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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1373 to 1422 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
172 splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Rooted 1 56.7592 65.9889 1.16261
trophinin. [swissprot;acc:q12816] Measured 23693.7 18263 1.29736
williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158] 0 112.666 141.702 1.25772
zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] Ranked 12225.7 13893.1 1.13638
173 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Rooted 1 145.551 168.796 1.1597
60s ribosomal protein l7. [swissprot;acc:p18124] 0 27.512 31.7228 1.15305
breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] Measured 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
cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] Squared 48.239 75.2348 1.55963
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] 1 82624.3 115061 1.39258
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Ranked 227.032 193.056 1.17599
suppressor of actin 1. [refseq;acc:nm_014016] 0 19088.1 16804.6 1.13589
174 bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] Rooted 15.8745 18.303 1.15298
cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] Squared 48.3438 75.3968 1.5596
dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] Ranked 1 335 286 1.17133
dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2] Measured 0 488.43 612.604 1.25423
mad protein (max dimerizer). [swissprot;acc:q05195] 1 4455.95 5774.03 1.2958
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] Rooted 145.551 168.796 1.1597
ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916] Ranked 0 13248.5 11666.4 1.13561
sedlin. [swissprot;acc:o14582] Squared 1 112820 157033 1.39189
175 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] Ranked 199.949 234.187 1.17123
cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247] Measured 0 1382.5 1107 1.24887
cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] Squared 48.5538 75.7214 1.55954
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Measured 1 4456.67 5773.77 1.29553
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] Rooted 0 61.6393 70.9983 1.15183
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] 1 145.551 168.796 1.1597
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Squared 112820 157033 1.39189
thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445] Ranked 0 13248.5 11666.4 1.13561
176 bet3 homolog. [swissprot;acc:o43617] Squared 1 112820 157033 1.39189
cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] 0 48.5538 75.7214 1.55954
dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] Ranked 13068 11528 1.13359
dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959] Rooted 20.3469 17.7078 1.14904
dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] Ranked 1 275.754 235.908 1.1689
max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Measured 4456.93 5773.67 1.29544
pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] Rooted 145.551 168.796 1.1597
small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] Measured 0 3023.85 2436.4 1.24111
177 acrc protein; putative nuclear protein. [refseq;acc:nm_052957] 4131.06 3340.03 1.23683
dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Ranked 1 229.406 196.695 1.1663
dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325] Rooted 0 20.3458 17.7104 1.14881
hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934] Squared 73.1683 109.766 1.50019
max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Measured 1 4457.06 5773.63 1.29539
mitochondrial solute carrier protein. [refseq;acc:nm_145305] Rooted 145.551 168.796 1.1597
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Ranked 0 14922.7 13174.5 1.1327
septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] Squared 1 78383 108483 1.38401
178 carboxypeptidase b precursor. [refseq;acc:nm_020361] 25326.4 18354.1 1.37988
collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400] Rooted 0 35.0775 30.5361 1.14872
dc11 protein. [refseq;acc:nm_020186] Squared 73.1683 109.766 1.50019
dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7] Measured 498.07 615.233 1.23523
formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Ranked 1 226.887 194.72 1.1652
integral membrane protein cii-3b. [sptrembl;acc:o75609] 0 14951.6 13204.2 1.13234

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/