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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measured Hugo Gene expected final description Rank
Results: HTML CSV LaTeX Showing element 1001 to 1050 of 3206 in total
measured
Hugo
expected
final
description
Rank
0.0649343 ACRC 0.256212 0.25343973 ACRC PROTEIN; PUTATIVE NUCLEAR PROTEIN. [RefSeq;Acc:NM_052957] 1025
0.0649384 MAGEC1 0.993221 0.065381622 MELANOMA-ASSOCIATED ANTIGEN C1 (MAGE-C1 ANTIGEN) (CANCER-TESTIS ANTIGEN CT7). [SWISSPROT;Acc:O60732] 3150
0.0649797 MAGEA6 0.993851 0.065381732 MELANOMA-ASSOCIATED ANTIGEN 6 (MAGE-6 ANTIGEN) (MAGE3B). [SWISSPROT;Acc:P43360] 3141
0.0650415 MAGEA9 0.994797 0.065381681 MELANOMA-ASSOCIATED ANTIGEN 9 (MAGE-9 ANTIGEN). [SWISSPROT;Acc:P43362] 3145
0.0651212 PUS7 0.285217 0.228321594 2108
0.0651239 no value 0.996058 0.065381634 MELANOMA-ASSOCIATED ANTIGEN 4 (MAGE-4 ANTIGEN) (MAGE-X2) (MAGE-41). [SWISSPROT;Acc:P43358] 3149
0.0651336 HNRNPU 0.285702 0.227977403 HETEROGENOUS NUCLEAR RIBONUCLEOPROTEIN U (HNRNP U) (SCAFFOLD ATTACHMENT FACTOR A) (SAF-A). [SWISSPROT;Acc:Q00839] 2135
0.0651843 no value 0.250194 0.260535025 KINESIN-LIKE PROTEIN KIF13B (KINESIN-LIKE PROTEIN GAKIN). [SWISSPROT;Acc:Q9NQT8] 852
0.0652476 MAGEA8 0.997949 0.065381698 MELANOMA-ASSOCIATED ANTIGEN 8 (MAGE-8 ANTIGEN). [SWISSPROT;Acc:P43361] 3144
0.0653044 CLSTN2 0.338193 0.193098024 CALSYNTENIN-2 PRECURSOR. [SWISSPROT;Acc:Q9H4D0] 2832
0.0653411 no value 0.271247 0.240891512 HURPIN (HACAT UV-REPRESSIBLE SERPIN) (PROTEASE INHIBITOR 13) (HEADPIN) (SERPIN B13). [SWISSPROT;Acc:Q9UIV8] 1584
0.0653467 INTS8 0.286165 0.228353223 2102
0.0653647 GON4L 0.286244 0.228353083 2103
PRKCE "PROTEIN KINASE C, EPSILON TYPE (EC 2.7.1.-) (NPKC-EPSILON). [SWISSPROT;Acc:Q02156]" 2104
0.0654179 no value 0.277203 0.235992756 HEAT SHOCK 70 KDA PROTEIN 1 (HSP70.1) (HSP70-1/HSP70-2). [SWISSPROT;Acc:P08107] 1772
0.0654684 RELB 0.269399 0.243016492 TRANSCRIPTION FACTOR RELB (I-REL). [SWISSPROT;Acc:Q01201] 1469
0.0654743 MAGEB6B 1.00142 0.065381458 "MELANOMA ANTIGEN, FAMILY B, 6. [RefSeq;Acc:NM_173523]" 3152
NDN NECDIN. [SWISSPROT;Acc:Q99608] 3153
0.0655808 TSG101 0.417367 0.157129816 TUMOR SUSCEPTIBILITY GENE 101 PROTEIN. [SWISSPROT;Acc:Q99816] 2937
0.0656049 KIAA0430 0.159562 0.411156165 LIMKAIN B1. [RefSeq;Acc:NM_019081] 51
0.0656147 PYCRL 1.32794 0.049410892 3184
0.0656459 DEAF1 0.270114 0.24303035 DEFORMED EPIDERMAL AUTOREGULATORY FACTOR 1 HOMOLOG (NUCLEAR DEAF-1 RELATED TRANSCRIPTIONAL REGULATOR) (NUDR) (SUPPRESSIN) (ZINC FINGER MYND DOMAIN CONTAINING PROTEIN 5). [SWISSPROT;Acc:O75398] 1464
0.0657247 SAPS1 0.324347 0.202636991 2761
0.0658169 SYNCRIP 0.213303 0.308560592 NS1-ASSOCIATED PROTEIN 1. [RefSeq;Acc:NM_006372] 260
0.0658246 MAGEA11 1.00678 0.065381315 MELANOMA-ASSOCIATED ANTIGEN 11 (MAGE-11 ANTIGEN). [SWISSPROT;Acc:P43364] 3156
0.0659071 MAGEB18 1.00804 0.065381433 3154
0.0659913 DAB2IP 0.639469 0.103197028 DAB2 INTERACTING PROTEIN; NGAP-LIKE PROTEIN; DOC-2/DAB2 INTERACTIVE PROTEIN. [RefSeq;Acc:NM_032552] 3072
0.066057 MYO7A 0.270441 0.244256603 MYOSIN VIIA. [SWISSPROT;Acc:Q13402] 1395
0.0660691 HSPA2 0.279962 0.235993099 HEAT SHOCK-RELATED 70 KDA PROTEIN 2 (HEAT SHOCK 70 KDA PROTEIN 2). [SWISSPROT;Acc:P54652] 1770
0.0661338 MAGEA10 1.0115 0.065381908 MELANOMA-ASSOCIATED ANTIGEN 10 (MAGE-10 ANTIGEN). [SWISSPROT;Acc:P43363] 3137
0.0661546 DNAJB11 0.191372 0.345685889 DNAJ HOMOLOG SUBFAMILY B MEMBER 11 PRECURSOR (ER-ASSOCIATED DNAJ PROTEIN 3) (ERJ3) (ER-ASSOCIATED HSP40 CO-CHAPERONE) (HDJ9) (PWP1- INTERACTING PROTEIN 4). [SWISSPROT;Acc:Q9UBS4] 162
0.066175 MAGEB10 1.01213 0.065381917 3136
MAGED4 "MELANOMA ANTIGEN, FAMILY D, 4 ISOFORM 1; MAGE1 PROTEIN; MAGE-E1 PROTEIN; MAGED4 PROTEIN. [RefSeq;Acc:NM_030801]" 3135
0.0662042 MAN2B1 0.380173 0.174142298 "LYSOSOMAL ALPHA-MANNOSIDASE PRECURSOR (EC 3.2.1.24) (MANNOSIDASE, ALPHA B) (LYSOSOMAL ACID ALPHA-MANNOSIDASE) (LAMAN) (MANNOSIDASE ALPHA CLASS 2B MEMBER 1). [SWISSPROT;Acc:O00754]" 2906
0.0662574 MAGED1 1.01339 0.065381936 MELANOMA-ASSOCIATED ANTIGEN D1 (MAGE-D1 ANTIGEN) (NEUROTROPHIN RECEPTOR-INTERACTING MAGE HOMOLOG) (PRO2292). [SWISSPROT;Acc:Q9Y5V3] 3134
0.0662986 TRO 1.01402 0.065381945 TROPHININ. [SWISSPROT;Acc:Q12816] 3133
0.0663724 SMAD5 0.266132 0.24939654 MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG 5 (SMAD 5) (MOTHERS AGAINST DPP HOMOLOG 5) (SMAD5) (HSMAD5) (JV5-1). [SWISSPROT;Acc:Q99717] 1173
0.0666089 SNTB2 0.26852 0.248059362 "BETA-2-SYNTROPHIN (59 KDA DYSTROPHIN-ASSOCIATED PROTEIN A1, BASIC COMPONENT 2) (SYNTROPHIN 3) (SNT3) (SYNTROPHIN-LIKE) (SNTL). [SWISSPROT;Acc:Q13425]" 1210
0.0666911 CAPSL 0.23892 0.279135694 381
0.066752 MAGEB4 1.02096 0.065381602 MELANOMA-ASSOCIATED ANTIGEN B1 (MAGE-B1 ANTIGEN) (MAGE-XP ANTIGEN) (DSS-AHC CRITICAL INTERVAL MAGE SUPERFAMILY 10) (DAM10). [SWISSPROT;Acc:P43366] 3151
0.0669169 MAGED2 1.02348 0.065381737 MELANOMA-ASSOCIATED ANTIGEN D2 (MAGE-D2 ANTIGEN) (BREAST CANCER ASSOCIATED GENE 1 PROTEIN) (BCG-1) (11B6) (HEPATOCELLULAR CARCINOMA ASSOCIATED PROTEIN JCL-1). [SWISSPROT;Acc:Q9UNF1] 3140
0.0669581 no value 1.02411 0.065381746 HEPATOCELLULAR CARCINOMA-ASSOCIATED PROTEIN HCA1. [RefSeq;Acc:NM_020932] 3138
0.0670247 TIMM10 0.262934 0.254910738 MITOCHONDRIAL IMPORT INNER MEMBRANE TRANSLOCASE SUBUNIT TIM10. [SWISSPROT;Acc:Q9Y5J8] 1001
0.0670488 PGD 0.303687 0.220782582 "6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING (EC 1.1.1.44). [SWISSPROT;Acc:P52209]" 2339
0.0670742 MAP1LC3B 0.647682 0.103560389 MICROTUBULE-ASSOCIATED PROTEINS 1A/1B LIGHT CHAIN 3B (MAP1A/MAP1B LC3 B) (MAP1A/1B LIGHT CHAIN 3 B). [SWISSPROT;Acc:Q9GZQ8] 3066
0.0671204 RPS6KA6 0.252671 0.265643465 RIBOSOMAL PROTEIN S6 KINASE ALPHA 6 (EC 2.7.1.37) (S6K-ALPHA 6) (90 KDA RIBOSOMAL PROTEIN S6 KINASE 6) (P90-RSK 6) (RIBOSOMAL S6 KINASE 4) (RSK-4) (PP90RSK4). [SWISSPROT;Acc:Q9UK32] 690
0.0671866 no value 0.25292 0.265643682 SIGNAL-INDUCED PROLIFERATION-ASSOCIATED 1-LIKE 1. [RefSeq;Acc:NM_015556] 688
0.0671887 ZNHIT3 0.24133 0.278410061 THYROID RECEPTOR INTERACTING PROTEIN 3 (TRIP-3) (FRAGMENT). [SWISSPROT;Acc:Q15649] 399
0.0673124 POLS 0.302153 0.222775878 POLYMERASE (DNA DIRECTED) SIGMA; TOPOISOMERASE-RELATED FUNCTION PROTEIN 4-1; POLYMERASE (DNA-DIRECTED) SIGMA. [RefSeq;Acc:NM_006999] 2267
0.0673151 NUFIP1 0.241784 0.278410068 NUCLEAR FRAGILE X MENTAL RETARDATION PROTEIN INTERACTING PROTEIN 1; NUCLEAR FRAGILE X MENTAL RETARDATION INTERCATING PROTEIN 1; NUCLEAR FRAGILE X MENTAL RETARDATION PROTEIN-INTERACTING PROTEIN 1. [RefSeq;Acc:NM_012345] 398

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/