C 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 15.586 48.1615
RALGDS Measured ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] 14021.4 2498.4 11523
SEPT1 Squared septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] 78383 30100 108483
SLC39A6 Ranked liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] 209.299 39.888 249.187
109 Divided CACNG8 Rooted voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] 49.2923 1.26585 62.3969
GNB4 Ranked guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] 266.933 1.24856 333.281
MYH4 Squared myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] 19321 1.54043 12542.6
REV1 Measured rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] 4366.44 1.35116 5899.76
Subtracted no value Squared cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] 88432.6 30009.3 58423.3
C10orf83 Measured 44050 protein. [refseq;acc:nm_178832] 17385.9 2496.7 14889.2
GAD2 Ranked glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] 209.299 39.888 249.187
NDUFS4 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] 30.8986 15.5633 46.4619
110 Divided CACNG4 voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] 49.293 1.26585 62.3973
DTX2 Ranked deltex 2. [refseq;acc:nm_020892] 333.144 1.2459 267.393
MYH8 Squared myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] 19321 1.54043 12542.6
PRMT1 Measured protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] 4366.44 1.35116 5899.76
Subtracted no value Squared pnas-18. [sptrembl;acc:q9bzu3] 87787.3 29631.5 58155.8
JPH3 Rooted junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 33.9632 15.5377 18.4255
NAPG Ranked gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] 209.299 39.888 249.187
PPP1R8 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] 17385.9 2496.7 14889.2
111 Divided CACNG3 Rooted voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] 49.2923 1.26585 62.3969
DTX1 Ranked deltex homolog 1; hdx-1. [refseq;acc:nm_004416] 332.925 1.24563 267.274
MYH2 Squared myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] 19321 1.54043 12542.6
PRMT8 Measured protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] 4366.44 1.35116 5899.76
Subtracted ACADVL Squared acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] 79779.8 28304.2 108084

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/