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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 5208 to 5257 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
326 dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [refseq;acc:nm_030655] Ranked Divided 0 11948.4 11295.6 1.05779
germ cell-less. [refseq;acc:nm_022471] Squared 3567.33 3084.18 1.15665
glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [swissprot;acc:q06210] Ranked Subtracted 12953.2 12273.2 680
ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] Rooted Divided 1 50.3803 45.4193 1.10923
myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] Squared Subtracted 19321 12542.6 6778.4
protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156] Measured 11773 10733.2 1039.8
putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544] Rooted 0 23.6959 25.0734 1.3775
transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Squared 177.23 126.355 50.875
u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Rooted 1 56.0466 63.4808 7.4342
327 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] Ranked Divided 0 9897.29 10466.5 1.05751
60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] Subtracted 1 241.83 263.615 21.785
60s ribosomal protein l18a. [swissprot;acc:q02543] Rooted 0 30.8547 32.2238 1.3691
actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] Squared Divided 178.482 205.335 1.15045
basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811] Subtracted 33.0303 83.901 50.8707
bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [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:o43252] Rooted Divided 1 50.3803 45.4193 1.10923
blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] Measured Subtracted 0 375.07 306.727 68.343
dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355] Divided 175.644 161.091 1.09034
dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5] Ranked Subtracted 10768.5 11444 675.5
dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] Divided 1 243.817 267.962 1.09903
luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Squared 16424.1 20645.8 1.25704
max protein. [swissprot;acc:p25912] Rooted Subtracted 56.3054 63.7148 7.4094
myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] Squared 19321 12542.6 6778.4
peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [swissprot;acc:p23284] Measured 11773 10733.2 1039.8
putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544] Rooted Divided 0 23.6959 25.0734 1.05813
septin 10 isoform 1. [refseq;acc:nm_144710] Measured 1 16067.4 19094.4 1.18839
328 26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232] Squared 0 6747.71 5878.56 1.14785
60s ribosomal protein l12. [swissprot;acc:p30050] Measured 1657.78 1805.05 1.08884
adp-ribosylation factor 3. [swissprot;acc:p16587] Ranked Subtracted 11627.8 10958.2 669.6
atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] Divided 1 258.437 235.183 1.09888
brain protein 44. [swissprot;acc:o95563] Measured 15999.1 19007.1 1.18801
far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [refseq;acc:nm_003902] Subtracted 0 604.529 538.094 66.435
histone h4. [swissprot;acc:p02304] Rooted Divided 98.5525 104.126 1.05655
kappa b-ras 1. [refseq;acc:nm_020345] Subtracted 21.0189 22.3788 1.3599
luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Squared Divided 1 16442.8 20662.7 1.25664
myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Subtracted 19321 12542.6 6778.4
nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] Rooted Divided 50.3803 45.4193 1.10923
putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] Ranked Subtracted 240.801 262.34 21.539
putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] Divided 0 10897 11520 1.05717
ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] Rooted Subtracted 1 124.41 117.043 7.367
tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [refseq;acc:nm_015975] Squared 0 354.23 402.944 48.714
udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294] Measured 1 11773 10733.2 1039.8
329 anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5] Squared Divided 0 195397 170319 1.14724
cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] Rooted 1 50.3803 45.4193 1.10923
clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] Ranked Subtracted 0 10301.4 10957.5 656.1
cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [swissprot;acc:p13073] Measured 1 11773 10733.2 1039.8
dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] Divided 0 1658.07 1805.36 1.08883
lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Ranked Subtracted 1 191.644 170.192 21.452
likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] Squared 0 605.501 557.57 47.931
low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] Measured 161 95 66
metaxin 2. [swissprot;acc:o75431] Squared Divided 1 41236 51807 1.25635

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/