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 Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


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Hugo Gene description Rank measured final expected
Results: HTML CSV LaTeX Showing element 301 to 350 of 3206 in total
Hugo  : no value
description
Rank
measured
final
expected
RIBULOSE-5-PHOSPHATE-3-EPIMERASE; RIBULOSE 5-PHOSPHATE 3-EPIMERASE. [RefSeq;Acc:NM_006916] 2372 0.327497 0.220049184 1.48829
RNA HELICASE-RELATED PROTEIN; RNA HELICASE-LIKE PROTEIN; SF3B125 DEAD-BOX PROTEIN. [RefSeq;Acc:NM_007372] 1433 0.038631 0.243657992 0.158546
RNA-BINDING PROTEIN. [RefSeq;Acc:NM_019027] 263 0.0560669 0.308560029 0.181705
SCRATCH; SCRATCH 1. [RefSeq;Acc:NM_031309] 1775 0.322861 0.235895694 1.36866
SECRETED MODULAR CALCIUM-BINDING PROTEIN 1. [RefSeq;Acc:NM_022137] 659 0.0285187 0.267114063 0.106766
SERPIN B11. [SWISSPROT;Acc:Q96P15] 2326 0.0194204 0.221795594 0.0875599
SEVEN IN ABSENTIA HOMOLOG 1. [RefSeq;Acc:NM_003031] 499 0.563143 0.274221006 2.05361
SH3 DOMAIN-BINDING GLUTAMIC ACID-RICH-LIKE PROTEIN 2 (FOVEA-ASSOCIATED SH3 DOMAIN BINDING PROTEIN). [SWISSPROT;Acc:Q9UJC5] 554 0.0368814 0.270999456 0.136094
SIGNAL RECOGNITION PARTICLE RECEPTOR ALPHA SUBUNIT (SR-ALPHA) (DOCKING PROTEIN ALPHA) (DP-ALPHA). [SWISSPROT;Acc:P08240] 2074 0.411592 0.229287668 1.79509
SIGNAL-INDUCED PROLIFERATION-ASSOCIATED 1-LIKE 1. [RefSeq;Acc:NM_015556] 688 0.0671866 0.265643682 0.25292
SIMILAR TO ZINC FINGER PROTEIN 277. [SPTREMBL;Acc:Q8WWA6] 2769 0.0486609 0.201617133 0.241353
SMALL GLUTAMINE RICH PROTEIN WITH TETRATRICOPEPTIDE REPEATS 2. [RefSeq;Acc:NM_019072] 2852 0.839834 0.191276958 4.39067
SMALL NUCLEAR RIBONUCLEOPROTEIN E (SNRNP-E) (SM PROTEIN E) (SM-E) (SME). [SWISSPROT;Acc:P08578] 534 0.0399967 0.271366443 0.14739
SPLICING FACTOR 3B SUBUNIT 3 (SPLICEOSOME ASSOCIATED PROTEIN 130) (SAP 130) (SF3B130) (PRE-MRNA SPLICING FACTOR SF3B 130 KDA SUBUNIT). [SWISSPROT;Acc:Q15393] 269 1.08194 0.306378809 3.53138
SPROUTY HOMOLOG 4 (SPRY-4). [SWISSPROT;Acc:Q9C004] 1151 0.0568291 0.249717015 0.227574
STEROL REGULATORY ELEMENT BINDING PROTEIN-2 (SREBP-2) (STEROL REGULATORY ELEMENT-BINDING TRANSCRIPTION FACTOR 2). [SWISSPROT;Acc:Q12772] 2151 0.0569865 0.227323135 0.250685
SUPPRESSOR OF TY 5 HOMOLOG; SUPPRESSOR OF TY (S.CEREVISIAE) 5 HOMOLOG. [RefSeq;Acc:NM_003169] 1906 1.04135 0.23220836 4.48455
SURVIVAL MOTOR NEURON PROTEIN (COMPONENT OF GEMS 1) (GEMIN1). [SWISSPROT;Acc:Q16637] 1473 0.270547 0.242976461 1.11347
SYNBINDIN (TRS23 HOMOLOG) (HEMATOPOIETIC STEM/PROGENITOR CELL PROTEIN 172) (HSPC172) (PTD009) (CGI-104). [SWISSPROT;Acc:Q9Y296] 3024 0.0250043 0.119322081 0.209553
TAX INTERACTION PROTEIN 1. [RefSeq;Acc:NM_014604] 1075 0.281064 0.252267648 1.11415
TETRATRICOPEPTIDE REPEAT PROTEIN 4 (MY044 PROTEIN). [SWISSPROT;Acc:O95801] 2565 0.061947 0.213525671 0.290115
TFIIH BASAL TRANSCRIPTION FACTOR COMPLEX P44 SUBUNIT (BASIC TRANSCRIPTION FACTOR 2 44 KDA SUBUNIT) (BTF2-P44) (GENERAL TRANSCRIPTION FACTOR IIH POLYPEPTIDE 2). [SWISSPROT;Acc:Q13888] 3034 0.146213 0.114763273 1.27404
TGF BETA-INDUCIBLE NUCLEAR PROTEIN 1; HAIRY CELL LEUKEMIA PROTEIN 1. [RefSeq;Acc:NM_014886] 1316 0.448528 0.24569876 1.82552
THIAMIN PYROPHOSPHOKINASE 1; MOUSE THIAMIN PYROPHOSPHOKINASE HOMOLOG; THIAMINE PYROPHOSPHOKINASE. [RefSeq;Acc:NM_022445] 2375 0.0258973 0.220048603 0.117689
TRANSCRIPTION ELONGATION FACTOR A PROTEIN 1 (TRANSCRIPTION ELONGATION FACTOR S-II PROTEIN 1) (TRANSCRIPTION ELONGATION FACTOR TFIIS.O). [SWISSPROT;Acc:P23193] 2423 0.0637011 0.218132041 0.29203
TRANSCRIPTION FACTOR BTF3 HOMOLOG 3. [SWISSPROT;Acc:Q13892] 247 0.625831 0.312379769 2.00343
TRANSCRIPTION FACTOR DP-1 (E2F DIMERIZATION PARTNER 1) (DRTF1- POLYPEPTIDE-1) (DRTF1). [SWISSPROT;Acc:Q14186] 85 0.788778 0.388723357 2.02915
TRANSCRIPTION FACTOR MAFG (V-MAF MUSCULOAPONEUROTIC FIBROSARCOMA ONCOGENE HOMOLOG G) (HMAF). [SWISSPROT;Acc:O15525] 2670 0.0798317 0.209233273 0.381544
TRANSCRIPTION FACTOR MAFK (ERYTHROID TRANSCRIPTION FACTOR NF-E2 P18 SUBUNIT). [SWISSPROT;Acc:O60675] 2672 0.0897053 0.209232998 0.428734
TRANSCRIPTION FACTOR-LIKE PROTEIN MORF4 (MORTALITY FACTOR 4) (CELLULAR SENESCENCE-RELATED PROTEIN 1) (SEN1). [SWISSPROT;Acc:Q9Y690] 1472 0.217383 0.242982412 0.894645
TRANSDUCIN-LIKE ENHANCER PROTEIN 1 (ESG1). [SWISSPROT;Acc:Q04724] 995 0.357881 0.255026331 1.40331
TRANSFORMER-2 PROTEIN HOMOLOG (TRA-2 ALPHA). [SWISSPROT;Acc:Q13595] 438 0.345566 0.276953532 1.24774
TRANSFORMING PROTEIN N-RAS. [SWISSPROT;Acc:P01111] 2962 0.217355 0.146163261 1.48707
TRANSLIN. [SWISSPROT;Acc:Q15631] 1600 0.218752 0.240009128 0.911432
TRINUCLEOTIDE REPEAT CONTAINING 15. [RefSeq;Acc:NM_015575] 180 0.0561104 0.336776904 0.16661
TYROSINE AMINOTRANSFERASE (EC 2.6.1.5) (L-TYROSINE:2-OXOGLUTARATE AMINOTRANSFERASE) (TAT). [SWISSPROT;Acc:P17735] 2902 0.174557 0.174700429 0.999179
U2 SMALL NUCLEAR RIBONUCLEOPROTEIN AUXILIARY FACTOR 35 KDA SUBUNIT RELATED-PROTEIN 1. [SWISSPROT;Acc:Q15695] 658 0.20255 0.267251969 0.757899
U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM2 (SMALL NUCLEAR RIBONUCLEAR PROTEIN D HOMOLOG) (G7B) (SNRNP CORE SM-LIKE PROTEIN SM-X5). [SWISSPROT;Acc:Q9Y333] 1487 0.390142 0.242827979 1.60666
U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM7. [SWISSPROT;Acc:Q9UK45] 1937 0.268923 0.231690359 1.1607
UBA/UBX 33.3 KDA PROTEIN. [SWISSPROT;Acc:Q04323] 126 0.375086 0.3550505 1.05643
UBIQUITIN ACTIVATING ENZYME E1-LIKE PROTEIN. [RefSeq;Acc:NM_006395] 2892 0.151451 0.178121277 0.850269
UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 3 (EC 6.3.2.19) (UBIQUITIN- PROTEIN LIGASE) (UBIQUITIN CARRIER PROTEIN) (E2(17)KB 3). [SWISSPROT;Acc:P47986] 2920 0.126707 0.16882224 0.750535
UBIQUITIN-LIKE PROTEIN SMT3B (SENTRIN 2) (HSMT3). [SWISSPROT;Acc:P55855] 1024 0.0979873 0.253442086 0.386626
UBIQUITIN. [SWISSPROT;Acc:P02248] 304 0.241123 0.298782679 0.807018
URIDINE KINASE-LIKE 1. [SWISSPROT;Acc:Q9NWZ5] 2097 0.180388 0.228414704 0.789739
VACUOLAR ATP SYNTHASE SUBUNIT G 2 (EC 3.6.3.14) (V-ATPASE G SUBUNIT 2) (VACUOLAR PROTON PUMP G SUBUNIT 2) (V-ATPASE 13 KDA SUBUNIT 2). [SWISSPROT;Acc:O95670] 1751 0.0861167 0.236716356 0.363797
WILLIAMS-BEUREN SYNDROME CRITICAL REGION PROTEIN 20 COPY B. [RefSeq;Acc:NM_145645] 2401 0.0801834 0.219053395 0.366045
WISKOTT-ALDRICH SYNDROME PROTEIN FAMILY MEMBER 2 (WASP-FAMILY PROTEIN MEMBER 2) (VERPROLIN HOMOLOGY DOMAIN-CONTAINING PROTEIN 2). [SWISSPROT;Acc:Q9Y6W5] 703 0.1433 0.26514745 0.540454
ZINC FINGER IMPRINTED 2. [SWISSPROT;Acc:Q9NZV7] 2827 0.161283 0.193483258 0.833576
ZINC FINGER PROTEIN 277. [SWISSPROT;Acc:Q9NRM2] 2768 0.0570468 0.20161727 0.282946

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 bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/