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 measured Gene expected Rank description final
Results: HTML CSV LaTeX Showing element 2558 to 2607 of 3206 in total
Hugo
measured
expected
Rank
description
final
RRP1 0.213008 0.867932 1331 NNP-1 PROTEIN (NOVEL NUCLEAR PROTEIN 1) (NUCLEOLAR PROTEIN NOP52) (NOP52) (D21S2056E). [SWISSPROT;Acc:P56182] 0.245420148
RRP12 0.6803 2.74555 1230 0.247782776
RRS1 0.0322443 0.145754 2334 RIBOSOME BIOGENESIS REGULATORY PROTEIN HOMOLOG. [SWISSPROT;Acc:Q15050] 0.221224117
RSL1D1 0.485772 2.00168 1505 PBK1 PROTEIN. [SPTREMBL;Acc:O76021] 0.242682147
RSPH10B 0.113583 0.451392 1089 0.251628296
RSRC2 0.11907 0.44632 669 0.266781681
RSU1 0.214312 0.997879 2508 RAS SUPPRESSOR PROTEIN 1 (RSU-1) (RSP-1). [SWISSPROT;Acc:Q15404] 0.214767522
RTN1 0.268811 1.29069 2691 RETICULON 1 (NEUROENDOCRINE-SPECIFIC PROTEIN). [SWISSPROT;Acc:Q16799] 0.20826922
RTN2 0.175589 0.842838 2685 RETICULON PROTEIN 2 (NEUROENDOCRINE-SPECIFIC PROTEIN-LIKE 1) (NSP-LIKE PROTEIN 1) (NSPLI). [SWISSPROT;Acc:O75298] 0.208330664
RTN3 0.203468 0.976589 2683 RETICULON PROTEIN 3 (NEUROENDOCRINE-SPECIFIC PROTEIN-LIKE 2) (NSP-LIKE PROTEIN II) (NSPLII). [SWISSPROT;Acc:O95197] 0.208345578
RTN4 0.267978 1.28698 2692 RETICULON 4 (NEURITE OUTGROWTH INHIBITOR) (NOGO PROTEIN) (FOOCEN) (NEUROENDOCRINE-SPECIFIC PROTEIN) (NSP) (NEUROENDOCRINE SPECIFIC PROTEIN C HOMOLOG) (RTN-X) (RETICULON 5) (MY043 PROTEIN). [SWISSPROT;Acc:Q9NQC3] 0.20822235
RUNX2 0.0548378 0.24054 2130 "RUNT-RELATED TRANSCRIPTION FACTOR 2 (CORE-BINDING FACTOR, ALPHA 1 SUBUNIT) (CBF-ALPHA 1) (ACUTE MYELOID LEUKEMIA 3 PROTEIN) (ONCOGENE AML-3) (POLYOMAVIRUS ENHANCER BINDING PROTEIN 2 ALPHA A SUBUNIT) (PEBP2-ALPHA A) (PEA2-ALPHA A) (SL3-3 ENHANCER FACTOR 1 " 0.227977883
RUVBL1 0.185296 0.809316 2085 RUVB-LIKE 1 (EC 3.6.1.-) (49-KDA TATA BOX-BINDING PROTEIN-INTERACTING PROTEIN) (49 KDA TBP-INTERACTING PROTEIN) (TIP49A) (PONTIN 52) (NUCLEAR MATRIX PROTEIN 238) (NMP 238) (54 KDA ERYTHROCYTE CYTOSOLIC PROTEIN) (ECP-54) (TIP60-ASSOCIATED PROTEIN 54-ALPHA) 0.228953833
RUVBL2 0.245894 1.04017 1762 RUVB-LIKE 2 (EC 3.6.1.-) (48-KDA TATA BOX-BINDING PROTEIN-INTERACTING PROTEIN) (48-KDA TBP-INTERACTING PROTEIN) (TIP49B) (REPRESSING PONTIN 52) (REPTIN 52) (51 KDA ERYTHROCYTE CYTOSOLIC PROTEIN) (ECP-51) (TIP60-ASSOCIATED PROTEIN 54-BETA) (TAP54-BETA) (CG 0.236397896
SALL1 0.176985 0.63809 429 SAL-LIKE PROTEIN 1 (ZINC FINGER PROTEIN SALL1) (SPALT-LIKE TRANSCRIPTION FACTOR 1) (HSAL1). [SWISSPROT;Acc:Q9NSC2] 0.277366829
SALL2 0.13272 0.478487 414 SAL-LIKE PROTEIN 2 (ZINC FINGER PROTEIN SALL2) (HSAL2). [SWISSPROT;Acc:Q9Y467] 0.277374307
SALL3 0.148125 0.534032 419 SAL-LIKE PROTEIN 3 (ZINC FINGER PROTEIN SALL3) (HSALL3). [SWISSPROT;Acc:Q9BXA9] 0.277371019
SALL4 0.135171 0.487324 415 SAL-LIKE PROTEIN 4 (ZINC FINGER PROTEIN SALL4). [SWISSPROT;Acc:Q9UJQ4] 0.277373985
SAP18 0.0937258 0.450013 2690 SIN3 ASSOCIATED POLYPEPTIDE P18 (2HOR0202). [SWISSPROT;Acc:O00422] 0.208273539
SAP30 0.0253172 0.145382 2904 "SIN3 ASSOCIATED POLYPEPTIDE P30; SIN3-ASSOCIATED POLYPEPTIDE, 30KD. [RefSeq;Acc:NM_003864]" 0.174142604
SAP30L 0.0326222 0.187331 2908 0.174142027
SAPS1 0.0657247 0.324347 2761 0.202636991
SAPS2 0.0721926 0.356265 2758 0.202637363
SAPS3 0.0957295 0.472418 2759 SPORULATION-INDUCED TRANSCRIPT 4-ASSOCIATED PROTEIN. [RefSeq;Acc:NM_018312] 0.202637283
SARM1 0.305359 1.11055 467 "STERILE ALPHA AND TIR MOTIF CONTAINING 1; STERILE ALPHA AND HEAT/ARMADILLO MOTIF PROTEIN, ORTHOLOG OF DROSOPHILA. [RefSeq;Acc:NM_015077]" 0.274961956
SARS 0.293395 1.25677 1848 SERYL-TRNA SYNTHETASE (EC 6.1.1.11) (SERINE--TRNA LIGASE) (SERRS). [SWISSPROT;Acc:P49591] 0.233451626
SARS2 0.215775 0.924279 1847 "SERYL-TRNA SYNTHETASE, MITOCHONDRIAL PRECURSOR (EC 6.1.1.11) (SERINE--TRNA LIGASE) (SERRSMT). [SWISSPROT;Acc:Q9NP81]" 0.233452237
SART1 0.35534 1.28928 457 SQUAMOUS CELL CARCINOMA ANTIGEN RECOGNIZED BY T CELLS 1; U4/U6.U5 TRI-SNRNP-ASSOCIATED 110 KDA PROTEIN; IGE AUTOANTIGEN; SART1(259) PROTEIN; SART1(800) PROTEIN. [RefSeq;Acc:NM_005146] 0.275611194
SBDS 0.149637 0.671325 2265 SHWACHMAN-BODIAN-DIAMOND SYNDROME PROTEIN (CGI-97). [SWISSPROT;Acc:Q9Y3A5] 0.222898
SCAMP1 0.0466014 0.221972 2656 SECRETORY CARRIER-ASSOCIATED MEMBRANE PROTEIN 1. [SWISSPROT;Acc:O15126] 0.209942695
SCAMP2 0.0366237 0.174446 2655 SECRETORY CARRIER-ASSOCIATED MEMBRANE PROTEIN 2. [SWISSPROT;Acc:O15127] 0.209942905
SCAMP3 0.0359383 0.171181 2654 SECRETORY CARRIER-ASSOCIATED MEMBRANE PROTEIN 3. [SWISSPROT;Acc:O14828] 0.209943276
SCAP 0.0868591 0.389405 2255 STEROL REGULATORY ELEMENT BINDING PROTEIN CLEAVAGE-ACTIVATING PROTEIN (SREBP CLEAVAGE-ACTIVATING PROTEIN) (SCAP). [SWISSPROT;Acc:Q12770] 0.223055944
SCAPER 0.0194686 0.0842001 1961 ZINC FINGER PROTEIN 291. [SWISSPROT;Acc:Q9BY12] 0.231218253
SCOC 0.0348108 0.135208 931 SHORT COILED-COIL PROTEIN; SHORT COILED COIL PROTEIN. [RefSeq;Acc:NM_032547] 0.257461097
SCP2 0.192957 0.526194 108 "NONSPECIFIC LIPID-TRANSFER PROTEIN, MITOCHONDRIAL PRECURSOR (NSL-TP) (STEROL CARRIER PROTEIN 2) (SCP-2) (STEROL CARRIER PROTEIN X) (SCP-X) (SCPX). [SWISSPROT;Acc:P22307]" 0.366703155
SCRIB 0.163652 0.629348 884 SCRIBBLE. [RefSeq;Acc:NM_015356] 0.260034194
SCYE1 0.388823 1.9597 2803 MULTISYNTHETASE COMPLEX AUXILIARY COMPONENT P43 [CONTAINS: ENDOTHELIAL-MONOCYTE ACTIVATING POLYPEPTIDE II (EMAP-II) (SMALL INDUCIBLE CYTOKINE SUBFAMILY E MEMBER 1)]. [SWISSPROT;Acc:Q12904] 0.19840945
SCYL1 0.0350787 0.154573 2174 SCY1-LIKE 1; TELOMERASE REGULATION-ASSOCIATED PROTEIN; HT019 PROTEIN; TELOMERASE REGULATION-ASSOCIATED PROTEIN; N-TERMINAL KINASE-LIKE PROTEIN; TERATOMA-ASSOCIATED TYROSINE KINASE; N-TERMINAL KINASE-LIKE. [RefSeq;Acc:NM_020680] 0.226939375
SDF2 0.0275634 0.118439 1891 STROMAL CELL-DERIVED FACTOR 2 PRECURSOR (SDF-2). [SWISSPROT;Acc:Q99470] 0.23272233
SDF2L1 0.0221128 0.0950179 1890 STROMAL CELL-DERIVED FACTOR 2-LIKE PROTEIN 1 PRECURSOR (SDF2 LIKE PROTEIN 1) (PWP1-INTERACTING PROTEIN 8). [SWISSPROT;Acc:Q9HCN8] 0.232722466
SDF4 0.0737619 0.340556 2468 45 KDA CALCIUM-BINDING PROTEIN PRECURSOR (CAB45) (STROMAL CELL-DERIVED FACTOR 4) (SDF-4). [SWISSPROT;Acc:Q9BRK5] 0.216592572
SDHA 0.150581 0.655122 2053 "SUCCINATE DEHYDROGENASE [UBIQUINONE] FLAVOPROTEIN SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.3.5.1) (FP) (FLAVOPROTEIN SUBUNIT OF COMPLEX II). [SWISSPROT;Acc:P31040]" 0.229851844
SDHB 0.311095 1.34923 2017 "SUCCINATE DEHYDROGENASE [UBIQUINONE] IRON-SULFUR PROTEIN, MITOCHONDRIAL PRECURSOR (EC 1.3.5.1) (IP) (IRON-SULFUR SUBUNIT OF COMPLEX II). [SWISSPROT;Acc:P21912]" 0.230572252
SDHC 0.240428 1.04189 1996 "SUCCINATE DEHYDROGENASE CYTOCHROME B560 SUBUNIT, MITOCHONDRIAL PRECURSOR (INTEGRAL MEMBRANE PROTEIN CII-3) (QPS1) (QPS-1) (SUCCINATE DEHYDROGENASE COMPLEX SUBUNIT C) (SUCCINATE-UBIQUINONE OXIDOREDUCTASE CYTOCHROME B LARGE SUBUNIT) (CYBL). [SWISSPRO" 0.230761405
SEC13 0.126518 0.534471 1753 SEC13-RELATED PROTEIN. [SWISSPROT;Acc:P55735] 0.236716305
SEC16A 0.141581 0.511852 448 0.276605347
SEC16B 0.109365 0.395349 447 REGUCALCIN GENE PROMOTOR REGION RELATED PROTEIN; RGPR-P117. [RefSeq;Acc:NM_033127] 0.276629004
SEC31A 0.134029 0.566199 1746 YEAST SEC31P HOMOLOG. [RefSeq;Acc:NM_014933] 0.236717126
SEC31B 0.107954 0.456048 1752 SECRETORY PATHWAY COMPONENT SEC31B-1. [RefSeq;Acc:NM_015490] 0.236716311

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/