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 1051 to 1100 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
Network Comparison Type
red
green
network_comparison
132 Ranked dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Subtracted 229.406 196.695 32.711
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Divided 350 290 1.2069
Squared autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] 36359.2 24466.8 1.48606
protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] Subtracted 71062.2 95488.6 24426.4
Rooted histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] Divided 44.963 55.0576 1.22451
ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Subtracted 144.606 157.824 13.218
133 Measured cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] 12798.9 10887.2 1911.7
gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Divided 23421.5 17580.4 1.33225
Ranked formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Subtracted 226.887 194.72 32.167
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Divided 350 290 1.2069
Squared gbp protein isoform a. [refseq;acc:nm_017870] 1182.25 1726.55 1.46039
thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] Subtracted 71062.2 95488.6 24426.4
Rooted anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] 144.606 157.824 13.218
odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Divided 45.4558 55.5995 1.22316
134 Measured g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] Subtracted 12796.8 10886 1910.8
gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Divided 21785.2 16426.1 1.32626
Ranked dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] 350 290 1.2069
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Subtracted 226.884 194.79 32.094
Squared gk001 protein. [refseq;acc:nm_020198] 71062.2 95488.6 24426.4
p66 alpha. [refseq;acc:nm_017660] Divided 81888.8 56306.5 1.45434
Rooted dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] 44.849 54.7964 1.2218
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Subtracted 54.8203 67.934 13.1137
135 Measured apg3p; pc3-96 protein. [refseq;acc:nm_022488] Divided 21785.2 16426.1 1.32626
transcription factor jun-b. [swissprot;acc:p17275] Subtracted 5579.18 7488.4 1909.22
Ranked cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] Divided 350 290 1.2069
forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Subtracted 263.215 231.407 31.808
Squared calsyntenin-2 precursor. [swissprot;acc:q9h4d0] 71033.4 95440.2 24406.8
transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] Divided 81888.8 56306.5 1.45434
Rooted 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] 54.935 66.6101 1.21253
voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] Subtracted 49.2923 62.3969 13.1046
136 Measured cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] 12787.6 10880.5 1907.1
nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] Divided 3620.77 4763.34 1.31556
Ranked cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] 350 290 1.2069
forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Subtracted 263.215 231.407 31.808
Squared calsyntenin-3 precursor. [swissprot;acc:q9bqt9] 71030.1 95434.8 24404.7
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Divided 81888.8 56306.5 1.45434
Rooted adiponectin receptor 2. [refseq;acc:nm_024551] 41.8357 50.6469 1.21061
voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] Subtracted 49.2923 62.3969 13.1046
137 Measured ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] Divided 3620.77 4763.34 1.31556
g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] Subtracted 12786.6 10879.9 1906.7
Ranked forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] 263.191 231.394 31.797
ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Divided 350 290 1.2069
Squared cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] 81606.8 56215.8 1.45167
small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765] Subtracted 69549 92953.5 23404.5
Rooted musashi 2 isoform a. [refseq;acc:nm_138962] Divided 54.9787 66.2416 1.20486
voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] Subtracted 49.2925 62.397 13.1045
138 Measured kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Divided 2755.15 2094.3 1.31555
tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] Subtracted 15182.5 13277.9 1904.6
Ranked cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] 174.667 205.556 30.889
serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] Divided 194.372 234.204 1.20493

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/