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 Hugo description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1280 to 1329 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Interaction Map
red
green
network_comparison
320 SF3B1 splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Subtracted Low confidence 202.057 193.952 8.105
321 no value c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] Divided High confidence 241.892 265.959 1.09949
DYNC1I1 dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] Subtracted Low confidence 209.495 201.474 8.021
SNORD23 glioma tumor suppressor candidate region gene 2 protein (p60). [swissprot;acc:q9nzm5] Divided 207.402 199.219 1.04108
TRO trophinin. [swissprot;acc:q12816] Subtracted High confidence 88.2482 110.265 22.0168
322 DNASE2B deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Divided 86.7483 78.8995 1.09948
GGPS1 geranylgeranyl pyrophosphate synthetase (ggpp synthetase) (ggppsase) (geranylgeranyl diphosphate synthase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10); farnesyltranstransferase (ec 2.5.1.29)]. [swissprot;acc:o95749] Subtracted Low confidence 209.518 201.554 7.964
NUDT21 cleavage and polyadenylation specific factor 5, 25 kd subunit; pre-mrna cleavage factor im (25kd); pre-mrna cleavage factor im, 25kd subunit. [refseq;acc:nm_007006] Divided 212.262 203.991 1.04055
RRM2 ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] Subtracted High confidence 231.969 210.064 21.905
323 no value 60s ribosomal protein l23a. [swissprot;acc:p29316] Divided 241.884 265.945 1.09947
C20orf43 protein c20orf43 (hspc164/hspc169) (ad-007) (cda05). [swissprot;acc:q9by42] Subtracted Low confidence 200.482 208.446 7.964
ITGB1BP2 integrin beta-1 binding protein 2 (melusin) (mstp015). [swissprot;acc:q9ukp3] Divided 212.262 203.991 1.04055
RPS14 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] Subtracted High confidence 242.238 264.11 21.872
324 no value 40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232]
RAB3GAP2 rab3 gtpase-activating protein, non-catalytic subunit. [refseq;acc:nm_012414] Divided Low confidence 212.262 203.991 1.04055
RPS23 40s ribosomal protein s23. [swissprot;acc:p39028] High confidence 243.944 268.195 1.09941
SPSB4 spry domain-containing socs box protein ssb-4. [refseq;acc:nm_080862] Subtracted Low confidence 219.655 211.763 7.892
325 AFF2 fragile x mental retardation 2 protein (protein fmr-2) (fmr2p) (ox19 protein) (fragile x e mental retardation syndrome protein). [swissprot;acc:p51816] 219.599 211.723 7.876
MRPL13 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] High confidence 241.828 263.62 21.792
MRPS12 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] Divided 243.944 268.195 1.09941
STT3B source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Low confidence 199.905 192.123 1.04051
326 AFF3 laf-4 protein (lymphoid nuclear protein related to af4). [swissprot;acc:p51826] Subtracted 219.598 211.722 7.876
DDOST dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] Divided 199.343 191.59 1.04047
RPL5 60s ribosomal protein l5. [swissprot;acc:p46777] High confidence 241.899 265.924 1.09932
RPS16 40s ribosomal protein s16. [swissprot;acc:p17008] Subtracted 241.828 263.62 21.792
327 AFF4 all1 fused gene from 5q31. [refseq;acc:nm_014423] Low confidence 219.598 211.722 7.876
POLR2A dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] Divided High confidence 243.817 267.962 1.09903
RPL13A 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] Subtracted 241.83 263.615 21.785
TRAPPC3 bet3 homolog. [swissprot;acc:o43617] Divided Low confidence 197.221 189.574 1.04034
328 no value putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] Subtracted High confidence 240.801 262.34 21.539
AFF1 af-4 protein (proto-oncogene af4) (fel protein). [swissprot;acc:p51825] Low confidence 219.597 211.722 7.875
DDX24 atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] Divided High confidence 258.437 235.183 1.09888
SF3B2 splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] Low confidence 203.162 195.289 1.04031
329 EXOC7 exocyst complex component exo70. [swissprot;acc:q9upt5] 204.124 212.339 1.04025
LASS2 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Subtracted High confidence 191.644 170.192 21.452
NEUROD2 neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Divided 312 284 1.09859
SF3B2 splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] Subtracted Low confidence 203.162 195.289 7.873
330 BCAR1 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] High confidence 224.657 203.235 21.422
CHD3 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] Divided 312 284 1.09859
RGN senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493] Low confidence 221.437 212.889 1.04015
SPSB1 spry domain-containing socs box protein ssb-1. [refseq;acc:nm_025106] Subtracted 219.556 211.692 7.864
331 CCT4 t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] High confidence 224.647 203.242 21.405
CDK2AP2 doc-1 related protein (doc-1r). [swissprot;acc:o75956] Divided 312 284 1.09859
GALE udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] Low confidence 200.249 192.535 1.04007
NME7 nucleoside diphosphate kinase 7 (ec 2.7.4.6) (ndk 7) (ndp kinase 7) (nm23-h7). [swissprot;acc:q9y5b8] Subtracted 210.796 202.935 7.861
332 DYNC1I1 dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] Divided 209.495 201.474 1.03981
NEDD9 enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] Subtracted High confidence 224.633 203.251 21.382
NEUROD6 neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Divided 312 284 1.09859
SPG20 spartin; trans-activated by hepatitis c virus core protein 1. [refseq;acc:nm_015087] Subtracted Low confidence 210.796 202.935 7.861
333 no value transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] High confidence 265.634 244.304 21.33

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/